https://wiki.yeastgenome.org/api.php?action=feedcontributions&user=Kyla&feedformat=atomSGD-Wiki - User contributions [en]2024-03-29T05:54:03ZUser contributionsMediaWiki 1.31.14https://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399284SGD Quarterly Newsletter, Summer 20152015-08-26T20:25:12Z<p>Kyla: /* Workshop: Getting More out of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the ''Getting More Out of SGD'' workshop, we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Mike Cherry]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB. Come by to take a spin on our site, learn about various features of the database, and provide us with feedback regarding how we can improve SGD to be entered in a daily raffle for SGD <strong>prizes</strong>!</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD staff will present three posters - please stop by and chat with us!</p><br />
{| style="width: 80%; height: 100px;" border="1"<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|Edith Wong<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|Giltae Song<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Homology curation at SGD: budding yeast as a model for eukaryotic biology<br />
| style="text-align:center;"|Stacia Engel<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
==Upcoming meeting: Cell Biology of Yeast Meeting at Cold Spring Harbor Labs==<br />
SGD staff will be at the [https://meetings.cshl.edu/meetings.aspx?meet=YEAST&year=15 Cell Biology of Yeast Meeting] to showcase what's new at SGD. Come find us at the exhihit table!<br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can substitute for each other, they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff, and is incorporated into SGD with their generous permission. Curation of this type of data will continue at SGD going forward.<br />
<br />
As a starting point, we collected a very straightforward set of data: <br />
* the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; <br />
* the direction of complementation (human gene complements yeast mutation, or vice versa); <br />
* the source of curation (SGD or P-POD); <br />
* the PubMed ID of the reference; <br />
* an optional free-text note adding more details.<br />
<br />
In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two places: <br />
# new templates in SGD's [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] data warehouse;<br />
# SGD's [http://www.yeastgenome.org/download-data/curation Download] site.<br />
<br />
Please take a look, let us know what you think, and point us to any published data that might be missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC]-approved symbols) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions [https://www.youtube.com/watch?v=vT_ihoyVwNY Overview] and [https://www.youtube.com/watch?v=evUSAtIwTFI Network]<br />
* [https://www.youtube.com/watch?v=22j-KWR-1qA Genome Snapshot]<br />
* [https://www.youtube.com/watch?v=Ai4tOv20_YY Yeast-Human Functional Complementation Data]<br />
* [https://www.youtube.com/watch?v=y5ASL7rBulA Reserving a Gene Name]<br />
* [https://www.youtube.com/watch?v=RVtSYSYnDak Sequence pages]<br />
* [https://www.youtube.com/watch?v=oKlvNqpmWfM Protein pages]<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, these were some of the most popular Research Spotlight posts on our home page recently:<br />
<br />
[http://www.yeastgenome.org/private-nurses-help-birth-ribosomal-proteins '''Private Nurses Help Birth Ribosomal Proteins''']. [http://www.yeastgenome.org/reference/S000180748/overview Pausch and colleagues] show that some ribosomal proteins are such potential troublemakers that they need individual chaperones to keep them swaddled and safe until they settle into the mature ribosome.<br />
<br />
[http://www.yeastgenome.org/wheres-that-protein '''Where's That Protein?''']. We can now pinpoint the locations of more than 4,000 yeast proteins, thanks to nine BILLION measurements made at the University of Toronto, published by [http://www.yeastgenome.org/reference/S000180516/overview Chong ''et al.''] and [http://www.yeastgenome.org/reference/S000180515/overview Koh ''et al.''].<br />
<br />
[http://www.yeastgenome.org/yeast-are-people-too '''Yeast are People Too''']. A new study by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo ''et al.''] in the Marcotte lab at the University of Texas at Austin shows that when you look under the hood, yeast and human cells not only look similar but even have hundreds of interchangeable parts.<br />
<br />
==What did we do over the summer?==<br />
<br />
# Robert Nash, a Senior Biocuration Scientist at SGD, presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=15 YEAST GENETICS & GENOMICS] course at [http://www.cshl.edu CSHL], on what types of data are available at SGD, and how to use YeastMine. [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive Slides from his presentation] are available at SGD.<br />
# Travis Sheppard, a Senior Software Developer at SGD, attended the React.js Europe conference at Paris to learn more about techniques, best practices, and emerging technologies related to the use of React.js in web development and user interfaces. He also attended the Eyeo Festival in Minneapolis to an insight into the processes used by designers for data visualization.<br />
<br />
==Recent Publications by SGD staff==<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Epub 2015 Jul 3. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399283SGD Quarterly Newsletter, Summer 20152015-08-26T20:21:42Z<p>Kyla: /* Posters */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the ''Getting More Out of SGD'' workshop, we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB. Come by to take a spin on our site, learn about various features of the database, and provide us with feedback regarding how we can improve SGD to be entered in a daily raffle for SGD <strong>prizes</strong>!</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD staff will present three posters - please stop by and chat with us!</p><br />
{| style="width: 80%; height: 100px;" border="1"<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|Edith Wong<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|Giltae Song<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Homology curation at SGD: budding yeast as a model for eukaryotic biology<br />
| style="text-align:center;"|Stacia Engel<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
==Upcoming meeting: Cell Biology of Yeast Meeting at Cold Spring Harbor Labs==<br />
SGD staff will be at the [https://meetings.cshl.edu/meetings.aspx?meet=YEAST&year=15 Cell Biology of Yeast Meeting] to showcase what's new at SGD. Come find us at the exhihit table!<br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can substitute for each other, they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff, and is incorporated into SGD with their generous permission. Curation of this type of data will continue at SGD going forward.<br />
<br />
As a starting point, we collected a very straightforward set of data: <br />
* the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; <br />
* the direction of complementation (human gene complements yeast mutation, or vice versa); <br />
* the source of curation (SGD or P-POD); <br />
* the PubMed ID of the reference; <br />
* an optional free-text note adding more details.<br />
<br />
In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two places: <br />
# new templates in SGD's [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] data warehouse;<br />
# SGD's [http://www.yeastgenome.org/download-data/curation Download] site.<br />
<br />
Please take a look, let us know what you think, and point us to any published data that might be missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC]-approved symbols) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions [https://www.youtube.com/watch?v=vT_ihoyVwNY Overview] and [https://www.youtube.com/watch?v=evUSAtIwTFI Network]<br />
* [https://www.youtube.com/watch?v=22j-KWR-1qA Genome Snapshot]<br />
* [https://www.youtube.com/watch?v=Ai4tOv20_YY Yeast-Human Functional Complementation Data]<br />
* [https://www.youtube.com/watch?v=y5ASL7rBulA Reserving a Gene Name]<br />
* [https://www.youtube.com/watch?v=RVtSYSYnDak Sequence pages]<br />
* [https://www.youtube.com/watch?v=oKlvNqpmWfM Protein pages]<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, these were some of the most popular Research Spotlight posts on our home page recently:<br />
<br />
[http://www.yeastgenome.org/private-nurses-help-birth-ribosomal-proteins '''Private Nurses Help Birth Ribosomal Proteins''']. [http://www.yeastgenome.org/reference/S000180748/overview Pausch and colleagues] show that some ribosomal proteins are such potential troublemakers that they need individual chaperones to keep them swaddled and safe until they settle into the mature ribosome.<br />
<br />
[http://www.yeastgenome.org/wheres-that-protein '''Where's That Protein?''']. We can now pinpoint the locations of more than 4,000 yeast proteins, thanks to nine BILLION measurements made at the University of Toronto, published by [http://www.yeastgenome.org/reference/S000180516/overview Chong ''et al.''] and [http://www.yeastgenome.org/reference/S000180515/overview Koh ''et al.''].<br />
<br />
[http://www.yeastgenome.org/yeast-are-people-too '''Yeast are People Too''']. A new study by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo ''et al.''] in the Marcotte lab at the University of Texas at Austin shows that when you look under the hood, yeast and human cells not only look similar but even have hundreds of interchangeable parts.<br />
<br />
==What did we do over the summer?==<br />
<br />
# Robert Nash, a Senior Biocuration Scientist at SGD, presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=15 YEAST GENETICS & GENOMICS] course at [http://www.cshl.edu CSHL], on what types of data are available at SGD, and how to use YeastMine. [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive Slides from his presentation] are available at SGD.<br />
# Travis Sheppard, a Senior Software Developer at SGD, attended the React.js Europe conference at Paris to learn more about techniques, best practices, and emerging technologies related to the use of React.js in web development and user interfaces. He also attended the Eyeo Festival in Minneapolis to an insight into the processes used by designers for data visualization.<br />
<br />
==Recent Publications by SGD staff==<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Epub 2015 Jul 3. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399282SGD Quarterly Newsletter, Summer 20152015-08-26T20:20:12Z<p>Kyla: /* Workshop: Getting More out of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the ''Getting More Out of SGD'' workshop, we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB. Come by to take a spin on our site, learn about various features of the database, and provide us with feedback regarding how we can improve SGD to be entered in a daily raffle for SGD <strong>prizes</strong>!</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD staff will present three posters - please stop by and chat with us!</p><br />
{| style="width: 60%; height: 200px;" border="1"<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Homology curation at SGD: budding yeast as a model for eukaryotic biology<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
==Upcoming meeting: Cell Biology of Yeast Meeting at Cold Spring Harbor Labs==<br />
SGD staff will be at the [https://meetings.cshl.edu/meetings.aspx?meet=YEAST&year=15 Cell Biology of Yeast Meeting] to showcase what's new at SGD. Come find us at the exhihit table!<br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can substitute for each other, they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff, and is incorporated into SGD with their generous permission. Curation of this type of data will continue at SGD going forward.<br />
<br />
As a starting point, we collected a very straightforward set of data: <br />
* the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; <br />
* the direction of complementation (human gene complements yeast mutation, or vice versa); <br />
* the source of curation (SGD or P-POD); <br />
* the PubMed ID of the reference; <br />
* an optional free-text note adding more details.<br />
<br />
In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two places: <br />
# new templates in SGD's [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] data warehouse;<br />
# SGD's [http://www.yeastgenome.org/download-data/curation Download] site.<br />
<br />
Please take a look, let us know what you think, and point us to any published data that might be missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC]-approved symbols) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions [https://www.youtube.com/watch?v=vT_ihoyVwNY Overview] and [https://www.youtube.com/watch?v=evUSAtIwTFI Network]<br />
* [https://www.youtube.com/watch?v=22j-KWR-1qA Genome Snapshot]<br />
* [https://www.youtube.com/watch?v=Ai4tOv20_YY Yeast-Human Functional Complementation Data]<br />
* [https://www.youtube.com/watch?v=y5ASL7rBulA Reserving a Gene Name]<br />
* [https://www.youtube.com/watch?v=RVtSYSYnDak Sequence pages]<br />
* [https://www.youtube.com/watch?v=oKlvNqpmWfM Protein pages]<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.<br />
<br />
==Research Spotlight (Blog posts)==<br />
In case you missed them, these were some of the most popular Research Spotlight posts on our home page recently:<br />
<br />
[http://www.yeastgenome.org/private-nurses-help-birth-ribosomal-proteins '''Private Nurses Help Birth Ribosomal Proteins''']. [http://www.yeastgenome.org/reference/S000180748/overview Pausch and colleagues] show that some ribosomal proteins are such potential troublemakers that they need individual chaperones to keep them swaddled and safe until they settle into the mature ribosome.<br />
<br />
[http://www.yeastgenome.org/wheres-that-protein '''Where's That Protein?''']. We can now pinpoint the locations of more than 4,000 yeast proteins, thanks to nine BILLION measurements made at the University of Toronto, published by [http://www.yeastgenome.org/reference/S000180516/overview Chong ''et al.''] and [http://www.yeastgenome.org/reference/S000180515/overview Koh ''et al.''].<br />
<br />
[http://www.yeastgenome.org/yeast-are-people-too '''Yeast are People Too''']. A new study by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo ''et al.''] in the Marcotte lab at the University of Texas at Austin shows that when you look under the hood, yeast and human cells not only look similar but even have hundreds of interchangeable parts.<br />
<br />
==What did we do over the summer?==<br />
<br />
# Robert Nash, a Senior Biocuration Scientist at SGD, presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=15 YEAST GENETICS & GENOMICS] course at [http://www.cshl.edu CSHL], on what types of data are available at SGD, and how to use YeastMine. [http://wiki.yeastgenome.org/index.php/SGD_Poster_Archive Slides from his presentation] are available at SGD.<br />
# Travis Sheppard, a Senior Software Developer at SGD, attended the React.js Europe conference at Paris to learn more about techniques, best practices, and emerging technologies related to the use of React.js in web development and user interfaces. He also attended the Eyeo Festival in Minneapolis to an insight into the processes used by designers for data visualization.<br />
<br />
==Recent Publications by SGD staff==<br />
#Skrzypek MS, Nash RS (2015) Biocuration at the Saccharomyces Genome Database. Genesis. 2015 Aug;53(8):450-7. doi: 10.1002/dvg.22862. Epub 2015 Jul 3. [http://www.ncbi.nlm.nih.gov/pubmed/25997651 '''PMID: 25997651''']<br />
#Song G, Dickins BJ, Demeter J, Engel S, Dunn B, Cherry JM (2015) AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One. 2015 Mar 17;10(3):e0120671. doi: 10.1371/journal.pone.0120671. eCollection 2015. [http://www.ncbi.nlm.nih.gov/pubmed/25781462 '''PMID: 25781462''']</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399242SGD Quarterly Newsletter, Summer 20152015-08-25T18:30:33Z<p>Kyla: /* Posters */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| style="width: 60%; height: 200px;" border="1"<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Homology curation at SGD: budding yeast as a model for eukaryotic biology<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions Overview and Network<br />
* Genome Snapshot <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399241SGD Quarterly Newsletter, Summer 20152015-08-25T18:18:38Z<p>Kyla: /* Posters */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| style="width: 60%; height: 200px;" border="1"<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br><br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions Overview and Network<br />
* Genome Snapshot <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399240SGD Quarterly Newsletter, Summer 20152015-08-25T18:00:35Z<p>Kyla: /* SGD’s 60-second Help Videos */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| width="100%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br><br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Interactions Overview and Network<br />
* Genome Snapshot <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399239SGD Quarterly Newsletter, Summer 20152015-08-25T17:57:50Z<p>Kyla: /* Posters */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| width="100%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|Inferring Genome Variation Patterns in <i>Saccharomyces cerevisiae</i> using the Eukaryote Pan-Genome Toolset<br />
| style="text-align:center;"|[[File:giltae-song.png|center|100px|thumb|Giltae Song]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br><br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399238SGD Quarterly Newsletter, Summer 20152015-08-25T17:53:58Z<p>Kyla: /* Workshop: Getting More out of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| width="100%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="width:10%;text-align:center;"|Poster <br />
| style="text-align:center;"|Date and Time <br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|Innovative visualization tools to interconnect multiple data types at SGD<br />
| style="text-align:center;"|[[File:Rama-staff-pic.png|center|100px|thumb|Rama Balakrishnan]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br><br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=SGD_Quarterly_Newsletter,_Summer_2015&diff=399237SGD Quarterly Newsletter, Summer 20152015-08-25T17:53:18Z<p>Kyla: /* Workshop: Getting More out of SGD */</p>
<hr />
<div>[[Category:Newsletter]]<br />
'''About this newsletter:''' <br><br />
<br />
This is the Summer 2015 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.<br />
You can also subscribe to SGD's RSS feed to receive updates on SGD news:<br />
http://www.yeastgenome.org/feed<br><br />
<br />
==SGD at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)==<br />
[[File:yeast-meet.jpg|center|300px]]<br />
<br />
<p>SGD staff will be hosting a workshop, posters, and an exhibit table at the 27th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) to be held in Levico Terme, Trento, Italy, from 6th to 12th September 2015.</p> SGD will showcase the items mentioned below and more! At the workshop, ''Getting More Out of SGD'' we will be discussing our curation efforts in capturing yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine and more. Bring your questions and comments - we love feedback!<br />
<br />
===Workshop: ''Getting More out of SGD''===<br />
<p> '''Date:''' Sunday, September 6th, 4PM<br><br />
'''Room:'''<br><br />
'''Featured Topics''': Yeast-human functional complementation data, the new Variant Viewer, new data in YeastMine <br><br />
</p><br />
<p>Find these SGD staff members, as well as those presenting [[#Posters|posters]], at the Workshop and the Exhibit table:<br />
{| border="1" <br />
|- style="vertical-align:middle;" <br />
| style="text-align:center;"|[[File:mike-cherry.png|center|100px|thumb|Dr. Mike Cherry<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo<br> workshop speaker]]<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel<br>workshop speaker]]<br />
|-<br />
|}<br />
</p><br />
<br />
===Posters===<br />
<p>In addition to the Workshop, SGD curators will present 4 posters - please stop by and chat with us!</p><br />
{| width="100%" border="1" <br />
|- style="vertical-align:middle;"<br />
| style="width:10%;text-align:center;"|Poster <br />
| style="text-align:center;"|Date and Time <br />
| style="text-align:center;"|Poster Title <br />
| style="text-align:center;"|Presenter <br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|Integrating genome-wide datasets into the Saccharomyces Genome Database<br />
| style="text-align:center;"|[[File:Edith-staff_pic.png|center|100px|thumb|Edith Wong]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|Innovative visualization tools to interconnect multiple data types at SGD<br />
| style="text-align:center;"|[[File:Rama-staff-pic.png|center|100px|thumb|Rama Balakrishnan]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Stacia-staff_pic.png|center|100px|thumb|Stacia Engel]]<br />
|- style="vertical-align:middle;"<br />
| style="text-align:center;"|xx<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|<br />
| style="text-align:center;"|[[File:Maria-staff_pic.jpg|center|100px|thumb|Maria Costanzo]]<br><br />
|- style="vertical-align:middle;"<br />
|-<br />
|}<br />
<br />
===Exhibit Table===<br />
<p>SGD will also have an exhibit table at the ICYGMB Come by to take a spin on our site, learn about various features of the database, and provide us with feedback as to what we can do to improve SGD and receive a <strong>prize</strong>! Look for us wearing our SuperBud fleece jackets, and feel free to flag any of us down!</p><br />
<br />
==Yeast-Human Functional Complementation Data Now in SGD==<br />
Yeast and humans diverged about a billion years ago. So if there’s still enough functional conservation between a pair of similar yeast and human genes that they can be substituted for each other, we know they must be critically important for life. An added bonus is that if a human protein works in yeast, all of the awesome power of yeast genetics and molecular biology can be used to study it.<br />
<br />
To make it easier for researchers to identify these “swappable” yeast and human genes, we’ve started collecting functional complementation data in SGD. The data are all curated from the published literature, via two sources. One set of papers was curated at SGD, including the recent systematic study of functional complementation by [http://www.yeastgenome.org/reference/S000180316/overview Kachroo and colleagues]. Another set was curated by Princeton Protein Orthology Database ([http://ppod.princeton.edu/ P-POD]) staff and is incorporated into SGD with their generous permission.<br />
<br />
As a starting point, we’ve collected a relatively simple set of data: the yeast and human genes involved in a functional complementation relationship, with their respective identifiers; the direction of complementation (human gene complements yeast mutation, or vice versa); the source of curation (SGD or P-POD); the PubMed ID of the reference; and an optional free-text note adding more details. In the future we’ll incorporate more information, such as the disease involvement of the human protein and the sequence differences found in disease-associated alleles that fail to complement the yeast mutation.<br />
<br />
You can access these data in two ways: using two new templates in [http://yeastmine.yeastgenome.org/yeastmine/begin.do YeastMine] our data warehouse; or via our [http://www.yeastgenome.org/download-data Download] page. Please take a look, let us know what you think, and point us to any published data that’s missing. We always appreciate your feedback!<br />
<br />
===Accessing Functional Complementation Data===<br />
<p>YeastMine is a versatile tool that lets you customize searches and create and manipulate lists of search results. To help you get started with YeastMine we've created a series of short [http://www.yeastgenome.org/help/video-tutorials/yeastmine video tutorials] explaining its features.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=Gene_Complements&amp;scope=all Gene --> Functional Complementation template]<br />
<p>This template lets you query with a yeast gene or list of genes (either your own custom list, or a pre-made gene list) and retrieve the human gene(s) involved in cross-species complementation along with all of the data listed above.</p><br />
[http://yeastmine.yeastgenome.org/yeastmine/template.do?name=HumaGene_YeastGene_Complement&amp;scope=all Human Gene --> Functional Complementation template]<br />
<p>This template takes either human gene names ([http://www.genenames.org/ HGNC -approved symbols]) or [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] IDs for human genes and returns the yeast gene(s) involved in cross-species complementation, along with the data listed above. You can run the query using a single human gene as input, or create a custom list of human genes in YeastMine for the query. We've created two new pre-made lists of human genes that can also be used with this template. The list "Human genes complementing or complemented by yeast genes" includes only human genes that are currently included in the functional complementation data, while the list "Human genes with yeast homologs" includes all human genes that have a yeast homolog as predicted by any of several methods.</p><br />
<h3>Downloading Functional Complementation Data</h3><br />
<p>If you'd prefer to have all the data in one file, simply visit our [http://www.yeastgenome.org/download-data/curation Curated Data download page] and download the file "functional_complementation.tab".</p><br />
<br />
==SGD’s 60-second Help Videos==<br />
<br />
SGD is actively expanding its library of short video tutorials designed to help you use various SGD tools and pages. Check out the latest new videos available for the following topics: <br />
* Yeast-Human Functional Complementation Data<br />
* Reserving a Gene Name<br />
* Working with Lists in YeastMine<br />
All videos are accessible via the SGD [http://www.yeastgenome.org/help/video-tutorials Video Tutorials] page and through SGD’s [https://www.youtube.com/channel/UCnTiLvqP2aYeHEaJl7m9DUg YouTube] channel.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:mike-cherry.png&diff=399236File:mike-cherry.png2015-08-25T17:51:06Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:giltae-song.png&diff=399235File:giltae-song.png2015-08-25T17:50:32Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:Spring_Bay_Area_Yeast_Meeting_2014(2).pdf&diff=398860File:Spring Bay Area Yeast Meeting 2014(2).pdf2014-04-16T17:24:23Z<p>Kyla: Kyla uploaded a new version of &quot;File:Spring Bay Area Yeast Meeting 2014(2).pdf&quot;</p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:Spring_Bay_Area_Yeast_Meeting_2014(2).pdf&diff=398859File:Spring Bay Area Yeast Meeting 2014(2).pdf2014-04-16T17:15:16Z<p>Kyla: Kyla uploaded a new version of &quot;File:Spring Bay Area Yeast Meeting 2014(2).pdf&quot;</p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=Bay_Area_Yeast_Meeting&diff=398858Bay Area Yeast Meeting2014-04-16T17:12:30Z<p>Kyla: /* Program */</p>
<hr />
<div>=Spring 2014 Bay Area Yeast Meeting Information=<br />
The Spring Bay Area Yeast Meeting is hosted by the <i>Saccharomyces</i> Genome Database group at Stanford University and UC Berkeley.<br />
<br />
* Venue: M106, Alway Building, Stanford Medical Center (intersection of Roth and Campus Dr)<br />
* Location: Stanford University, CA<br />
* Date: April 19th, 2014<br />
<br />
==Registration==<br />
* Registration is free.<br />
<br />
==Program==<br />
9:00 - 10:00 Coffee and Registration (Courtyard outside M106) <br><br />
10:00 - 12:00 Research Talks M106 <br><br />
<br />
*FRET-based assay for monitoring septin filament assembly<br />
::''Elizabeth “Libby” Booth, Jeremy Thorner Lab, UC Berkeley''<br />
<br />
*Yeast's evil relative: a fungus that swims, crawls, and kills vertebrates<br />
::''Tim Stearns, Stanford University''<br />
<br />
*Number of Cln3 molecules determines budding probability in yeast<br />
::''Kurt Schmoller , J.M. Skotheim Lab, Stanford University''<br />
<br />
*Re-replication of a centromere induces whole-chromosomal instability and aneuploidy<br />
::''Stacey Hanlon, Joachim J. Li Lab, UCSF''<br />
<br />
*Heterozygote advantage in adapting diploids<br />
::''Diamantis Sellis, Dmitri Petrov Lab, Stanford University''<br />
<br />
* A Metabolomics Approach to Study Chardonnay Wine Fermentation<br />
::''Chandra Richter - Viticulture, Chemistry and Enology, E&J Gallo Winery''<br />
<br />
12:00 - 1:45 Lunch and Posters (Courtyard outside M106)<br><br />
1:50 - 3:45 Research Talks M106 <br><br />
<br />
*Investigating the functional defects of human p53 mutations in a yeast model system: an introductory molecular biology laboratory course for undergraduates<br />
::''Daria Hekmat-Scafe, Martha Cyert and Tim Stearns Lab, Stanford University''<br />
<br />
*Chromatin Remodeling as a Molecular Basis of Expression Noise<br />
::''Christopher Brown, Hinrich Boeger Lab, UC Santa Cruz''<br />
<br />
*Insights into yeast gene regulation though high-throughput and precision RNA boundary mapping<br />
::''Aino Järvelin, Lars Steinmetz Lab, EMBL''<br />
<br />
*Transient expression of intrinsically disordered proteins heritably transforms the phenotypic landscape of S. cerevisiae<br />
::''Daniel Jarosz, Stanford University''<br />
<br />
*Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation<br />
::''Carlo Artieri, Hunter B. Fraser Lab, Stanford University''<br />
<br />
*The role of nucleoporins specifically Nup2 during meiosis in budding yeast<br />
::''Daniel Chu, Sean Burgess Lab, UC Davis''<br />
<br />
3:50 - 4:50 Keynote Speaker M106<br><br />
:::“Genes and proteins that control secretion and autophagy.”<br />
''Randy Schekman, Howard Hughes Investigator and Professor of Cell and Developmental Biology, UC Berkeley''<Br><br />
''Nobel Prize in Physiology or Medicine, 2013''<br />
<br />
4:50 - 5:30 Wine reception (Courtyard outside M106)<br />
<br />
[[media:Spring_Bay_Area_Yeast_Meeting_2014(2).pdf|Printable Schedule]]<br />
<br />
==Keynote Speaker==<br />
Genes and proteins that control secretion and autophagy.<br />
<br><br />
''Randy Schekman, UC Berkeley (Nobel Prize in Physiology or Medicine, 2013)''<br />
<br />
==Maps & Parking==<br />
Parking is free during the weekend on Stanford campus.<br />
<br />
Parking structure closest to M106 is at the intersection of Roth and Campus drive.<br />
[http://maps.stanford.edu/maps_library Stanford University maps]<br />
<br />
==Campus Shuttle (Marguerite)==<br />
Free campus shuttle from downtown Palo Alto is available. The Palo Alto Train Station is the closest stop to Stanford University. <br />
A variety of maps for the [http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Marguerite Shuttle] are available.<br />
<br />
Realtime [http://lbre-apps.stanford.edu/transportation/stanford_ivl/ Shuttle Bus Service]. The Stanford Marguerite Shuttle is free.<br />
<br />
==Sponsors==<br />
* Amyris Biotechnologies<br />
* E&J Gallo Winery<br />
* School of Medicine, Stanford University<br />
<br />
==Need help?==<br />
* If you have any questions please contact us at [http://www.yeastgenome.org/cgi-bin/suggestion sgd-helpdesk]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome&diff=398856Meiotic Double-Stranded Breaks in the Yeast Genome2014-04-16T16:37:18Z<p>Kyla: </p>
<hr />
<div>The localization of the Spo11-dependent double-stranded break sites and the chromatin asssociation of Mre11p with double strand break sites during meiosis has been characterized at the genome-wide level in a subsequent paper (Borde et al. (2004) Association of Mre11p with Double-Strand Break Sites during Yeast Meiosis. [http://www.ncbi.nlm.nih.gov/pubmed/?term=14967146 Mol Cell (2004) 13(3):389-401]). <br />
<br><br />
<br />
The meiotic double-stranded breaks data on Chromosome III was kindly provided in both [[Tabular_Form_of_Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|tabular]] and graphical form by Dr. Frédéric Baudat and Dr. Alain Nicolas of the Institut Curie, Section de Recherche. For further information, please see their paper, [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volume:94!firstpage:5213!tyear:1998!fyear:1996!fmonth:Feb!tmonth:Apr!tdatedef:28%2520April%25201998!fdatedef:6%2520February%25201996!hits:10!sendit:Search Proc. Natl. Acad. Sci. (1997) USA 94:5213-5218]. This graphic represents '''Figure 2''' of this paper. The key and legend for this figure are located directly under the figure.<br />
For a commentary article on this topic, please see Nicolas, A. (1998). Relationship between transcription and initiation of meiotic recombination: Toward chromatin accessibility. [http://www.pnas.org/content/95/1/87.full Proc. Natl. Acad. Sci. (1998) USA 95:87-89].<br />
<br><br />
<br />
<center>[[file:chrIII.dsbreak.png|900px|link=http://www.yeastgenome.org/images/chrIII.dsbreak.gif]]</center><br />
<br />
<br><br />
Legend from '''Figure 2''' of [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volum%5c Proc. Natl. Acad. Sci. (1997) USA 94:5213-5218]:<br />
<br><br />
<br />
'''Location and amount of meiotic DSBs on chromosome III'''. For simplification, the ORF numbers (22) are indicated without YCL or YCR. The physical map is drawn to scale from the sequence (coordinates are in kb) and is corrected for the major differences found in ORD1181 derived from SK1 that lead chromosome III to a length of 340 kb instead of 315 kb in the published sequence (22): Ty2-17 near LEU2 is absent, as is the delta LTR between YCR6c and YCR7c; a Ty2 identified by PCR amplification and restriction analysis is inserted at coordinate 151,000; a Ty1 is inserted between RIM1 and YCR29c (25); additional 396 bp are in YCR89w; the right chromosomal end is 15-25 kb longer and of unknown sequence. Bar height represents the percent of meiotic DSBs per DNA molecule. Generally, two measurements were made at each region, with different restriction digests and probes. Standard errors between different measurements of the same DSB sites depend on the DSB frequencies: 0.05-0.2% for DSB 0.5%, 0.2-0.5% for DSB between 0.5% and 1.5%, and 0.5-1% for DSB > 1.5%. Red, green, and blue bars represent DSBs in intergenic-promoter, intergenic terminators, and coding regions, respectively. Other information is provided in the legend box.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Historical_Systematic_Sequence_Information&diff=398855Historical Systematic Sequence Information2014-04-16T16:36:34Z<p>Kyla: /* Chromosomal Features */</p>
<hr />
<div>These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].<br />
<br />
=Chromosomal Features=<br />
[[Modified_Nucleotides_within_RNAs_in_S._cerevisiae|Modified Nucleotides within RNAs in S. cerevisiae]]<br />
<br />
[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]<br />
<br />
[[Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|Meiotic Double-Stranded Breaks in the Yeast Genome]]<br />
<br />
[[Tabular_Form_of_Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|Tabular For of Meiotic Double Stranded Breaks in the Yeast Genome]]<br />
<br />
[[S._cerevisiae_Codon_Usage_Tables|Codon Usage Tables]]<br />
<br />
=Reagents=<br />
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]<br />
<br />
[[Commonly_used_auxotrophic_markers|Commonly Used Auxotrophic Markers]]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Tabular_Form_of_Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome&diff=398854Tabular Form of Meiotic Double-Stranded Breaks in the Yeast Genome2014-04-16T16:35:44Z<p>Kyla: Created page with "The meiotic double-stranded breaks data on Chromosome III was kindly provided in both tabular and graphical form by Dr. Frédéric Baudat and Dr. Alain Nicolas of the Institut..."</p>
<hr />
<div>The meiotic double-stranded breaks data on Chromosome III was kindly provided in both tabular and graphical form by Dr. Frédéric Baudat and Dr. Alain Nicolas of the Institut Curie, Section de Recherche. For further information, please see their paper, [http://www.pnas.org/content/94/10/5213.long Proc. Natl. Acad. Sci. (1997) USA 94:5213-5218]. Please note that the coordinates given for the double stranded breaks are based on the chromosome III sequence of 1/31/97. Due to sequence changes on chromosome III since this time, the coordinates shown in the table below are not identical to the current coordinates for chromosome III.<br />
<center>***[[Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|Return to graphical display of double stranded breaks on Chromosome III]]***</center><br />
<br><br />
{| {{table}} border="1"<br />
|-<br />
! '''Coordinates of double stranded break sites on chromosome III (using 01/31/97 sequence)''' !! '''(bp)''' !! '''DSBs located 5' of this ORF (or in other relative locations, where indicated):''' !! '''% of cells containing double-stranded break'''<br />
|-<br />
| 17140<br />
| 300<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL063W YCL063W]<br />
| 0.2<br />
|- <br />
| 22241<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL061C YCL061C]<br />
| 0.1<br />
|- <br />
| 24341<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL058C YCL058C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PRD1 YCL057W/PRD1]<br />
| 0.2<br />
|- <br />
| 24541<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL058C YCL058C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PRD1 YCL057W/PRD1]<br />
| 0.3<br />
|- <br />
| 38995<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=DTP1 DTP1]<br />
| 0.7<br />
|- <br />
| 39200<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=DTP1 DTP1]<br />
| 0.2<br />
|- <br />
| 40845<br>40945<br />
| 150<br>150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL049C YCL049C]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL049C YCL049C]<br />
| combined value <br>of 2.0<br />
|- <br />
| 41245<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL049C YCL049C]<br />
| 0.1<br />
|- <br />
| 41995<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL048W YCL048W]<br />
| 0.4<br />
|- <br />
| 44578<br />
| 500<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL047C YCL047C]<br />
| 0.2<br />
|- <br />
| 46987<br />
| 40<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL045C YCL045C]<br />
| 0.4<br />
|- <br />
| 47057<br />
| 40<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL045C YCL045C]<br />
| 0.5<br />
|- <br />
| 48402<br />
| 75<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL044C YCL044C]<br />
| 0.4<br />
|- <br />
| 50254<br>50604<br>50727<br />
| 125<br>125<br>100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PDI1 PDI1], [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1]<br>[http://www.yeastgenome.orgcgi-bin/seqTools?seqname=PDI1 PDI1], [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PDI1 PDI1], [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1]<br />
| combined value<br>of 5.0<br />
|- <br />
| 51377<br>51627<br>51827<br />
| 100<br>150<br>200<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1] coding region<br>in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1] coding region<br>in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=GLK1 GLK1] coding region<br />
| combined value<br>of 2.0<br />
|- <br />
| 52427<br />
| 300<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL039W YCL039W]<br />
| 2.0<br />
|- <br />
| 56763<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL038C YCL038C]<br />
| 0.6<br />
|- <br />
| 58803<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL037C YCL037C/SRO9]<br />
| 0.03<br />
|- <br />
| 58893<br />
| 40<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL037C YCL037C/SRO9]<br />
| 0.1<br />
|- <br />
| 61251<br>61476<br>61526<br />
| 75<br>100<br>100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL035C YCL035C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL034W YCL034W]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL035C YCL035C][http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL034W YCL034W]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL035C YCL035C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL034W YCL034W]<br />
| combined value<br>of 0.9<br />
|- <br />
| 63269<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL033C YCL033C];<br />
[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=STE50 STE50]<br />
| 0.1<br />
|- <br />
| 65600<br />
| 350<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL031C YCL031C/RRP7]<br />
| 0.3<br />
|- <br />
| 68351<br>68501<br>68601<br />
| 50<br>50<br>50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=HIS4 HIS4]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=HIS4 HIS4]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=HIS4 HIS4]<br />
| combined value<br>of 0.9<br />
|- <br />
| 70078<br />
| 125<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=BIK1 BIK1]<br />
| 0.3<br />
|- <br />
| 71551<br />
| 250<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=FUS1 FUS1] (spread across 300 bp)<br />
| 0.3<br />
|- <br />
| 74208<br />
| 200<br />
| 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=FUS1 FUS1]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL026C-A YCL026C-A/FRM2]<br> (previously called YCL0X8C)<br />
| 2.7<br />
|- <br />
| 75951<br />
| 650<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL026C-A YCL026C-A/FRM2]<br />
| 0.7<br />
|- <br />
| 78054<br>78104<br>78204<br>78304<br>78381<br>78431<br />
| 50<br>50<br>50<br>50<br>75<br>75<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL025C YCL025C/AGP1]<br />
| combined value<br>of 5.0<br />
|- <br />
| 90667<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=LEU2 LEU2]<br />
| 1.6<br />
|- <br />
| 94120<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=NFS1 NFS1]<br />
| 0.3<br />
|- <br />
| 95568<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL016C YCL016C]-[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL014W YCL014W/BUD3]<br />
| 0.9<br />
|- <br />
| 101456<br />
| 100<br />
| 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL012W YCL012W]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL011C YCL011C/GBP2]<br />
| 0.02<br />
|- <br />
| 101556<br />
| 100<br />
| 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL012W YCL012W]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL011C YCL011C/GBP2]<br />
| 0.1<br />
|- <br />
| 103081<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL011C YCL011C/GBP2]<br />
| 0.02<br />
|- <br />
| 103181<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL011C YCL011C/GBP2]<br />
| 0.03<br />
|- <br />
| 104081<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL010C YCL010C]<br />
| 1.2<br />
|- <br />
| 105331<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL009C YCL009C/ILV6]<br />
| 1.2<br />
|- <br />
| 106581<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL008C YCL008C/STP22]<br />
| 0.4<br />
|- <br />
| 107531<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL007C YCL007C/CWH36]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL006C YCL006C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL005W YCL005W]<br />
| 0.4<br />
|- <br />
| 108610<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PEL1 PEL1]<br />
| 0.3<br />
|- <br />
| 111400<br />
| 250<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL002C YCL002C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCL001W YCL001W/RER1]<br />
| 0.2<br />
|- <br />
| 163369<br>164069<br><br />
| 150<br>350<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PMP1 PMP1]; in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR025C YCR025C] coding region<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PMP1 PMP1]; in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR025C YCR025C] coding region<br />
| combined value <br>of 1.6<br />
|- <br />
| 184890<br />
| 125<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR033W YCR033W]<br />
| 0<br />
|- <br />
| 189183<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR034W YCR034W/FEN1]<br />
| 0<br />
|- <br />
| 190563<br />
| 450<br />
| 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR034W YCR034W/FEN1]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR035C YCR035C/RRP43]<br />
| 0<br />
|- <br />
| 191900<br />
| 400<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR035C YCR035C/RRP43]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR036W YCR036W/RBK1]<br />
| 0.5<br />
|- <br />
| 196016<br />
| 125<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR037C YCR037C/PHO87]<br />
| 1.7<br />
|- <br />
| 198284<br />
| 75<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=BUD5 BUD5]<br />
| 0<br />
|- <br />
| 198959<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=a2 a2]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=a1 a1]<br />
| 0<br />
|- <br />
| 199550<br />
| 150<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=a1 a1] coding region; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR041W YCR041W]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=a1 a1]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=TSM1 TSM1]<br />
| 0.6<br />
|- <br />
| 201300<br />
| 100<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=TSM1 TSM1] coding region<br />
| 0.3<br />
|- <br />
| 204200<br />
| 250<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=TSM1 TSM1]<br />
| 0.4<br />
|- <br />
| 204342<br />
| 350<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR043C YCR043C]<br />
| 0.3<br />
|- <br />
| 206692<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR044C YCR044C]<br />
| 0.4<br />
|- <br />
| 208442<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR045C YCR045C]<br />
| 0.6<br />
|- <br />
| 209292<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR046C YCR046C/IMG1]<br />
| 1.8<br />
|- <br />
| 209942<br />
| 100<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR047C YCR047C] coding region<br />
| 0.1<br />
|- <br />
| 210425<br>210525<br><br />
| 50<br>50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR047C YCR047C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR048W YCR048W/ARE1]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR047C YCR047C][http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR048W YCR048W/ARE1]<br />
| combined value <br>of 8.8<br />
|- <br />
| 210942<br />
| 50<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR048W YCR048W/ARE1] and [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR049C YCR049C] coding regions<br />
| 0.02<br />
|- <br />
| 211092<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR049C YCR049C]; in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR048W" YCR048W/ARE1] coding region<br />
| 0.1<br />
|- <br />
| 212727<br />
| 250<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR051W YCR051W]<br />
| 0.8<br />
|- <br />
| 213580<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR052W YCR052W/RSC6]<br />
| 0.6<br />
|-<br />
| 215327<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=THR4 THR4]<br />
| 1.0<br />
|- <br />
| 219049<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=CTR86 CTR86]<br />
| 0.7<br />
|- <br />
| 222049<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=PWP2 PWP2]<br />
| 0.2<br />
|- <br />
| 222154<br />
| 35<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR058C PWP2]<br />
| 0.4<br />
|- <br />
| 223075<br />
| 65<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR059C YCR059C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR060W YCR060W] (spread across 100 bp)<br />
| 0.6<br />
|- <br />
| 224035<br>223695<br><br />
| 75<br>35<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR061W YCR061W]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR061W YCR061W]<br />
| combined value <br>of 1.0<br />
|- <br />
| 224110<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR061W YCR061W]<br />
| 4.7<br />
|- <br />
| 227110<br />
| 300<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR063W YCR063W]<br />
| 1.4<br />
|- <br />
| 227160<br />
| 250<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR064C YCR064C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR065W YCR065W/HCM1]<br />
| 3.9<br />
|- <br />
| 230010<br />
| 600<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=RAD18 RAD18]<br />
| 0.3<br />
|- <br />
| 231610<br />
| 1000<br />
| 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=RAD18 RAD18]; 3' of [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR067C YCR067C/SED4]<br />
| 0.4<br />
|- <br />
| 235200<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR067C YCR067C/SED4]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR068W YCR068W]<br />
| 2.0<br />
|- <br />
| 235500<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR067C YCR067C/SED4]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR068W YCR068W]<br />
| 0.8<br />
|- <br />
| 237500<br />
| 150<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR069W YCR069W/SCC3]<br />
| 0.7<br />
|- <br />
| 239450<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR071C YCR071C/IMG2]<br />
| 0.7<br />
|- <br />
| 241200<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR072C YCR072C]<br />
| 0.6<br />
|- <br />
| 245550<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR073C YCR073C/SSK22]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR073W-A YCR073W-A/SOL2]<br />
| 2.8<br />
|- <br />
| 247550<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=ERS1 ERS1]<br />
| 0.5<br />
|- <br />
| 248832<br />
| 75<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR076C YCR076C]<br />
| 0.3<br />
|- <br />
| 251483<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR077C YCR077C/PAT1]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR079W YCR079W]<br />
| 1.3<br />
|- <br />
| 257383<br />
| 1000<br />
| in [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR081W YCR081W/SRB8] coding region;<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR082W YCR082W] or [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR083W YCR083W]<br />
| 0.5<br />
|- <br />
| 260883<br />
| 500<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=TUP1 TUP1]<br />
| 0<br />
|- <br />
| 261433<br />
| 450<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=TUP1 TUP1]<br />
| 0<br />
|- <br />
| 265583<br />
| 200<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR089W YCR089W/FIG2]<br />
| 0<br />
|- <br />
| 271764<br />
| 400<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR090C YCR090C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=KIN28 KIN28]<br />
| 0<br />
|- <br />
| 273014<br />
| 350<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR090C YCR090C]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=KIN28 KIN28]<br />
| 0<br />
|- <br />
| 278632<br>278717<br><br />
| 35<br>50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=MSH3 MSH3]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR093W YCR093W/CDC39]<br>[http://www.yeastgenome.org/cgi-bin/seqTools?seqname=MSH3 MSH3]; [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR093W YCR093W/CDC39]<br />
| combined value<br>of 1.2<br />
|- <br />
| 285391<br />
| 100<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR094W YCR094W/CDC50]<br />
| 0.6<br />
|- <br />
| 288050<br />
| 50<br />
| [http://www.yeastgenome.org/cgi-bin/seqTools?seqname=YCR095C YCR095C]<br />
| 0<br />
|}</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Methods&diff=398853Methods2014-04-16T16:11:05Z<p>Kyla: </p>
<hr />
<div>*[http://labs.fhcrc.org/breeden/Methods/index.html Yeast Lab Protocols] from the Breeden Lab, Fred Hutchinson Cancer Research Center.<br />
<br />
*[http://labs.fhcrc.org/gottschling/Yeast%20Protocols/index.html Yeast Lab Protocols] from the Gottschling Lab, Fred Hutchinson Cancer Research Center.<br />
<br />
*[http://gasch.genetics.wisc.edu/protocols.html Yeast & Microarray Protocols] from the Gasch Lab, University of Wisconsin-Madison.<br />
<br />
*[http://home.cc.umanitoba.ca/~gietz/ The Definitive Yeast Transformation Homepage] from the University of Manitoba.<br />
<br />
*[http://fangman-brewer.genetics.washington.edu/index.html DNA Replication Protocols] from the Fangman and Brewer Labs, University of Washington.<br />
<br />
*[http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide. Version 2.0], a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.<br />
<br />
*[http://gasch.genetics.wisc.edu/protocols/Gasch_MethEnzym.pdf Guide to Yeast Microarray Experiments], by Audrey Gasch, from <u>Guide to Yeast Genetics and Molecular and Cellular Biology</u>, Methods in Enzymology (2002)<br />
<br />
*[http://depts.washington.edu/yeastrc/ The NCRR Yeast Resource Center] at the University of Washington facilitates the study of yeast protein complexes by providing access to techniques such as mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction.<br />
<br />
* [http://genome.cshlp.org/content/7/12/1174.full PCR-Based Allele Replacement] (Erdeniz <i>et al.</i> (1997) Genome Res. 7:1174-1183). Available to the public without password restriction and at no charge, through a special arrangement with Genome Research arranged by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bärtsch on the W303 strain; derivatives were used in the study'').<br />
<br />
*[http://dunham.gs.washington.edu/home.shtml Chemostat Manual] from Maitreya Dunham's lab, University of Washington. <br />
<br />
*[http://www.phys.ksu.edu/gene/chapters.html A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University based on [http://www.rushessay.com essay writing].<br />
<br />
*[http://openwetware.org/wiki/The_mRNA_Decay_Resource:Protocols_and_Resources Protocols and Resources] from the RNA Decay Resource, a resource for the sharing of information, know-how, and wisdom among researchers who study mRNA decay.<br />
<br />
*[[SGA]] protocols and scoring software.<br />
<br />
*[http://Vadlo.com/ Molecular Biology Protocols Search Engine] from Life in Research, LLC. Also life sciences databases, online tools, software, and powerpoints. For example [http://www.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://www.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases]<br />
<br />
*[http://wiki.yeastgenome.org/index.php/Software Software tools] created by members of the scientific community.<br />
*[http://sbs.umkc.edu/yeastcommunity/ Yeast Community Site] from Honigberg Lab, University of Missouri Kansas City.<br />
<br />
*[http://www.magusto.com/ Concours Site] from concours Lab, University of Mousseaux sur seine (protocol in French).<br />
<br />
*[[Yeast_Cell_Micromanipulation|Yeast Cell Micromanipulation]] Protocol for Making Support Rod with Fiber Optic Needle Attached from Cora Styles<br />
<br />
*[http://yeastgenome.org/cgi-bin/geneticData/displayTwoPoint? Genetic Mapping (Two-Point) Data] for yeast genes.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Yeast_Cell_Micromanipulation&diff=398852Yeast Cell Micromanipulation2014-04-16T16:07:13Z<p>Kyla: Created page with "<center><big>Protocol for Making Support Rod with Fiber Optic Needle Attached</big></center> <center><big>from [http://www.corastyles.com Cora Styles]</big></center> ==Advan..."</p>
<hr />
<div><center><big>Protocol for Making Support Rod with Fiber Optic Needle Attached</big></center><br />
<br />
<center><big>from [http://www.corastyles.com Cora Styles]</big></center><br />
<br />
==Advantages:==<br />
*Perfectly flat and light-transmitting<br />
*Minimal time and effort to construct<br />
*Non-breakable support stem<br />
*Minimal shadow in field of view<br />
'''Materials Needed:'''<br />
*3/4 inch fiber-optic strand with polished ends (for source, see below)<br />
*closed end capillary 1 mm diam.<br />
*aluminum rod 2mm x 5 inches<br />
*superglue<br />
*tape<br />
*2 microscope slides 1 inch x 3 inches<br />
*small, steady flame (for example, a well-shielded pilot from Touch-o-matic burner)<br />
*small, non-serrated forceps (Millipore is preferable)<br />
*toothpick with Parafilm tip<br />
*Might need hacksaw or bolt cutter<br />
==Protocol:==<br />
#Make a right angle bend 3/8 inch from closed end of capillary tube. With the capillary tube secured to a horizontal support, heat the bend point with the tip of the flame. As the glass softens, the tip will fall by gravity straight down into the flame. Remove the flame.<br />
#This step is optional, but will reduce shadow. Stretch out the short closed-end segment to make it thinner. Direct the flame to the middle (not at the bend!) of the short segment. Grasp the closed-end tip with forceps and pull it gently and deliberately. Keep your line straight to preserve the 90 degree angle. Cut off excess glass to leave a suitable length of 5/16 to 1/2 inch.<br />
#Place the capillary tube parallel to the aluminum rod so that the bent end extends 1 inch beyond the rod. Tape them together. One short piece of tape is enough.<br />
#Check the length of your two-part needle support. Measure the distance between the viewing site of your microscope and the micromanipulator holder. Shorten your rod if necessary using a hacksaw or bolt cutter.<br />
#Attach a fiber optic strand to the short bent segment of the capillary tube using superglue.<br />
#*Working under good light, place a fiber optic strand on a glass slide. Strands are handled conveniently with forceps or a Parafilm-tipped toothpick. If convenient, check under low power (40-50X) magnification to be sure the ends are squared off (not broken).<br />
#*Move the fiber so that one end extends into open air beyond the edge of the slide, or even slants down off the slide. The opposite end will be the working tip.<br />
#*Apply a drop of super-glue to the second slide, and moisten the capillary bent segment in it. Bring the glue-moistened segment parallel to the optic fiber so that the bend meets it about 1/8 inch from the non-working end (the end off the slide). On contact, the fiber will attach by surface tension. Caution: Avoid touching the slide with glue - the fiber may stick to the slide! And avoid getting glue on the bottom end of the fiber - light transmission will be impaired (but the needle will still function).<br />
#Adjust the angle and height of the fiber needle. While the glue is still moist, you can make small adjustments with a toothpick or your fingertip. Try to perfect the right angle. The distance from the bend to working tip should be a little over 1/2 inch.<br />
'''Sources:'''<br />
*Fiber optic needle source:<br />
<br />
[http://corastyles.com Cora Styles Lab Supplies, LLC]<br />
<Br><br />
PO Box 431<br />
<br><br />
Talent, OR 97540<br />
<br><br />
Phone: 541-535-6775<br />
<br><br />
Fax: 678-693-5704<br />
<br><br />
E-mail: products@CoraStyles.com</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Bay_Area_Yeast_Meeting&diff=398833Bay Area Yeast Meeting2014-04-10T16:13:46Z<p>Kyla: /* Program */</p>
<hr />
<div>=Spring 2014 Bay Area Yeast Meeting Information=<br />
The Spring Bay Area Yeast Meeting is hosted by the <i>Saccharomyces</i> Genome Database group at Stanford University and UC Berkeley.<br />
<br />
* Venue: M106, Alway Building, Stanford Medical Center (intersection of Roth and Campus Dr)<br />
* Location: Stanford University, CA<br />
* Date: April 19th, 2014<br />
<br />
==Registration==<br />
* Registration is free.<br />
* To help us get a head count for food and to prepare the meeting agenda, please enter your information using this [https://docs.google.com/forms/d/1a8GTekOulC5C-oshJ4Y30CvqXELTxJQxh2q_EVOC0kY/viewform? Registration Form]<br />
<br />
==Program==<br />
9:00 - 10:00 Coffee and Registration (Courtyard outside M106) <br><br />
10:00 - 12:00 Research Talks M106 <br><br />
<br />
*FRET-based assay for monitoring septin filament assembly<br />
::''Elizabeth “Libby” Booth, Jeremy Thorner Lab, UC Berkeley''<br />
<br />
*Yeast's evil relative: a fungus that swims, crawls, and kills vertebrates<br />
::''Tim Stearns, Stanford University''<br />
<br />
*Number of Cln3 molecules determines budding probability in yeast<br />
::''Kurt Schmoller , J.M. Skotheim Lab, Stanford University''<br />
<br />
*Re-replication of a centromere induces whole-chromosomal instability and aneuploidy<br />
::''Stacey Hanlon, Joachim J. Li Lab, UCSF''<br />
<br />
*Heterozygote advantage in adapting diploids<br />
::''Diamantis Sellis, Dmitri Petrov Lab, Stanford University''<br />
<br />
*TBA<br />
::''Chandra Richter - Gallo Research''<br />
<br />
12:00 - 1:45 Lunch and Posters (Courtyard outside M106)<br><br />
1:50 - 3:45 Research Talks M106 <br><br />
<br />
*Investigating the functional defects of human p53 mutations in a yeast model system: an introductory molecular biology laboratory course for undergraduates<br />
::''Daria Hekmat-Scafe, Martha Cyert and Tim Stearns Lab, Stanford University''<br />
<br />
*Chromatin Remodeling as a Molecular Basis of Expression Noise<br />
::''Christopher Brown, Hinrich Boeger Lab, UC Santa Cruz''<br />
<br />
*Insights into yeast gene regulation though high-throughput and precision RNA boundary mapping<br />
::''Aino Järvelin, Lars Steinmetz Lab, EMBL''<br />
<br />
*Transient expression of intrinsically disordered proteins heritably transforms the phenotypic landscape of S. cerevisiae<br />
::''Daniel Jarosz, Stanford University''<br />
<br />
*Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation<br />
::''Carlo Artieri, Hunter B. Fraser Lab, Stanford University''<br />
<br />
*The role of nucleoporins specifically Nup2 during meiosis in budding yeast<br />
::''Daniel Chu, Sean Burgess Lab, UC Davis''<br />
<br />
3:50 - 4:50 Keynote Speaker M106<br><br />
:::“Genes and proteins that control secretion and autophagy.”<br />
''Randy Schekman, Howard Hughes Investigator and Professor of Cell and Developmental Biology, UC Berkeley''<Br><br />
''Nobel Prize in Physiology or Medicine, 2013''<br />
<br />
4:50 - 5:30 Wine reception (Courtyard outside M106)<br />
<br />
[[media:Spring_Bay_Area_Yeast_Meeting_2014(2).pdf|Printable Schedule]]<br />
<br />
==Keynote Speaker==<br />
Genes and proteins that control secretion and autophagy.<br />
<br><br />
''Randy Schekman, UC Berkeley (Nobel Prize in Physiology or Medicine, 2013)''<br />
<br />
==Maps & Parking==<br />
Parking is free during the weekend on Stanford campus.<br />
<br />
Parking structure closest to M106 is at the intersection of Roth and Campus drive.<br />
[http://maps.stanford.edu/maps_library Stanford University maps]<br />
<br />
==Campus Shuttle (Marguerite)==<br />
Free campus shuttle from downtown Palo Alto is available. The Palo Alto Train Station is the closest stop to Stanford University. <br />
A variety of maps for the [http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Marguerite Shuttle] are available.<br />
<br />
Realtime [http://lbre-apps.stanford.edu/transportation/stanford_ivl/ Shuttle Bus Service]. The Stanford Marguerite Shuttle is free.<br />
<br />
==Sponsors==<br />
* Amyris Biotechnologies<br />
* E&J Gallo Winery<br />
* School of Medicine, Stanford University<br />
<br />
==Need help?==<br />
* If you have any questions please contact us at [http://www.yeastgenome.org/cgi-bin/suggestion sgd-helpdesk]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:Spring_Bay_Area_Yeast_Meeting_2014(2).pdf&diff=398832File:Spring Bay Area Yeast Meeting 2014(2).pdf2014-04-10T16:09:10Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=Bay_Area_Yeast_Meeting&diff=398831Bay Area Yeast Meeting2014-04-10T16:07:14Z<p>Kyla: /* Program */</p>
<hr />
<div>=Spring 2014 Bay Area Yeast Meeting Information=<br />
The Spring Bay Area Yeast Meeting is hosted by the <i>Saccharomyces</i> Genome Database group at Stanford University and UC Berkeley.<br />
<br />
* Venue: M106, Alway Building, Stanford Medical Center (intersection of Roth and Campus Dr)<br />
* Location: Stanford University, CA<br />
* Date: April 19th, 2014<br />
<br />
==Registration==<br />
* Registration is free.<br />
* To help us get a head count for food and to prepare the meeting agenda, please enter your information using this [https://docs.google.com/forms/d/1a8GTekOulC5C-oshJ4Y30CvqXELTxJQxh2q_EVOC0kY/viewform? Registration Form]<br />
<br />
==Program==<br />
9:00 - 10:00 Coffee and Registration (Courtyard outside M106) <br><br />
10:00 - 12:00 Research Talks M106 <br><br />
<br />
*FRET-based assay for monitoring septin filament assembly<br />
::''Elizabeth “Libby” Booth, Jeremy Thorner Lab, UC Berkeley''<br />
<br />
*Yeast's evil relative: a fungus that swims, crawls, and kills vertebrates<br />
::''Tim Stearns, Stanford University''<br />
<br />
*Number of Cln3 molecules determines budding probability in yeast<br />
::''Kurt Schmoller , J.M. Skotheim Lab, Stanford University''<br />
<br />
*Re-replication of a centromere induces whole-chromosomal instability and aneuploidy<br />
::''Stacey Hanlon, Joachim J. Li Lab, UCSF''<br />
<br />
*Heterozygote advantage in adapting diploids<br />
::''Diamantis Sellis, Dmitri Petrov Lab, Stanford University''<br />
<br />
*TBA<br />
::''Chandra Richter - Gallo Research''<br />
<br />
12:00 - 1:45 Lunch and Posters (Courtyard outside M106)<br><br />
1:50 - 3:45 Research Talks M106 <br><br />
<br />
*Investigating the functional defects of human p53 mutations in a yeast model system: an introductory molecular biology laboratory course for undergraduates<br />
::''Daria Hekmat-Scafe, Martha Cyert and Tim Stearns Lab, Stanford University''<br />
<br />
*Chromatin Remodeling as a Molecular Basis of Expression Noise<br />
::''Christopher Brown, Hinrich Boeger Lab, UC Santa Cruz''<br />
<br />
*Insights into yeast gene regulation though high-throughput and precision RNA boundary mapping<br />
::''Aino Järvelin, Lars Steinmetz Lab, EMBL''<br />
<br />
*Transient expression of intrinsically disordered proteins heritably transforms the phenotypic landscape of S. cerevisiae<br />
::''Daniel Jarosz, Stanford University''<br />
<br />
*Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation<br />
::''Carlo Artieri, Hunter B. Fraser Lab, Stanford University''<br />
<br />
*The role of nucleoporins specifically Nup2 during meiosis in budding yeast<br />
::''Daniel Chu, Sean Burgess Lab, UC Davis''<br />
<br />
3:50 - 4:50 Keynote Speaker M106<br><br />
:::“Genes and proteins that control secretion and autophagy.”<br />
''Randy Schekman, Howard Hughes Investigator and Professor of Cell and Developmental Biology, UC Berkeley''<Br><br />
''Nobel Prize in Physiology or Medicine, 2013''<br />
<br />
4:50 - 5:30 Wine reception (Courtyard outside M106)<br />
<br />
[[media:SBAYM2014.pdf|Printable Schedule]]<br />
<br />
==Keynote Speaker==<br />
Genes and proteins that control secretion and autophagy.<br />
<br><br />
''Randy Schekman, UC Berkeley (Nobel Prize in Physiology or Medicine, 2013)''<br />
<br />
==Maps & Parking==<br />
Parking is free during the weekend on Stanford campus.<br />
<br />
Parking structure closest to M106 is at the intersection of Roth and Campus drive.<br />
[http://maps.stanford.edu/maps_library Stanford University maps]<br />
<br />
==Campus Shuttle (Marguerite)==<br />
Free campus shuttle from downtown Palo Alto is available. The Palo Alto Train Station is the closest stop to Stanford University. <br />
A variety of maps for the [http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Marguerite Shuttle] are available.<br />
<br />
Realtime [http://lbre-apps.stanford.edu/transportation/stanford_ivl/ Shuttle Bus Service]. The Stanford Marguerite Shuttle is free.<br />
<br />
==Sponsors==<br />
* Amyris Biotechnologies<br />
* E&J Gallo Winery<br />
* School of Medicine, Stanford University<br />
<br />
==Need help?==<br />
* If you have any questions please contact us at [http://www.yeastgenome.org/cgi-bin/suggestion sgd-helpdesk]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Historical_Systematic_Sequence_Information&diff=398830Historical Systematic Sequence Information2014-04-10T16:06:25Z<p>Kyla: </p>
<hr />
<div>These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].<br />
<br />
=Chromosomal Features=<br />
[[Modified_Nucleotides_within_RNAs_in_S._cerevisiae|Modified Nucleotides within RNAs in S. cerevisiae]]<br />
<br />
[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]<br />
<br />
[[Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|Meiotic Double-Stranded Breaks in the Yeast Genome]]<br />
<br />
[[S._cerevisiae_Codon_Usage_Tables|Codon Usage Tables]]<br />
<br />
<br />
<br />
=Reagents=<br />
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]<br />
<br />
[[Commonly_used_auxotrophic_markers|Commonly Used Auxotrophic Markers]]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Historical_Systematic_Sequence_Information&diff=398829Historical Systematic Sequence Information2014-04-10T16:05:07Z<p>Kyla: </p>
<hr />
<div>These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].<br />
<br />
=Chromosomal Features=<br />
[[Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome|Modified Nucleotides within RNAs in S. cerevisiae]]<br />
<br />
[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]<br />
<br />
[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]<br />
<br />
[[S._cerevisiae_Codon_Usage_Tables|Codon Usage Tables]]<br />
<br />
<br />
<br />
=Reagents=<br />
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]<br />
<br />
[[Commonly_used_auxotrophic_markers|Commonly Used Auxotrophic Markers]]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Historical_Systematic_Sequence_Information&diff=398828Historical Systematic Sequence Information2014-04-10T15:52:31Z<p>Kyla: /* Chromosomal Features */</p>
<hr />
<div>These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].<br />
<br />
=Chromosomal Features=<br />
[http://wiki.yeastgenome.org/index.php/Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome Modified Nucleotides within RNAs in S. cerevisiae]<br />
<br />
[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]<br />
<br />
[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]<br />
<br />
[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]<br />
<br />
=Reagents=<br />
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]<br />
<br />
[[Commonly_used_auxotrophic_markers|Commonly Used Auxotrophic Markers]]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Bay_Area_Yeast_Meeting&diff=398827Bay Area Yeast Meeting2014-04-10T15:01:51Z<p>Kyla: /* Program */</p>
<hr />
<div>=Spring 2014 Bay Area Yeast Meeting Information=<br />
The Spring Bay Area Yeast Meeting is hosted by the <i>Saccharomyces</i> Genome Database group at Stanford University and UC Berkeley.<br />
<br />
* Venue: M106, Alway Building, Stanford Medical Center (intersection of Roth and Campus Dr)<br />
* Location: Stanford University, CA<br />
* Date: April 19th, 2014<br />
<br />
==Registration==<br />
* Registration is free.<br />
* To help us get a head count for food and to prepare the meeting agenda, please enter your information using this [https://docs.google.com/forms/d/1a8GTekOulC5C-oshJ4Y30CvqXELTxJQxh2q_EVOC0kY/viewform? Registration Form]<br />
<br />
==Program==<br />
9:00 - 10:00 Coffee and Registration (Courtyard outside M106) <br><br />
10:00 - 12:00 Research Talks M106 <br><br />
<br />
*FRET-based assay for monitoring septin filament assembly<br />
::''Elizabeth “Libby” Booth, Jeremy Thorner Lab, UC Berkeley''<br />
<br />
*Yeast's evil relative: a fungus that swims, crawls, and kills vertebrates<br />
::''Tim Stearns, Stanford University''<br />
<br />
*Number of Cln3 molecules determines budding probability in yeast<br />
::''Kurt Schmoller , J.M. Skotheim Lab, Stanford University''<br />
<br />
*Re-replication of a centromere induces whole-chromosomal instability and aneuploidy<br />
::''Stacey Hanlon, Joachim J. Li Lab, UCSF''<br />
<br />
*Heterozygote advantage in adapting diploids<br />
::''Diamantis Sellis, Dmitri Petrov Lab, Stanford University''<br />
<br />
*TBA<br />
::''Chandra Richter - Gallo Research''<br />
<br />
12:00 - 1:45 Lunch and Posters (Courtyard outside M106)<br><br />
1:50 - 3:45 Research Talks M106 <br><br />
<br />
*Investigating the functional defects of human p53 mutations in a yeast model system: an introductory molecular biology laboratory course for undergraduates<br />
::''Daria Hekmat-Scafe, Martha Cyert and Tim Stearns Lab, Stanford University''<br />
<br />
*Chomatin Remodeling as a Molecular Basis of Expression Noise<br />
::''Christopher Brown, Hinrich Boeger Lab, UC Santa Cruz''<br />
<br />
*Insights into yeast gene regulation though high-throughput and precision RNA boundary mapping<br />
::''Aino Järvelin, Lars Steinmetz Lab, EMBL''<br />
<br />
*Transient expression of intrinsically disordered proteins heritably transforms the phenotypic landscape of S. cerevisiae<br />
::''Daniel Jarosz, Stanford University''<br />
<br />
*Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation<br />
::''Carlo Artieri, Hunter B. Fraser Lab, Stanford University''<br />
<br />
*The role of nucleoporins specifically Nup2 during meiosis in budding yeast<br />
::''Daniel Chu, Sean Burgess Lab, UC Davis''<br />
<br />
3:50 - 4:50 Keynote Speaker M106<br><br />
:::“Genes and proteins that control secretion and autophagy.”<br />
''Randy Schekman, Howard Hughes Investigator and Professor of Cell and Developmental Biology, UC Berkeley''<Br><br />
''Nobel Prize in Physiology or Medicine, 2013''<br />
<br />
4:50 - 5:30 Wine reception (Courtyard outside M106)<br />
<br />
[[media:SBAYM2014.pdf|Printable Schedule]]<br />
<br />
==Keynote Speaker==<br />
Genes and proteins that control secretion and autophagy.<br />
<br><br />
''Randy Schekman, UC Berkeley (Nobel Prize in Physiology or Medicine, 2013)''<br />
<br />
==Maps & Parking==<br />
Parking is free during the weekend on Stanford campus.<br />
<br />
Parking structure closest to M106 is at the intersection of Roth and Campus drive.<br />
[http://maps.stanford.edu/maps_library Stanford University maps]<br />
<br />
==Campus Shuttle (Marguerite)==<br />
Free campus shuttle from downtown Palo Alto is available. The Palo Alto Train Station is the closest stop to Stanford University. <br />
A variety of maps for the [http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Marguerite Shuttle] are available.<br />
<br />
Realtime [http://lbre-apps.stanford.edu/transportation/stanford_ivl/ Shuttle Bus Service]. The Stanford Marguerite Shuttle is free.<br />
<br />
==Sponsors==<br />
* Amyris Biotechnologies<br />
* E&J Gallo Winery<br />
* School of Medicine, Stanford University<br />
<br />
==Need help?==<br />
* If you have any questions please contact us at [http://www.yeastgenome.org/cgi-bin/suggestion sgd-helpdesk]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome&diff=398826Meiotic Double-Stranded Breaks in the Yeast Genome2014-04-09T16:39:05Z<p>Kyla: </p>
<hr />
<div>The localization of the Spo11-dependent double-stranded break sites and the chromatin asssociation of Mre11p with double strand break sites during meiosis has been characterized at the genome-wide level in a subsequent paper (Borde et al. (2004) Association of Mre11p with Double-Strand Break Sites during Yeast Meiosis. [http://www.ncbi.nlm.nih.gov/pubmed/?term=14967146 Mol Cell (2004) 13(3):389-401]). <br />
<br><br />
<br />
The meiotic double-stranded breaks data on Chromosome III was kindly provided in both tabular and graphical form by Dr. Frédéric Baudat and Dr. Alain Nicolas of the Institut Curie, Section de Recherche. For further information, please see their paper, [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volume:94!firstpage:5213!tyear:1998!fyear:1996!fmonth:Feb!tmonth:Apr!tdatedef:28%2520April%25201998!fdatedef:6%2520February%25201996!hits:10!sendit:Search Proc. Natl. Acad. Sci. (1997) USA 94:5213-5218]. This graphic represents '''Figure 2''' of this paper. The key and legend for this figure are located directly under the figure.<br />
For a commentary article on this topic, please see Nicolas, A. (1998). Relationship between transcription and initiation of meiotic recombination: Toward chromatin accessibility. [http://www.pnas.org/content/95/1/87.full Proc. Natl. Acad. Sci. (1998) USA 95:87-89].<br />
<br><br />
<br />
<center>[[file:chrIII.dsbreak.png|900px|link=http://www.yeastgenome.org/images/chrIII.dsbreak.gif]]</center><br />
<br />
<br><br />
Legend from '''Figure 2''' of [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volum%5c Proc. Natl. Acad. Sci. (1997) USA 94:5213-5218]:<br />
<br><br />
<br />
'''Location and amount of meiotic DSBs on chromosome III'''. For simplification, the ORF numbers (22) are indicated without YCL or YCR. The physical map is drawn to scale from the sequence (coordinates are in kb) and is corrected for the major differences found in ORD1181 derived from SK1 that lead chromosome III to a length of 340 kb instead of 315 kb in the published sequence (22): Ty2-17 near LEU2 is absent, as is the delta LTR between YCR6c and YCR7c; a Ty2 identified by PCR amplification and restriction analysis is inserted at coordinate 151,000; a Ty1 is inserted between RIM1 and YCR29c (25); additional 396 bp are in YCR89w; the right chromosomal end is 15-25 kb longer and of unknown sequence. Bar height represents the percent of meiotic DSBs per DNA molecule. Generally, two measurements were made at each region, with different restriction digests and probes. Standard errors between different measurements of the same DSB sites depend on the DSB frequencies: 0.05-0.2% for DSB 0.5%, 0.2-0.5% for DSB between 0.5% and 1.5%, and 0.5-1% for DSB > 1.5%. Red, green, and blue bars represent DSBs in intergenic-promoter, intergenic terminators, and coding regions, respectively. Other information is provided in the legend box.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome&diff=398825Meiotic Double-Stranded Breaks in the Yeast Genome2014-04-09T16:16:59Z<p>Kyla: </p>
<hr />
<div>The localization of the Spo11-dependent double-stranded break sites and the chromatin asssociation of Mre11p with double strand break sites during meiosis has been characterized at the genome-wide level in a subsequent paper ([http://www.ncbi.nlm.nih.gov/pubmed/?term=14967146 Borde et al. (2004) Association of Mre11p with Double-Strand Break Sites during Yeast Meiosis. Mol Cell 13(3):389-401]). <br />
<br><br />
<br />
The meiotic double-stranded breaks data on Chromosome III was kindly provided in both tabular and graphical form by Dr. Frédéric Baudat and Dr. Alain Nicolas of the Institut Curie, Section de Recherche. For further information, please see their paper, [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volume:94!firstpage:5213!tyear:1998!fyear:1996!fmonth:Feb!tmonth:Apr!tdatedef:28%2520April%25201998!fdatedef:6%2520February%25201996!hits:10!sendit:Search Proc. Natl. Acad. Sci. USA 94:5213-5218 (1997)]. This graphic represents '''Figure 2''' of this paper. The key and legend for this figure are located directly under the figure.<br />
For a commentary article on this topic, please see Nicolas, A. (1998). Relationship between transcription and initiation of meiotic recombination: Toward chromatin accessibility. [http://www.pnas.org/content/95/1/87.full Proc. Natl. Acad. Sci. USA 95:87-89 (1998)].<br />
<br><br />
<br />
<center>[[file:chrIII.dsbreak.png|900px|link=http://www.yeastgenome.org/images/chrIII.dsbreak.gif]]</center><br />
<br />
<br><br />
Legend from '''Figure 2''' of [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volum%5c Proc. Natl. Acad. Sci. USA 94:5213-5218 (1997)]:<br />
<br><br />
<br />
'''Location and amount of meiotic DSBs on chromosome III'''. For simplification, the ORF numbers (22) are indicated without YCL or YCR. The physical map is drawn to scale from the sequence (coordinates are in kb) and is corrected for the major differences found in ORD1181 derived from SK1 that lead chromosome III to a length of 340 kb instead of 315 kb in the published sequence (22): Ty2-17 near LEU2 is absent, as is the delta LTR between YCR6c and YCR7c; a Ty2 identified by PCR amplification and restriction analysis is inserted at coordinate 151,000; a Ty1 is inserted between RIM1 and YCR29c (25); additional 396 bp are in YCR89w; the right chromosomal end is 15-25 kb longer and of unknown sequence. Bar height represents the percent of meiotic DSBs per DNA molecule. Generally, two measurements were made at each region, with different restriction digests and probes. Standard errors between different measurements of the same DSB sites depend on the DSB frequencies: 0.05-0.2% for DSB 0.5%, 0.2-0.5% for DSB between 0.5% and 1.5%, and 0.5-1% for DSB > 1.5%. Red, green, and blue bars represent DSBs in intergenic-promoter, intergenic terminators, and coding regions, respectively. Other information is provided in the legend box.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Meiotic_Double-Stranded_Breaks_in_the_Yeast_Genome&diff=398824Meiotic Double-Stranded Breaks in the Yeast Genome2014-04-09T15:37:12Z<p>Kyla: Created page with "The localization of the Spo11-dependent double-stranded break sites and the chromatin asssociation of Mre11p with double strand break sites during meiosis has been characteriz..."</p>
<hr />
<div>The localization of the Spo11-dependent double-stranded break sites and the chromatin asssociation of Mre11p with double strand break sites during meiosis has been characterized at the genome-wide level in a subsequent paper (Borde et al. (2004) Association of Mre11p with Double-Strand Break Sites during Yeast Meiosis. Mol Cell 13(3):389-401). <br />
<br><br />
<br />
The meiotic double-stranded breaks data on Chromosome III was kindly provided in both tabular and graphical form by Dr. Frédéric Baudat and [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch?id=4257 Dr. Alain Nicolas] of the Institut Curie, Section de Recherche. For further information, please see their paper, [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volume:94!firstpage:5213!tyear:1998!fyear:1996!fmonth:Feb!tmonth:Apr!tdatedef:28%2520April%25201998!fdatedef:6%2520February%25201996!hits:10!sendit:Search Proc. Natl. Acad. Sci. USA 94:5213-5218]. This graphic represents '''Figure 2''' of this paper. The key and legend for this figure are located directly under the figure.<br />
For a commentary article on this topic, please see Nicolas, A. (1998). Relationship between transcription and initiation of meiotic recombination: Toward chromatin accessibility. [http://www.pnas.org/content/95/1/87.full Proc. Natl. Acad. Sci. USA 95:87-89].<br />
<br><br />
<br />
<center>[[file:chrIII.dsbreak.png|900px|link=http://www.yeastgenome.org/images/chrIII.dsbreak.gif]]</center><br />
<br />
<br><br />
Legend from '''Figure 2''' of [http://www.pnas.org/content/94/10/5213.full?terms=&searchqstr=volum%5c Proc. Natl. Acad. Sci. USA 94:5213-5218]:<br />
<br><br />
<br />
'''Location and amount of meiotic DSBs on chromosome III'''. For simplification, the ORF numbers (22) are indicated without YCL or YCR. The physical map is drawn to scale from the sequence (coordinates are in kb) and is corrected for the major differences found in ORD1181 derived from SK1 that lead chromosome III to a length of 340 kb instead of 315 kb in the published sequence (22): Ty2-17 near LEU2 is absent, as is the delta LTR between YCR6c and YCR7c; a Ty2 identified by PCR amplification and restriction analysis is inserted at coordinate 151,000; a Ty1 is inserted between RIM1 and YCR29c (25); additional 396 bp are in YCR89w; the right chromosomal end is 15-25 kb longer and of unknown sequence. Bar height represents the percent of meiotic DSBs per DNA molecule. Generally, two measurements were made at each region, with different restriction digests and probes. Standard errors between different measurements of the same DSB sites depend on the DSB frequencies: 0.05-0.2% for DSB 0.5%, 0.2-0.5% for DSB between 0.5% and 1.5%, and 0.5-1% for DSB > 1.5%. Red, green, and blue bars represent DSBs in intergenic-promoter, intergenic terminators, and coding regions, respectively. Other information is provided in the legend box.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:chrIII.dsbreak.png&diff=398823File:chrIII.dsbreak.png2014-04-09T15:36:24Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=S._cerevisiae_Codon_Usage_Tables&diff=398822S. cerevisiae Codon Usage Tables2014-04-09T15:35:40Z<p>Kyla: Created page with "==These tables are from 1999 and were built using the known or predicted ORF sequences contained within the complete yeast genomic sequence.== *[http://downloads.yeastgenome.o..."</p>
<hr />
<div>==These tables are from 1999 and were built using the known or predicted ORF sequences contained within the complete yeast genomic sequence.==<br />
*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.gene.cod ''Saccharomyces cerevisiae''] from 3,222 ORFs which have been assigned a gene name by the community as listed within SGD as of January 1999.<br />
*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.orf.cod ''Saccharomyces cerevisiae''] from 6,222 ORFs listed within SGD as of January 1999.<br />
<br><br />
<br />
==These tables are from 1993 and produced with the GCG program CodonFrequency.==<br />
Duplicates, pseudogenes, mutant and synthetic genes were not included. Coding regions were specified using the Feature Table of each entry, then checked for accuracy. If more than one stop codon was found the sequence was not included.<br />
*[http://downloads.yeastgenome.org/unpublished_data/codon/ysc.g63.cod ''Saccharomyces cerevisiae''] from 435 genes found in GenBank 63.<br />
*[http://downloads.yeastgenome.org/unpublished_data/codon/yscmt.cod ''Saccharomyces cerevisiae'' mitochondrion] 17 genes found in GenBank 63.<br />
*[http://www.kazusa.or.jp/codon/ Codon Usage Database] from Yasukazu Nakamura using the latest GenBank Release.</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Modified_Nucleotides_within_RNAs_in_S._cerevisiae&diff=398821Modified Nucleotides within RNAs in S. cerevisiae2014-04-09T15:31:50Z<p>Kyla: Created page with "These tables list positions of nucleotide modifications, both pseudouridylation and ribose 2'-O-methylation, within ribosomal RNAs (5S rRNA, [[#5.8SrRNA|5.8S rRNA]..."</p>
<hr />
<div>These tables list positions of nucleotide modifications, both pseudouridylation and ribose 2'-O-methylation, within ribosomal RNAs ([[#5SrRNA|5S rRNA]], [[#5.8SrRNA|5.8S rRNA]], [[#18SrRNA|18S rRNA]], and [[#25SrRNA|25S rRNA]]) and snRNAs ([[#U1snRNA|U1 snRNA]], [[#U2snRNA|U2 snRNA]], and [[#U5snRNA|U5 snRNA]]). Many of these modifications are performed by small nucleolar ribonucleic acid complexes (snoRNPs) where a specific snoRNA guides the position of modification; in these cases, only the snoRNA is listed, though the proteins of the snoRNP complex are required to catalyze the modification. For a list of all snoRNAs, see the table of [http://yeastmine.yeastgenome.org/yeastmine/results.do?trail=%7Cresults.517&table=results.517&queryBuilder=snoRNAs snoRNAs in ''S. cerevisiae'']. Other modifications are directed and catalyzed by a protein enzyme without snoRNA guidance. Within the sequence context column, the modified nucleotide is shown in red.<br />
<br><br />
<br />
Many thanks to Wayne Decatur and Dorota Piekna-Przybylska for providing the coordinates of the modification sites within the 18S and 25S rRNAs with respect to the genome of ''S. cerevisiae''. Note that older papers have used alternate coordinate systems; links to tables providing the correspondance between old and current coordinates are provided within these two tables. For more detailed information about the snoRNAs, see the SGD Locus Summaries for each or the [http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/main.php snoRNA database at UMass Amherst].<br />
<br />
{| {{table}} border="1"<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=5SrRNA|'''Modified Position within the 5S rRNA'''<br>''compiled June 2008''<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
|50<sup>1</sup><br />
|pseudouridylation<br />
|AACUG<span style="color:#FF0000">'''U'''</span>AGUUA<br />
|[http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=PUS7 PUS7]<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
| colspan=4|1. '''Decatur WA and Schnare MN, et al.''' (2008) Different mechanisms for Pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 28(10):3089-100<br>[http://www.yeastgenome.org/reference/S000125816/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/18332121?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=5.8SrRNA|'''Modified Position within the 5.8S rRNA'''<br>''compiled June 2008''<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
|73<sup>1</sup><br />
|pseudouridylation<br />
|GUGAA<span style="color:#FF0000">'''U'''</span>UGCAG<br />
|[http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR43 snR43]<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
| colspan=4|1. '''Decatur WA and Schnare MN, et al.''' (2008) Different mechanisms for Pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 28(10):3089-100<br>[http://www.yeastgenome.org/reference/S000125816/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/18332121?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=18srRNA|'''Modified Position within the 18S rRNA'''<br>''compiled June 2007''<br>[http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/nm18s.php ''see alternate numbering systems for the 18S ribose methylations'']<br>[http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/psi18s.php ''see alternate numbering systems for the 18S pseudouridylations'']<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
|28<br />
|ribose 2'-O-methylation (on A)<br />
|GUCAU<span style="color:#FF0000">'''A'''</span>UGCUU<br />
|[http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR74 snR74]<br />
|-<br />
| 100<br />
| ribose 2'-O-methylation (on A)<br />
| GGCUC<font color="red"><b>A</b></font>UUAAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR51 snR51]<br />
|- <br />
| 106<br />
| pseudouridylation<br />
| UUAAA<font color="red"><b>U</b></font>CAGUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR44 snR44]<br />
|- <br />
| 120<br />
| pseudouridylation<br />
| GUUUA<font color="red"><b>U</b></font>UUGAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR49 snR49]<br />
|- <br />
| 211<br />
| pseudouridylation<br />
| AUUUA<font color="red"><b>U</b></font>UAGAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR49 snR49]<br />
|- <br />
| 302<br />
| pseudouridylation<br />
| UCAAA<font color="red"><b>U</b></font>UUCUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR49 snR49]<br />
|- <br />
| 414<br />
| ribose 2'-O-methylation (on C)<br />
| CACAU<font color="red"><b>C</b></font>CAAGG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR128 snR128]<br />
|- <br />
| 420<br />
| ribose 2'-O-methylation (on A)<br />
| CAAGG<font color="red"><b>A</b></font>AGGCA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR52 snR52]<br />
|- <br />
| 436<br />
| ribose 2'-O-methylation (on A)<br />
| CGCGC<font color="red"><b>A</b></font>AAUUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR87 snR87]<br />
|- <br />
| 466<br />
| pseudouridylation<br />
| GGUAG<font color="red"><b>U</b></font>GACAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR189 snR189]<br />
|- <br />
| 541<br />
| ribose 2'-O-methylation (on A)<br />
| CGAGG<font color="red"><b>A</b></font>ACAAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR41 snR41]<br />
|- <br />
| 578<br />
| ribose 2'-O-methylation (on U)<br />
| CGCGG<font color="red"><b>U</b></font>AAUUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR77 snR77]<br />
|- <br />
| 619<br />
| ribose 2'-O-methylation (on A)<br />
| CAGUU<font color="red"><b>A</b></font>AAAAG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR47 snR47]<br />
|- <br />
| 632<br />
| pseudouridylation<br />
| CGUAG<font color="red"><b>U</b></font>UGAAC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR161 snR161]<br />
|- <br />
| 759<br />
| pseudouridylation<br />
| AAAAU<font color="red"><b>U</b></font>AGAGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR80 snR80]<br />
|- <br />
| 766<br />
| pseudouridylation<br />
| GAGUG<font color="red"><b>U</b></font>UCAAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR161 snR161]<br />
|- <br />
| 796<br />
| ribose 2'-O-methylation (on A)<br />
| AUAUU<font color="red"><b>A</b></font>GCAUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR53 snR53]<br />
|- <br />
| 974<br />
| ribose 2'-O-methylation (on A)<br />
| CAAGA<font color="red"><b>A</b></font>CGAAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR54 snR54]<br />
|- <br />
| 999<br />
| pseudouridylation<br />
| GAUGA<font color="red"><b>U</b></font>CAGAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR31 snR31]<br />
|- <br />
| 1007<br />
| ribose 2'-O-methylation (on C)<br />
| GAUAC<font color="red"><b>C</b></font>GUCGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR79 snR79]<br />
|- <br />
| 1126<br />
| ribose 2'-O-methylation (on G)<br />
| CGCAA<font color="red"><b>G</b></font>GCUGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR41 snR41]<br />
|- <br />
| 1181<br />
| pseudouridylation<br />
| GCGGC<font color="red"><b>U</b></font>UAAUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR85 snR85]<br />
|- <br />
| 1187<br />
| pseudouridylation<br />
| UAAUU<font color="red"><b>U</b></font>GACUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR36 snR36]<br />
|- <br />
| 1191<br />
| pseudouridylation<br> Note that subsequent additional modifications generate m<sup>1</sup>acp<sup>3</sup>-psi.<br />
| UUGAC<font color="red"><b>U</b></font>CAACA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR35 snR35]<br />
|- <br />
| 1269<br />
| ribose 2'-O-methylation (on U)<br />
| GGUGG<font color="red"><b>U</b></font>GGUGC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR55 snR55]<br />
|- <br />
| 1271<br />
| ribose 2'-O-methylation (on G)<br />
| UGGUG<font color="red"><b>G</b></font>UGCAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR40 snR40]<br />
|- <br />
| 1290<br />
| pseudouridylation<br />
| UUAGU<font color="red"><b>U</b></font>GGUGG <br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR83 snR83]<br />
|- <br />
| 1415<br />
| pseudouridylation<br />
| AAGUU<font color="red"><b>U</b></font>GAGGC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR83 snR83]<br />
|- <br />
| 1428<br />
| ribose 2'-O-methylation (on G)<br />
| UAACA<font color="red"><b>G</b></font>GUCUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR56 snR56]<br />
|- <br />
| 1572<br />
| ribose 2'-O-methylation (on G)<br />
| UCAAC<font color="red"><b>G</b></font>AGGAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR57 nR57]<br />
|- <br />
| 1639<br />
| ribose 2'-O-methylation (on C)<br />
| CACCG<font color="red"><b>C</b></font>CCGUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR70 snR70]<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
|colspan=4|1. All information in this table courtesy of Wayne Decatur and Dorota Piekna-Przybylska; also see the table of snoRNAs or the locus summary and literature guide pages for each specific gene to view references.<br />
|-<br />
|colspan=4|2. Piekna-Przybylska D, et al. (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12<br>[http://www.yeastgenome.org/reference/S000120772/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/17283215?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=25SrRNA|'''Modified Position within the 25S rRNA'''<br>''compiled June 2007''<br>[http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/nm25s.php ''see alternate numbering systems for the 25S ribose methylations'']<br>[http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/psi25s.php see alternate numbering systems for the 25S pseudouridylations]<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|- <br />
| 649<br />
| ribose 2'-O-methylation (on A)<br />
| GAAAC<font color="red"><b>A</b></font>CGGAC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR1 snR18]<br />
|- <br />
| 650<br />
| ribose 2'-O-methylation (on C)<br />
| AAACA<font color="red"><b>C</b></font>GGACC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR18 snR18]<br />
|- <br />
| 663<br />
| ribose 2'-O-methylation (on C)<br />
| GGAGU<font color="red"><b>C</b></font>UAACG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR58 snR58]<br />
|- <br />
| 776<br />
| pseudouridylation<br />
| AUGGA<font color="red"><b>U</b></font>UUGAG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR80 snR80]<br />
|- <br />
| 805<br />
| ribose 2'-O-methylation (on G)<br />
| GACCC<font color="red"><b>G</b></font>AAAGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR39B snR39B]<br />
|- <br />
| 807<br />
| ribose 2'-O-methylation (on A)<br />
| CCCGA<font color="red"><b>A</b></font>AGAUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR39 snR39]<br> [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR59 snR59]<br />
|- <br />
| 817<br />
| ribose 2'-O-methylation (on A)<br />
| GGUGA<font color="red"><b>A</b></font>CUAUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR60 snR60]<br />
|- <br />
| 867<br />
| ribose 2'-O-methylation (on G)<br />
| UCGUA<font color="red"><b>G</b></font>CGGUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR50 snR50]<br />
|- <br />
| 876<br />
| ribose 2'-O-methylation (on A)<br />
| UUCUG<font color="red"><b>A</b></font>CGUGC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR72 snR72]<br />
|- <br />
| 898<br />
| ribose 2'-O-methylation (on U)<br />
| CGAAU<font color="red"><b>U</b></font>UGGGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR40 snR40]<br />
|- <br />
| 908<br />
| ribose 2'-O-methylation (on G)<br />
| UAUAG<font color="red"><b>G</b></font>GGCGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR60 snR60]<br />
|- <br />
| 960<br />
| pseudouridylation<br />
| UUCCC<font color="red"><b>U</b></font>CAGGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR8 snR8]<br />
|- <br />
| 966<br />
| pseudouridylation<br />
| CAGGA<font color="red"><b>U</b></font>AGCAG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR43 snR43]<br />
|- <br />
| 986<br />
| pseudouridylation<br />
| UCAGU<font color="red"><b>U</b></font>UUAUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR8 snR8]<br />
|- <br />
| 990<br />
| pseudouridylation<br />
| UUUUA<font color="red"><b>U</b></font>GAGGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR49 snR49]<br />
|- <br />
| 1004<br />
| pseudouridylation<br />
| GCGAA<font color="red"><b>U</b></font>GAUUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR5 snR5]<br />
|- <br />
| 1042<br />
| pseudouridylation<br />
| CCUAU<font color="red"><b>U</b></font>CUCAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR33 snR33]<br />
|- <br />
| 1052<br />
| pseudouridylation<br />
| AACUU<font color="red"><b>U</b></font>AAAUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR81 snR81]<br />
|- <br />
| 1056<br />
| pseudouridylation<br />
| UUAAA<font color="red"><b>U</b></font>AUGUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR44 snR44]<br />
|- <br />
| 1110<br />
| pseudouridylation<br />
| AGCUU<font color="red"><b>U</b></font>UAGUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR82 snR82]<br />
|- <br />
| 1124<br />
| pseudouridylation<br />
| CAUUU<font color="red"><b>U</b></font>UGGUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR5 snR5]<br />
|- <br />
| 1133<br />
| ribose 2'-O-methylation (on A)<br />
| UAAGC<font color="red"><b>A</b></font>GAACU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR61 snR61]<br />
|- <br />
| 1437<br />
| ribose 2'-O-methylation (on C)<br />
| CAGAU<font color="red"><b>C</b></font>UUGGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR24 snR24]<br />
|- <br />
| 1449<br />
| ribose 2'-O-methylation (on C)<br />
| GUAGU<font color="red"><b>A</b></font>GCAAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR24 snR24]<br />
|- <br />
| 1450<br />
| ribose 2'-O-methylation (on C)<br />
| UAGUA<font color="red"><b>G</b></font>CAAAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR24 snR24]<br />
|- <br />
| 1888<br />
| ribose 2'-O-methylation (on U)<br />
| AAUAA<font color="red"><b>U</b></font>GUAGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR62 snR62]<br />
|- <br />
| 2129<br />
| pseudouridylation<br />
| GAAUC<font color="red"><b>U</b></font>GACUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR3 snR3]<br />
|- <br />
| 2133<br />
| pseudouridylation<br />
| CUGAC<font color="red"><b>U</b></font>GUCUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR3 snR3]<br />
|- <br />
| 2191<br />
| pseudouridylation<br />
| UGAUU<font color="red"><b>U</b></font>CUGCC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR32 snR32]<br />
|- <br />
| 2197<br />
| ribose 2'-O-methylation (on C)<br />
| CUGCC<font color="red"><b>C</b></font>AGUGC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR76 snR76]<br />
|- <br />
| 2220<br />
| ribose 2'-O-methylation (on A)<br />
| AGUGA<font color="red"><b>A</b></font>GAAAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR47 snR47]<br />
|- <br />
| 2256<br />
| ribose 2'-O-methylation (on A)<br />
| GAGUA<font color="red"><b>A</b></font>CUAUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR63 snR63]<br />
|- <br />
| 2258<br />
| pseudouridylation<br />
| GUAAC<font color="red"><b>U</b></font>AUGAC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR191 snR191]<br />
|- <br />
| 2260<br />
| pseudouridylation<br />
| AACUA<font color="red"><b>U</b></font>GACUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR191 snR191]<br />
|- <br />
| 2264<br />
| pseudouridylation<br />
| AUGAC<font color="red"><b>U</b></font>CUCUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR3 snR3]<br />
|- <br />
| 2266<br />
| pseudouridylation<br />
| GACUC<font color="red"><b>U</b></font>CUUAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR84 snR84]<br />
|- <br />
| 2314<br />
| pseudouridylation<br />
| AUGAA<font color="red"><b>U</b></font>GGAUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR86 snR86]<br />
|- <br />
| 2340<br />
| pseudouridylation<br />
| GUCCC<font color="red"><b>U</b></font>AUCUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR9 snR9]<br />
|- <br />
| 2349<br />
| pseudouridylation<br />
| UACUA<font color="red"><b>U</b></font>CUAGC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR82 snR82]<br />
|- <br />
| 2280<br />
| ribose 2'-O-methylation (on A)<br />
| AGCCA<font color="red"><b>A</b></font>AUGCC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR13 snR13]<br />
|- <br />
| 2281<br />
| ribose 2'-O-methylation (on A)<br />
| GCCAA<font color="red"><b>A</b></font>UGCCU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR13 snR13]<br />
|- <br />
| 2288<br />
| ribose 2'-O-methylation (on G)<br />
| GCCUC<font color="red"><b>G</b></font>UCAUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR75 snR75]<br />
|- <br />
| 2337<br />
| ribose 2'-O-methylation (on C)<br />
| ACUGU<font color="red"><b>C</b></font>CCUAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR64 snR64]<br />
|- <br />
| 2347<br />
| ribose 2'-O-methylation (on U)<br />
| UCUAC<font color="red"><b>U</b></font>AUCUA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR65 snR65]<br />
|- <br />
| 2351<br />
| pseudouridylation<br />
| CUAUC<font color="red"><b>U</b></font>AGCGA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR82 snR82]<br />
|- <br />
| 2416<br />
| pseudouridylation<br />
| UGAGC<font color="red"><b>U</b></font>UGACU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR11 snR11]<br />
|- <br />
| 2417<br />
| ribose 2'-O-methylation (on U)<br />
| GAGCU<font color="red"><b>U</b></font>GACUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR66 snR66]<br />
|- <br />
| 2421<br />
| ribose 2'-O-methylation (on U)<br />
| UUGAC<font color="red"><b>U</b></font>CUAGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR78 snR78]<br />
|- <br />
| 2619<br />
| ribose 2'-O-methylation (on G)<br />
| GGCUG<font color="red"><b>G</b></font>GGCGG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR67 snR67]<br />
|- <br />
| 2640<br />
| ribose 2'-O-methylation (on A)<br />
| AAACG<font color="red"><b>A</b></font>UAACG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR68 snR68]<br />
|- <br />
| 2724<br />
| ribose 2'-O-methylation (on U)<br />
| UGAUU<font color="red"><b>U</b></font>UCAGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR67 snR67]<br />
|- <br />
| 2729<br />
| ribose 2'-O-methylation (on U)<br />
| UUCAG<font color="red"><b>U</b></font>GUGAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR51 snR51]<br />
|- <br />
| 2735<br />
| pseudouridylation<br />
| GUGAA<font color="red"><b>U</b></font>ACAAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR189 snR189]<br />
|- <br />
| 2791<br />
| ribose 2'-O-methylation (on G)<br />
| GGCUA<font color="red"><b>G</b></font>AGGUG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR48 snR48]<br />
|- <br />
| 2793<br />
| ribose 2'-O-methylation (on G)<br />
| CUAGA<font color="red"><b>G</b></font>GUGCC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR48 snR48]<br />
|- <br />
| 2815<br />
| ribose 2'-O-methylation (on G)<br />
| CACAG<font color="red"><b>G</b></font>GAUAA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR38 nR38]<br />
|- <br />
| 2826<br />
| pseudouridylation<br />
| CUGGC<font color="red"><b>U</b></font>UGUGG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR34 snR34]<br />
|- <br />
| 2865<br />
| pseudouridylation<br />
| UUUGA<font color="red"><b>U</b></font>UCUUC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR46 snR46]<br />
|- <br />
| 2880<br />
| pseudouridylation<br />
| UCGGC<font color="red"><b>U</b></font>CUUCC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR34 snR34]<br />
|- <br />
| 2921<br />
| ribose 2'-O-methylation (on U)<br />
| UGGAU<font color="red"><b>U</b></font>GUUCA<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR52 snR52]<br />
|- <br />
| 2922<br />
| ribose 2'-O-methylation (on G)<br />
| GGAUU<font color="red"><b>G</b></font>UUCAC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SPB1 SPB1]<br />
|- <br />
| 2923<br />
| pseudouridylation<br />
| GAUUG<font color="red"><b>U</b></font>UCACC<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR10 snR10]<br />
|- <br />
| 2944<br />
| pseudouridylation<br />
| GAACG<font color="red"><b>U</b></font>GAGCU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR37 snR37]<br />
|- <br />
| 2946<br />
| ribose 2'-O-methylation (on A)<br />
| ACGUG<font color="red"><b>A</b></font>GCUGG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR71 snR71]<br />
|- <br />
| 2948<br />
| ribose 2'-O-methylation (on C)<br />
| GUGAG<font color="red"><b>C</b></font>UGGGU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR69 snR69]<br />
|- <br />
| 2959<br />
| ribose 2'-O-methylation (on C)<br />
| UUAGA<font color="red"><b>C</b></font>CGUCG<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR73 snR73]<br />
|- <br />
| 2975<br />
| pseudouridylation<br />
| CAGGU<font color="red"><b>U</b></font>AGUUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=snR42 snR42]<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
|colspan=4|1. All information in this table courtesy of Wayne Decatur and Dorota Piekna-Przybylska; also see the table of snoRNAs or the locus summary and literature guide pages for each specific gene to view references.<br />
|-<br />
|colspan=4|2. Piekna-Przybylska D, et al. (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12<br>[http://www.yeastgenome.org/reference/S000120772/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/17283215?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=U1snRNA|'''Modified Position within the [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000007295 U1 snRNA]'''<br>''compiled June 2007''<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
| 5<sup>1</sup><br />
| pseudouridylation<br />
| AUAC<font color="red"><b>U</b></font>UACCU<br />
| not yet known<br />
|-<br />
| 6<sup>1</sup><br />
| pseudouridylation<br />
| AUACU<font color="red"><b>U</b></font>ACCUU<br />
| not yet known<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
|colspan=4|1. '''Massenet S, ''et al''.''' (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 [http://www.yeastgenome.org/reference/S000054022/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/10022901?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=U2snRNA|'''Modified Position within the [http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000006478 U2 snRNA]'''<br>''compiled June 2007''<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
| 35<sup>1</sup><br />
| pseudouridylation<br />
| AAGUG<font color="red"><b>U</b></font>AGUAU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=PUS7 PUS7]<br />
|-<br />
| 42<sup>1</sup><br />
| pseudouridylation<br />
| GUAUC<font color="red"><b>U</b></font>GUUCU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR81 snR81]<br />
|-<br />
| 44<sup>1</sup><br />
| pseudouridylation<br />
| UCUGU<font color="red"><b>U</b></font>CUUUU<br />
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=PUS1 PUS1]<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
|colspan=4|1. '''Massenet S, ''et al''.''' (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 [http://www.yeastgenome.org/reference/S000054022/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/10022901?dopt=Abstract PubMed]<br />
|-<br />
|colspan=4|2. '''Ma X, ''et al''.''' (2003) Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J 22(8):1889-97 [http://www.yeastgenome.org/reference/S000072999/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/12682021?dopt=Abstract PubMed]<br />
|-<br />
|colspan=4|3. '''Ma X, ''et al''.''' (2005) Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism. EMBO J 24(13):2403-13 [http://www.yeastgenome.org/reference/S000082374/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/15962000?dopt=Abstract PubMed]<br />
|-<br />
| align="center" style="background:#FFDEAD;" colspan=4 id=U5snRNA|'''Modified Position within the [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR7 U5 snRNA]'''<br>''compiled June 2007''<br />
|-<br />
| align="center" style="background:#819FF7;"|'''Position'''<br />
| align="center" style="background:#819FF7;"|'''Modification Type'''<br />
| align="center" style="background:#819FF7;"|'''Sequence Context of Modification'''<br />
| align="center" style="background:#819FF7;"|'''Gene Associated with Modification'''<br />
|-<br />
| 99<sup>1</sup><br />
| pseudouridylation<br />
| CCUUU<font color="red"><b>U</b></font>ACCAG<br />
| not yet known<br />
|-<br />
| align="center" style="background:#819FF7;" colspan=4|'''References'''<br />
|-<br />
|colspan=4|1. '''Massenet S, ''et al''.''' (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 [http://www.yeastgenome.org/reference/S000054022/overview SGD Paper] | [http://www.ncbi.nlm.nih.gov/pubmed/10022901?dopt=Abstract PubMed]<br />
|}</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Historical_Systematic_Sequence_Information&diff=398820Historical Systematic Sequence Information2014-04-09T15:14:20Z<p>Kyla: </p>
<hr />
<div>These pages refer to the systematic sequence of S288C prior to Release 64. Before Release 64, there were [[Guidelines_for_changing_systematic_sequence | guidelines for changing systematic sequence]].<br />
<br />
=Chromosomal Features=<br />
[http://www.yeastgenome.org/community/RNAmodTable.shtml Modified Nucleotides within RNAs in S. cerevisiae]<br />
<br />
[http://www.yeastgenome.org/archive/newORF-sage.shtml SGD ORF Additions based on SAGE]<br />
<br />
[http://www.yeastgenome.org/community/DSB_graphic.shtml Meiotic Double-Stranded Breaks in the Yeast Genome]<br />
<br />
[http://www.yeastgenome.org/community/codon_usage.shtml Codon Usage Tables]<br />
<br />
=Reagents=<br />
[http://www.yeastgenome.org/community/primerPage.shtml Primer sets for amplifying yeast ORFs]<br />
<br />
[[Commonly_used_auxotrophic_markers|Commonly Used Auxotrophic Markers]]</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Yeast_Images&diff=398814Yeast Images2014-04-04T17:13:10Z<p>Kyla: </p>
<hr />
<div>''S. cerevisiae'' images available from The Cell: An Image Library<br />
[[Image:TheCell.png|100px|link=http://www.cellimagelibrary.org]]<br />
<br />
'''The Cell: An Image Library™ is a public repository of images and videos. These images have been reviewed and many have been annotated. You will find that The Cell provides a large collection of yeast images and videos.'''<br />
'''The Cell is funded by NIGMS Grand Opportunities grant RC2GM092708 to the American Society for Cell Biology (ASCB). We encourage you to submit images from your work to The Cell.'''<br />
<br />
The following images were previously provided by the yeast community for distribution bu SGD. You are welcome to use these images, however please be respectful and cite the person(s) who provided the image as the source. If you have images you would be willing to make available for public use, please contribute them to The Cell Library mentioned above.<br />
<br />
{| {{table}} border="1"<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Diane Nowicki and Ryan Liermann<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|DY150 cells in stationary phase. [electron micrograph]||[[Image:STcontrol.jpg|100px|link=http://wiki.yeastgenome.org/images/0/05/STcontrol.jpg]]<br />
|-<br />
|DY150 cells undergoing detergent mediated (Y-PER) lysis. [electron micrograph, 12,000X]||[[Image:1504pea.jpg|100px|link=http://wiki.yeastgenome.org/images/b/bf/1504pea.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Peter Hollenhorst and Catherine Fox<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type cells (W303 derivative). [light micrograph]||[[Image:wildtype.gif|100px|link=http://wiki.yeastgenome.org/images/8/85/wildtype.GIF]]<br />
|-<br />
|fkh1 delete cells (W303 derivative). [light micrograph]||[[image:fkh1delete.gif|100px|link=http://wiki.yeastgenome.org/images/2/2d/fkh1delete.GIF]]<br />
|-<br />
|fkh2 delete cells (W303 derivative). [light micrograph]||[[image:fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/7/7c/fkh2delete.GIF]]<br />
|-<br />
|fkh1 fkh2 double delete cells showing pseudohyphal growth (W303 derivative). [light micrograph]||[[image:fkh1fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/c/cc/fkh1fkh2delete.GIF]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Carsten Kettner<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type YCC588 cells stained with Calcofluor White. [fluorescent micrograph, 1000X]||[[image:protoplast1.jpg|100px|link=http://wiki.yeastgenome.orgu/images/6/61/protoplast1.jpg]]<br />
|-<br />
|Wild type YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast2.jpg|100px|link=http://wiki.yeastgenome.org/images/8/8d/protoplast2.jpg]][[image:protoplast3.jpg|100px|link=http://wiki.yeastgenome.org/images/9/9e/protoplast3.jpg]]<br />
|-<br />
|Wild type YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast4.jpg|100px|link=http://wiki.yeastgenome.org/images/4/40/protoplast4.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Dan Eshel<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Axial-budding cells with oval, rounded mother tips.||[[image:ovals.jpg|100px|link=http://wiki.yeastgenome.org/images/a/ac/ovals.jpg]]<br />
|-<br />
|Bi-polar budding cells with "lemon"-shaped mother tips.||[[image:lemons.jpg|100px|link=http://wiki.yeastgenome.org/images/f/fa/lemons.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' image provided by Teresa Rinaldi<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type W303 cells, with GFP imported into mitochondria and DNA stained with dapi. [fluorescence microscopy image, 100X]||[[image:w303dapimitogfp.JPG|100px|link=http://wiki.yeastgenome.org/images/6/61/w303dapimitogfp.JPG]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movies provided by Kerry Bloom<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Fluorescent tufts of kinetochore microtubules shortening to the pole.||[[image:flourescent_tufts.png|100px|link=http://www.yeastgenome.org/images/flourescent_tufts.mov]]<br />
|-<br />
|gRNA-ASH1 in bud6 cells. (Strain JZY1345)||[[image:gRNA-ASH1_in_bud6_cells_(Strain_JZY1345).png|100px|link=http://www.yeastgenome.org/images/gRNA_JZY1345.mov]]<br />
|-<br />
|Kar9-GFP in WT (Strain YEF473A).||[[image:Kar9-GFP_in_WT_(Strain_YEF473A).png|100px|link=http://www.yeastgenome.org/images/Kar9_strainYEF473A.mov]]<br />
|-<br />
|[http://labs.bio.unc.edu/Bloom/bloomyeast.htm Bloom Lab]||<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movie provided by Michel Jacquet<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Oscillatory nucleocytoplasmic shuttling of Msn2-GFP in W303.||[[image:Oscillatory_nucleocytoplasmic_shuttling_of_Msn2-GFP_in_W303.png|100px|link=http://www.yeastgenome.org/images/msn2_oscillatory.mov]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Schizosaccharomyces pombe'' pictures available from the [http://www-bcf.usc.edu/~forsburg/index.html '''Forsburg lab page''']<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Maxim Zakhartsev<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type Saccharomyces cerevisiae strain BY4742 (EUROSCARF) in continuous culture at 22.5 degrees C. Instrument: confocal laser microscope Carl Zeiss LSM 510 Meta, phase contrast imaging. Authors: Dr. Maxim Zakhartsev and Doris Petroi, International University Bremen, Germany.||[[image:yeast_2.jpg|100px|link=http://wiki.yeastgenome.org/images/5/5f/yeast_2.jpg]]<br />
|-<br />
|Saccharomyces cerevisiae strain InvSC1 (Invitrogen) transformed with pYES2-eGFP expressing intracellularly recombinant eGFP (enhanced green fluorescent protein from jellyfish Aequorea victoria). Top, large eGFP fluorescence image; Bottom, composite image: upper left, eGFP fluorescence; upper right, phase contrast image; lower left, superimposed image. Instrument: confocal laser microscope Carl Zeiss LSM 510; Meta. eGFP has been excited by argon laser at 488 nm. Authors: Dr. Maxim Zakhartsev, Dr. Sergei Rarozin, Carmen Momeu, International University Bremen, Germany.||[[image:eGFP_full-zoom_large.png|100px|link=http://wiki.yeastgenome.org/images/3/35/eGFP_full-zoom_large.png]]<br />
|}</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Yeast_Images&diff=398813Yeast Images2014-04-04T17:10:28Z<p>Kyla: </p>
<hr />
<div>''S. cerevisiae'' images available from The Cell: An Image Library<br />
[[Image:TheCell.png|100px|link=http://www.cellimagelibrary.org]]<br />
<br />
'''The Cell: An Image Library™ is a public repository of images and videos. These images have been reviewed and many have been annotated. You will find that The Cell provides a large collection of yeast images and videos.'''<br />
'''The Cell is funded by NIGMS Grand Opportunities grant RC2GM092708 to the American Society for Cell Biology (ASCB). We encourage you to submit images from your work to The Cell.'''<br />
<br />
The following images were previously provided by the yeast community for distribution bu SGD. You are welcome to use these images, however please be respectful and cite the person(s) who provided the image as the source. If you have images you would be willing to make available for public use, please contribute them to The Cell Library mentioned above.<br />
<br />
{| {{table}} border="1"<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Diane Nowicki and Ryan Liermann<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|DY150 cells in stationary phase. [electron micrograph]||[[Image:STcontrol.jpg|100px|link=http://wiki.yeastgenome.org/images/0/05/STcontrol.jpg]]<br />
|-<br />
|DY150 cells undergoing detergent mediated (Y-PER) lysis. [electron micrograph, 12,000X]||[[Image:1504pea.jpg|100px|link=http://wiki.yeastgenome.org/images/b/bf/1504pea.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Peter Hollenhorst and Catherine Fox<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype cells (W303 derivative). [light micrograph]||[[Image:wildtype.gif|100px|link=http://wiki.yeastgenome.org/images/8/85/wildtype.GIF]]<br />
|-<br />
|fkh1 delete cells (W303 derivative). [light micrograph]||[[image:fkh1delete.gif|100px|link=http://wiki.yeastgenome.org/images/2/2d/fkh1delete.GIF]]<br />
|-<br />
|fkh2 delete cells (W303 derivative). [light micrograph]||[[image:fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/7/7c/fkh2delete.GIF]]<br />
|-<br />
|fkh1 fkh2 double delete cells showing pseudohyphal growth (W303 derivative). [light micrograph]||[[image:fkh1fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/c/cc/fkh1fkh2delete.GIF]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Carsten Kettner<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype YCC588 cells stained with Calcofluor White. [fluorescent micrograph, 1000X]||[[image:protoplast1.jpg|100px|link=http://wiki.yeastgenome.orgu/images/6/61/protoplast1.jpg]]<br />
|-<br />
|wildtype YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast2.jpg|100px|link=http://wiki.yeastgenome.org/images/8/8d/protoplast2.jpg]][[image:protoplast3.jpg|100px|link=http://wiki.yeastgenome.org/images/9/9e/protoplast3.jpg]]<br />
|-<br />
|wildtype YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast4.jpg|100px|link=http://wiki.yeastgenome.org/images/4/40/protoplast4.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Dan Eshel<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Axial-budding cells with oval, rounded mother tips||[[image:ovals.jpg|100px|link=http://wiki.yeastgenome.org/images/a/ac/ovals.jpg]]<br />
|-<br />
|Bi-polar budding cells with "lemon"-shaped mother tips||[[image:lemons.jpg|100px|link=http://wiki.yeastgenome.org/images/f/fa/lemons.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' image provided by Teresa Rinaldi<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype W303 cells, with GFP imported into mitochondria and DNA stained with dapi. [fluorescence microscopy image, 100X]||[[image:w303dapimitogfp.JPG|100px|link=http://wiki.yeastgenome.org/images/6/61/w303dapimitogfp.JPG]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movies provided by Kerry Bloom<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Fluorescent tufts of kinetochore microtubules shortening to the pole||[[image:flourescent_tufts.png|100px|link=http://www.yeastgenome.org/images/flourescent_tufts.mov]]<br />
|-<br />
|gRNA-ASH1 in bud6 cells (Strain JZY1345)||[[image:gRNA-ASH1_in_bud6_cells_(Strain_JZY1345).png|100px|link=http://www.yeastgenome.org/images/gRNA_JZY1345.mov]]<br />
|-<br />
|Kar9-GFP in WT (Strain YEF473A)||[[image:Kar9-GFP_in_WT_(Strain_YEF473A).png|100px|link=http://www.yeastgenome.org/images/Kar9_strainYEF473A.mov]]<br />
|-<br />
|[http://labs.bio.unc.edu/Bloom/bloomyeast.htm Bloom Lab]||<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movie provided by Michel Jacquet<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Oscillatory nucleocytoplasmic shuttling of Msn2-GFP in W303||[[image:Oscillatory_nucleocytoplasmic_shuttling_of_Msn2-GFP_in_W303.png|100px|link=http://www.yeastgenome.org/images/msn2_oscillatory.mov]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Schizosaccharomyces pombe'' pictures available from the [http://www-bcf.usc.edu/~forsburg/index.html '''Forsburg lab page''']<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Maxim Zakhartsev<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type Saccharomyces cerevisiae strain BY4742 (EUROSCARF) in continuous culture at 22.5 degrees C. Instrument: confocal laser microscope Carl Zeiss LSM 510 Meta, phase contrast imaging. Authors: Dr. Maxim Zakhartsev and Doris Petroi, International University Bremen, Germany||[[image:yeast_2.jpg|100px|link=http://wiki.yeastgenome.org/images/5/5f/yeast_2.jpg]]<br />
|-<br />
|Saccharomyces cerevisiae strain InvSC1 (Invitrogen) transformed with pYES2-eGFP expressing intracellularly recombinant eGFP (enhanced green fluorescent protein from jellyfish Aequorea victoria). Top, large eGFP fluorescence image; Bottom, composite image: upper left, eGFP fluorescence; upper right, phase contrast image; lower left, superimposed image. Instrument: confocal laser microscope Carl Zeiss LSM 510; Meta. eGFP has been excited by argon laser at 488 nm. Authors: Dr. Maxim Zakhartsev, Dr. Sergei Rarozin, Carmen Momeu, International University Bremen, Germany||[[image:eGFP_full-zoom_large.png|100px|link=http://wiki.yeastgenome.org/images/3/35/eGFP_full-zoom_large.png]]<br />
|}</div>Kylahttps://wiki.yeastgenome.org/index.php?title=Yeast_Images&diff=398812Yeast Images2014-04-04T17:09:59Z<p>Kyla: Created page with "''S. cerevisiae'' images available from The Cell: An Image Library link=http://www.cellimagelibrary.org '''The Cell: An Image Library™ is a p..."</p>
<hr />
<div>''S. cerevisiae'' images available from The Cell: An Image Library<br />
[[Image:TheCell.png|100px|link=http://www.cellimagelibrary.org]]<br />
<br />
'''The Cell: An Image Library™ is a public repository of images and videos. These images have been reviewed and many have been annotated. You will find that The Cell provides a large collection of yeast images and videos.'''<br />
'''The Cell is funded by NIGMS Grand Opportunities grant RC2GM092708 to the American Society for Cell Biology (ASCB). We encourage you to submit images from your work to The Cell.'''<br />
<br />
The following images were previously provided by the yeast community for distribution bu SGD. You are welcome to use these images, however please be respectful and cite the person(s) who provided the image as the source. If you have images you would be willing to make available for public use, please contribute them to The Cell Library mentioned above.<br />
<br />
{| {{table}} border="1"<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Diane Nowicki and Ryan Liermann<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|DY150 cells in stationary phase. [electron micrograph]||[[Image:STcontrol.jpg|100px|link=http://wiki.yeastgenome.org/images/0/05/STcontrol.jpg]]<br />
|-<br />
|DY150 cells undergoing detergent mediated (Y-PER) lysis. [electron micrograph, 12,000X]||[[Image:1504pea.jpg|100px|link=http://wiki.yeastgenome.org/images/b/bf/1504pea.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Peter Hollenhorst and Catherine Fox<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype cells (W303 derivative). [light micrograph]||[[Image:wildtype.gif|100px|link=http://wiki.yeastgenome.org/images/8/85/wildtype.GIF]]<br />
|-<br />
|fkh1 delete cells (W303 derivative). [light micrograph]||[[image:fkh1delete.gif|100px|link=http://wiki.yeastgenome.org/images/2/2d/fkh1delete.GIF]]<br />
|-<br />
|fkh2 delete cells (W303 derivative). [light micrograph]||[[image:fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/7/7c/fkh2delete.GIF]]<br />
|-<br />
|fkh1 fkh2 double delete cells showing pseudohyphal growth (W303 derivative). [light micrograph]||[[image:fkh1fkh2delete.gif|100px|link=http://wiki.yeastgenome.org/images/c/cc/fkh1fkh2delete.GIF]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Carsten Kettner<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype YCC588 cells stained with Calcofluor White. [fluorescent micrograph, 1000X]||[[image:protoplast1.jpg|100px|link=http://wiki.yeastgenome.orgu/images/6/61/protoplast1.jpg]]<br />
|-<br />
|wildtype YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast2.jpg|100px|link=http://wiki.yeastgenome.org/images/8/8d/protoplast2.jpg]][[image:protoplast3.jpg|100px|link=http://yeastgenome-devwiki.stanford.edu/images/9/9e/protoplast3.jpg]]<br />
|-<br />
|wildtype YCC588 protoplasts. [DIC image, 400X]||[[image:protoplast4.jpg|100px|link=http://wiki.yeastgenome.org/images/4/40/protoplast4.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Dan Eshel<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Axial-budding cells with oval, rounded mother tips||[[image:ovals.jpg|100px|link=http://wiki.yeastgenome.org/images/a/ac/ovals.jpg]]<br />
|-<br />
|Bi-polar budding cells with "lemon"-shaped mother tips||[[image:lemons.jpg|100px|link=http://wiki.yeastgenome.org/images/f/fa/lemons.jpg]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' image provided by Teresa Rinaldi<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|wildtype W303 cells, with GFP imported into mitochondria and DNA stained with dapi. [fluorescence microscopy image, 100X]||[[image:w303dapimitogfp.JPG|100px|link=http://wiki.yeastgenome.org/images/6/61/w303dapimitogfp.JPG]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movies provided by Kerry Bloom<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Fluorescent tufts of kinetochore microtubules shortening to the pole||[[image:flourescent_tufts.png|100px|link=http://www.yeastgenome.org/images/flourescent_tufts.mov]]<br />
|-<br />
|gRNA-ASH1 in bud6 cells (Strain JZY1345)||[[image:gRNA-ASH1_in_bud6_cells_(Strain_JZY1345).png|100px|link=http://www.yeastgenome.org/images/gRNA_JZY1345.mov]]<br />
|-<br />
|Kar9-GFP in WT (Strain YEF473A)||[[image:Kar9-GFP_in_WT_(Strain_YEF473A).png|100px|link=http://www.yeastgenome.org/images/Kar9_strainYEF473A.mov]]<br />
|-<br />
|[http://labs.bio.unc.edu/Bloom/bloomyeast.htm Bloom Lab]||<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' movie provided by Michel Jacquet<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Oscillatory nucleocytoplasmic shuttling of Msn2-GFP in W303||[[image:Oscillatory_nucleocytoplasmic_shuttling_of_Msn2-GFP_in_W303.png|100px|link=http://www.yeastgenome.org/images/msn2_oscillatory.mov]]<br />
|-<br />
| align="center" style="background:#819FF7;"|''Schizosaccharomyces pombe'' pictures available from the [http://www-bcf.usc.edu/~forsburg/index.html '''Forsburg lab page''']<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
| align="center" style="background:#819FF7;"|''Saccharomyces cerevisiae'' images provided by Maxim Zakhartsev<br />
| align="center" style="background:#819FF7;"|<br />
|-<br />
|Wild type Saccharomyces cerevisiae strain BY4742 (EUROSCARF) in continuous culture at 22.5 degrees C. Instrument: confocal laser microscope Carl Zeiss LSM 510 Meta, phase contrast imaging. Authors: Dr. Maxim Zakhartsev and Doris Petroi, International University Bremen, Germany||[[image:yeast_2.jpg|100px|link=http://wiki.yeastgenome.org/images/5/5f/yeast_2.jpg]]<br />
|-<br />
|Saccharomyces cerevisiae strain InvSC1 (Invitrogen) transformed with pYES2-eGFP expressing intracellularly recombinant eGFP (enhanced green fluorescent protein from jellyfish Aequorea victoria). Top, large eGFP fluorescence image; Bottom, composite image: upper left, eGFP fluorescence; upper right, phase contrast image; lower left, superimposed image. Instrument: confocal laser microscope Carl Zeiss LSM 510; Meta. eGFP has been excited by argon laser at 488 nm. Authors: Dr. Maxim Zakhartsev, Dr. Sergei Rarozin, Carmen Momeu, International University Bremen, Germany||[[image:eGFP_full-zoom_large.png|100px|link=http://wiki.yeastgenome.org/images/3/35/eGFP_full-zoom_large.png]]<br />
|}</div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:yeast_2.jpg&diff=398811File:yeast 2.jpg2014-04-04T17:05:55Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:wildtype.gif&diff=398810File:wildtype.gif2014-04-04T17:05:25Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:w303dapimitogfp.JPG&diff=398809File:w303dapimitogfp.JPG2014-04-04T17:04:50Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:TheCell.png&diff=398808File:TheCell.png2014-04-04T17:04:40Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:STcontrol.jpg&diff=398807File:STcontrol.jpg2014-04-04T17:04:32Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:protoplast4.jpg&diff=398806File:protoplast4.jpg2014-04-04T17:04:11Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:protoplast3.jpg&diff=398805File:protoplast3.jpg2014-04-04T17:04:03Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:protoplast2.jpg&diff=398804File:protoplast2.jpg2014-04-04T17:03:56Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:protoplast1.jpg&diff=398803File:protoplast1.jpg2014-04-04T17:03:49Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:ovals.jpg&diff=398802File:ovals.jpg2014-04-04T17:03:41Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:Oscillatory_nucleocytoplasmic_shuttling_of_Msn2-GFP_in_W303.png&diff=398801File:Oscillatory nucleocytoplasmic shuttling of Msn2-GFP in W303.png2014-04-04T17:03:35Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:lemons.jpg&diff=398800File:lemons.jpg2014-04-04T17:03:25Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:fkh2delete.gif&diff=398799File:fkh2delete.gif2014-04-04T17:02:17Z<p>Kyla: </p>
<hr />
<div></div>Kylahttps://wiki.yeastgenome.org/index.php?title=File:fkh1fkh2delete.gif&diff=398798File:fkh1fkh2delete.gif2014-04-04T17:02:09Z<p>Kyla: </p>
<hr />
<div></div>Kyla