New & Noteworthy

SGD Newsletter, Summer 2020

June 08, 2020

About this newsletter:

This is the Summer 2020 issue of the 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. You can view this newsletter as well as previous newsletters on our community Wiki.

Contents:

  1. Submit Data Form
  2. The Allied Genetics Conference (TAGC 2020)
  3. Explore SGD
  4. SGD Website Trailer
  5. Supplemental Data
  6. 26th Anniversary of the SGD Website
  7. A Note on COVID-19

Submit Data Form

Are you away from the bench right now and have a bit of extra time on your hands? SGD can use your help! Authors can submit data and information about their publications by pointing us to novel results, datasets (we appreciate GEO accession IDs!), or other important information, using SGD’s simple “Submit Data” form (https://www.yeastgenome.org/submitData). 

The Allied Genetics Conference (TAGC 2020)

Members of the SGD team virtually attended The Allied Genetics Conference in April 2020. Principal investigator Mike Cherry, PhD, gave a virtual workshop on using SGD and highlighted some of the useful tools and resources available to our users. SGD staff interacted with members of the yeast community through the conference Slack channels and also presented posters as part of the virtual poster sessions throughout the week (see below). We would like to thank the GSA for facilitating this successful change to a virtual conference and holding an accessible, well received event for the entire model organism community!

PresenterPoster Title
Suzi Aleksander“The Use of the Gene Ontology to Describe Biological Function at Saccharomyces Genome Database”
Micheal Alexander“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”
Joanna ArgasinskaSaccharomyces Genome Database (SGD) Through the Years”
Stacia Engel“SGD & the Alliance of Genome Resources”
Rob Nash“Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes”

Explore SGD

We recently added the new ‘Explore SGD’ button to the SGD homepage which allows for the exploration of data and pages without an initial search query. 

If you select the ‘Explore SGD’ button, you will be redirected to our search results page and can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike. New users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories. 

Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website. 

SGD Website Trailer

Subscribe to the SGD YouTube channel!
What are the basic features of SGD? Find out in our SGD Website Trailer

What are the basic features of SGD? Watch our new video to learn some of the key features that are available to help users with their research efforts. While this video does not include all of the many tools and resources that SGD has to offer, we have also generated a list of helpful SGD links which can be found on our help pages.

You can find this video, as well as other video tutorials on SGD resources, on our YouTube channel

Supplemental Data

SGD is now uploading and storing supplemental materials for our yeast papers! We are hosting data from past, present, and future papers on our literature pages. To access these data, simply search SGD with the paper’s PubMed ID and then look for the “Downloadable Files.”

26th Anniversary of the SGD Website

Screen Shot 2020-05-13 at 5.01.28 PM
The SGD Team zoomed in to celebrate the anniversary with cupcakes and fuzzy budders

Happy Birthday (Bud-day!) to Us! May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all! In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast. We’ve grown a lot since then, and have even migrated to the cloud! But as always, we’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 26 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.

A Note on COVID-19

We recognize that 2020 has brought many changes and challenges. Our thoughts go out to all those impacted by the novel coronavirus, SARS-CoV-2. Like many of you, we have found ourselves adjusting to these times, and the SGD team is currently working from home for the foreseeable future. Rest assured, we are still working just as hard to maintain the SGD resource and continuing to serve the amazing budding yeast community!

Categories: Newsletter

Tutorial on New SGD Features!

May 15, 2020

What are the basic features of SGD? In our new video you will learn some of the key features that are available to users to help with their research efforts.

We realize that there are many resources not included in this video (did you see that list at the end?), but we wanted to provide new users with a glimpse of some of the information they can expect to find on our detailed website.

The video is also located on our YouTube channel where we maintain other videos and tutorials regarding SGD features.

Categories: Tutorial

26th Anniversary of SGD Website

May 13, 2020


Happy Birthday to Us!  May 8, 2020 marked the 26th anniversary of the day the SGD website first went live, bringing yeast genome information to all!  In May 1994, the “World Wide Web” had only been in existence for about 22 months, but starting way back then, anyone (especially yeast researchers!) could easily access the “SacchDB” database from our old server “genome-www.stanford.edu” to find information on our favorite model organism, the budding yeast.  We’ve grown a lot since then, and have even migrated to the cloud!  But as always, we’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 26 years.  Without such a great community behind us, SGD would not be the fantastic resource it is today.

The SGD Team zoomed in to celebrate the anniversary with cupcakes and fuzzy budders:

Screen Shot 2020-05-13 at 5.01.28 PM

“26 years and still your best bud!” #APOYG!

Categories: Announcements

Submit Data to SGD

April 15, 2020

Help SGD annotate your paper by pointing us to your novel results, datasets, or other important information! Authors can submit their own data for their publications using SGD’s simple submit data form.

Be sure to contact us if you have any questions or feedback!

Categories: Announcements

Explore SGD with New Homepage Feature

April 06, 2020


SGD is excited to introduce the new ‘Explore SGD’ button on our homepage, which allows users to explore SGD data and pages without an initial search query.

After selecting the ‘Explore SGD’ button, users will be redirected to our search results page where they can browse all of the information SGD has to offer. The tool is designed for both new and veteran users alike, as new users are provided a glimpse into the warehouse of information SGD contains, while seasoned users may discover something new. After clicking on the ‘Explore SGD’ button, be sure to use the categories on the left to navigate through the various pages and examine areas of interest. If you are viewing this page on a mobile device, tap on “Categories” at the top of your screen to see the list of categories.

Additionally, an ‘Explore’ button has been added to the selection of links available in the black bar at the top of every page. This gives users the ability to access the search results page from anywhere on the SGD website.

Check out the new Explore features on the SGD homepage and be sure to contact us if you have any questions or feedback!

Categories: Website changes

SGD Newsletter, Fall 2019

December 05, 2019

About this newsletter:

This is the Fall 2019 issue of the 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.

Contents:

  1. SGD at ICYGMB 2019
  2. SGD Staff Out and About
  3. Alliance of Genome Resouces at Version 2.3
  4. Updated Metabolic Pathways at SGD
  5. Sequence Variant Tracks Added to JBrowse
  6. Recent Publications from SGD Staff
  7. Happy Holidays from SGD!
  8. Upcoming Meetings

SGD at ICYGMB 2019

From August 18th-22nd, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientists Barbara Dunn, Edith Wong, and Rob Nash, Biocuration Scientist Suzi Aleksander, Software Developer Felix Gondwe, and Associate Biocuration Scientist Patrick Ng attended the 29th International Conference on Yeast Genetics and Molecular Biology in Gothenburg, Sweden. Our attending staff presented at a workshop and poster sessions at the meeting, and presentation materials are downloadable at the links below. We had a great time interacting with users and getting their feedback on how to improve SGD as a resource for the budding yeast community.

Presentations

PresenterPresentation Title
Mike Cherry“Introduction to SGD Workshop”
Stacia Engel“SGD’s Collaboration with the Alliance of Genome Resources”
Rob Nash“Disease Associations and Protein Abundance”
Edith Wong“Macromolecular Complexes and Chemical Pages at SGD”
Suzi Aleksander“Gene Ontology at SGD: GO Slim Mapper”
Patrick Ng“Depicting the S288C Transcriptome at SGD”

Posters

PresenterPoster Title
Barbara Dunn“Beyond S288C: Incorporating Genomic Sequence Information from Large-Scale S. cerevisiae Population Surveys into SGD”
Felix Gondwe“Downloading Data from SGD”
Edith Wong“Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”
Patrick Ng“Representing Transcriptional Heterogeneity and Inter-Strain Variation at the Saccharomyces Genome Database”
Stacia Engel“SGD & the Alliance of Genome Resources”
Suzi Aleksander“The Use of the Gene Ontology to Describe Biological Function at SaccharomycesGenome Database”
Rob Nash“Yeast-Human Cross-Species Complementation and Associations with Disease-related Genes”

Alliance of Genome Resources at Version 2.3

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 2.3 in November. Notable improvements and new features include:

  • Disease Pages present individual genetic models and mutants, as well as groupings within Disease Association ribbons.
  • Automated Gene Descriptions use an improved algorithm and now include Expression annotations.
  • Expression sections on Gene pages link out to external repositories and MOD specific resources.
  • Variants with allele/molecular consequences are displayed for Gene/JBrowse pages and downloadable as files.
  • Molecular Interactions for individual or all Alliance species are also available as files.

Updated Metabolic Pathways at SGD

SGD recently updated the YeastPathways resource, containing more than 200 biochemical pathways, with help from the BioCyc group at SRI to provide an updated web portal and tools. You can query for metabolic network, pathway, enzyme, or metabolites, as well as access pathways from SGD’s Function menu or locus pages for genes with enzymatic roles.

Sequence Variant Tracks Added to JBrowse

Sequence tracks that depict single nucleotide polymorphisms and small insertion/deletions mapped relative to the reference strain S288C by Song et al. 2015 in 25 S.cerevisiae strains are now viewable in SGD JBrowse. They are accessible from the “variants” category when you click the “Select tracks” tab on the upper-left hand of the page.

SGD Staff Out and About

Barbara Dunn and Joanna Argasinska at the SGD booth at Cold Spring Harbor Laboratory
Mike Cherry enjoying talking yeast biology with Doug Bishop. Photos by Constance Brukin
  • On October 7th-11th PI Mike Cherry, Senior Biocuration Scientists Edith Wong and Joanna Argasinska, Biocuration Scientist Suzi Aleksander, and Software Developer Felix Gondwe attended the Gene Ontology Consortium meeting in UC Berkeley, CA.
  • On October 23rd-26th, PI Mike Cherry, Senior Biocuration Scientists Barbara Dunn and Joanna Argasinska attended the  Yeast Research: Origins, Insights, Breakthroughs meeting in Cold Spring Harbor Laboratory, NY. They presented the poster, Saccharomyces Genome Database (SGD) Through the Years”

Recent Publications from SGD Staff

  • The Alliance of Genome Resources Consortium (2019) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 2019 Sep 25. pii: gkz813. doi: 10.1093/nar/gkz813. PMID:31552413
  • Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM (2019) Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 2019 Oct 15. pii: gkz892. doi: 10.1093/nar/gkz892. PMID:31612944
  • The Alliance of Genome Resources Consortium (2019) The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. Genetics. 2019 Dec 1. vol. 213 no. 4 1189-1196. doi: 10.1534/genetics.119.302523. PMID: 31796553
  • Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM and the SGD Project (2020) Incorporation of a Unified Protein Abundance Dataset into the Saccharomyces Genome Database. Database (Oxford). Manuscript Submitted

Happy Holidays from SGD!

We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays. Stanford University will be closed for two weeks starting on December 24. Although SGD staff members will be taking time off, the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.

Upcoming Meetings

The Allied Genetics Conference – TAGC 2020
Metro Washington, DC
April 22 to April 26, 2020 

15th International Congress on Yeasts
University of Vienna, Vienna, Austria
August 23 to August 27, 2020

The 31st Fungal Genetics Conference
Asilomar Conference Grounds, Pacific Grove, CA
March 09 to March 14, 2021

Categories: Newsletter

Browse Metabolic Pathways at SGD

August 02, 2019

Did you know that SGD has over 200 curated biochemical pathways for you to explore? SGD’s YeastPathways is a database of metabolic pathways and enzymes in Saccharomyces cerevisiae. YeastPathways enables you to visualize yeast metabolism from large metabolic networks to individual pathways, and from biochemical reactions down to individual metabolites. Search tools and click-to-browse features in YeastPathways enable quick navigation and intuitive exploration of yeast metabolism.

As the first major content update to YeastPathways since 2012, we have recently updated 62 pathways with expertly-curated summaries on pathway biochemistry, genetics, regulation, and more. Compounds that were previously missing a structure have also now been updated, along with the stoichiometry and scheme of many pathway reactions. In addition to content updates, YeastPathways has also received a major software upgrade that provides new tools, pages, and visual aids.

With new content and software, YeastPathways is better than ever. Users new to YeastPathways will find that it’s easy to get started—simply access YeastPathways through the Function menu at SGD, then run a search for a pathway, compound, enzyme, or reaction on the YeastPathways homepage. You can also access YeastPathways through gene pages at SGD. Just run a search for your favorite metabolic enzyme at SGD (example: TPI1) and find the Pathways section on the locus summary page. Any pathways in which the protein is involved will be listed and linked to YeastPathways.

Check out YeastPathways and be sure to contact us if you have any questions or feedback!

Categories: Data updates

Sequence Variant Tracks Added to JBrowse

June 12, 2019

We are excited to announce that 50 new “Variants” data tracks are now available for use in our genome browsing tool JBrowse. Utilizing whole-genome sequencing data published by Song et al. (2015), these data tracks visualize how the sequences of 25 S. cerevisiae strains differ from that of the reference genome strain, S288C.

Two data tracks are available for each of the 25 strains: a track that indicates single nucleotide polymorphisms (SNPs) relative to strain S288C, and a track that shows insertions or deletions (“indels”) relative to S288C.

Accessing these new data tracks is easy—just enter JBrowse and click on the “Select tracks” tab on the upper-left hand part of the page. Then, select the “variants” category. You can also download the variants, annotation, and sequence files on these strains for use in your own analyses.

If you’re new to JBrowse, don’t miss out—getting started takes no time at all. For information on how to use this tool, be sure to check out the JBrowse playlist on the SGD YouTube Channel or visit the JBrowse help page. If you have any questions or feedback about the new “Variants” data tracks or about our genome browsing tool, please don’t hesitate to contact us.

Table of strains with “Variants” data tracks in JBrowse, along with links to download their respective dataset:

Strain (link to Variants tracks in JBrowse)File Download Link
BC187BC187_Stanford_2014_JRII00000000.zip
BY4741BY4741_Stanford_2014_JRIS00000000.zip
BY4742BY4742_Stanford_2014_JRIR00000000.zip
CEN_PK2-1CaCEN.PK2-1Ca_Stanford_2014_JRIV01000000.zip
D273-10BD273-10B_Stanford_2014_JRIY00000000.zip
DBVPG6044DBVPG6044_Stanford_2014_JRIG00000000.zip
FL100FL100_Stanford_2014_JRIT00000000.zip
FY1679FY1679_Stanford_2014_JRIN00000000.zip
JK9-3dJK9-3d_Stanford_2014_JRIZ00000000.zip
K11K11_Stanford_2014_JRIJ00000000.zip
L1528L1528_Stanford_2014_JRIK00000000.zip
RedStarRedStar_Stanford_2014_JRIL00000000.zip
RM11-1ARM11-1A_Stanford_2014_JRIP00000000.zip
SEY6210SEY6210_Stanford_2014_JRIW00000000.zip
Sigma1278b-10560-6BSigma1278b-10560-6B_Stanford_2014_JRIQ00000000.zip
SK1SK1_Stanford_2014_JRIH00000000.zip
UWOPS05_217_3UWOPS05-217-3_Stanford_2014_JRIM00000000.zip
W303W303_Stanford_2014_JRIU00000000.zip
X2180-1AX2180-1A_Stanford_2014_JRIX00000000.zip
Y55Y55_Stanford_2014_JRIF00000000.zip
YJM339YJM339_Stanford_2014_JRIE00000000.zip
YPH499YPH499_Stanford_2014_JRIO00000000.zip
YPS128YPS128_Stanford_2014_JRID00000000.zip
YPS163YPS163_Stanford_2014_JRIC00000000.zip
YS9YS9_Stanford_2014_JRIB00000000.zip

Categories: New Data

SGD Newsletter, Spring 2019

June 03, 2019

About this newsletter:

This is the Spring 2019 issue of the 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.

Contents:

  1. 25th Anniversary of the SGD Website
  2. JBrowse: S288C Transcriptome and New Data Tracks
  3. Proteome-wide Abundance Data
  4. Alliance of Genome Resources: 2.1 Release
  5. SGD at Biocuration 2019
  6. Recent publications from SGD Staff
  7. SGD Biocurators Out and About
  8. What else have we been up to lately?
  9. Upcoming Meetings

25th Anniversary of the SGD Website

SGD members in front of the 150-foot-diameter Stanford Dish.

SGD members in front of the 150-foot-diameter Stanford Dish.

Wednesday, May 8th, marked the 25th year that the SGD website has been live. Although we celebrated the 25th anniversary of the database last year, the actual website wasn’t online until the following year (when the “World Wide Web” had only been in existence for about 22 months). Starting in 1994, you could simply access SacchDB from our old server genome-www.stanford.edu to find information on your favorite model organism. We’d like to express our gratitude to all of our users, collaborators, advisors, staff, and anyone else who has supported SGD over the last 25 years. Without such a great community behind us, SGD would not be the fantastic resource it is today.

SGD staff celebrated the day by taking a tour around the Stanford campus and enjoying the beautiful California spring weather. Did you catch our throwback page for CDC6?

JBrowse: S288C Transcriptome and New Data Tracks

Access SGD’s “S288C Transcriptome Data Tracks in JBrowse” and other video tutorials on our YouTube Channel

We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.

SGD has also updated our JBrowse with an additional 157 new data tracks related to genome-wide experiments and omics data for you to explore. The categories added include: Transcription & Transcriptional Regulation; Histone Modification; Chromatin Organization; RNA Catabolism; Transposons; DNA Replication, Recombination, and Repair.

Proteome-wide Abundance Data

SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell. Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85).

Two new YeastMine templates have been created to provide access to these data: Gene → Protein Abundance and Gene → Median Protein Abundance.

Alliance of Genome Resources: 2.1 Release

In March, the Alliance released version 2.1. The release showcases the combined effort from SGD and the other core Alliance members. Notable improvements and new features include:

  • Disease Associations file on Downloads page
  • Gene Descriptions files on Downloads page
  • Updated Interactions table, including link outs to MOD pages
  • Updated Gene Ontology and Expression ribbon displays
  • Related Data links in Search results

SGD at Biocuration 2019

From April 7th-10th, PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the International Society for Biocuration’s 12th International Biocuration Conference in Cambridge, UK. Several of our staff presented posters, while Edith also gave a great talk on her recent Database publication: Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Below are the posters and the talk SGD staff presented at Biocuration 2019. Click on any of the links to download the presentation.

Presentation

Presenter Presentation Title
Edith Wong “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”

Posters

Presenter Poster Title
Suzi Aleksander “In the Know About GO: A Newly Redesigned Website for the Gene Ontology”
Felix Gondwe “Downloading Data from SGD”
Edith Wong “Integration of Macromolecular Complex Data into the Saccharomyces Genome Database”

Recent publications from SGD Staff

  • Wong ED, Skrzypek MS, Weng S, Binkley G, Meldal BHM, Perfetto L, Orchard SE, Engel SR, Cherry JM; SGD Project (2018). Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Database (Oxford). 2019 Jan 1; 2019. doi: 10.1093/database/baz008 PMID:30715277
  • Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (2019). Model organism data evolving in support of translational medicine. Lab Anim (NY). 2018 Oct; 47(10):277-289. doi: 10.1038/s41684-018-0150-4 PMID:30224793

SGD Biocurators Out and About

You might see some of our SGD members at these upcoming events:


Senior Biocuration Scientist Rob Nash will be conducting a workshop at the annual Yeast Genetics & Genomics course at Cold Spring Harbor Laboratory July 23 – August 12, 2019.




SGD will be attending ICYGMB2019, the 29th International Conference on Yeast Genetics and Molecular Biology in Göteborg, Sweden August 18-22, 2019. If you’re going, be sure to attend the SGD Workshop on the afternoon of Day 4, Wednesday August 21!


What Else Have We Been Up To Lately?

Kevin MacPherson telling the SGD classic about 'why did the yeast cross the road?' at the Fungal Genetics Conference.[Photo by Matt Sachs, GSA]

Kevin MacPherson telling the SGD classic about ‘why did the yeast cross the road?’ at the Fungal Genetics Conference. [Photo by Matt Sachs, GSA]

  • Biocuration Scientist Kevin MacPherson gave tutorials at the Fungal Pathogen Genomics course at the Wellcome Genome Campus in May. He taught students how to use tools and resources at both SGD and the Candida Genome Database.
  • PI Mike Cherry, Principal Biocuration Scientist Stacia Engel, Senior Biocuration Scientist Edith Wong, Biocuration Scientist Suzi Aleksander and Software Developer Felix Gondwe attended the 2019 Gene Ontology Consortium Meeting in Cambridge, UK, in early April.
  • In March, Senior Biocuration Scientist Barbara Dunn and Biocuration Scientist Kevin MacPherson attended the Genetics Society of America’s 30th Fungal Genetics Conference in Pacific Grove, CA. They both presented posters, which are available to download in the table below.
Presenter Poster Title
Barbara Dunn “Associating Yeast Genes with Human Disease-related Genes at SGD”
Kevin MacPherson “Comparative Genomics at the Saccharomyces Genome Database”

Upcoming Meetings

Categories: Newsletter

Explore the S288C Transcriptome in JBrowse

April 25, 2019

We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.

You can easily access these new tracks by entering JBrowse and clicking on the left-hand “Select tracks” tab. They are located in the Transcriptome category. In addition to viewing the data in JBrowse, you can also download the .gff3 and .bw files for these tracks for use in your own analyses.

Check out our video tutorial from the SGD YouTube channel at the top of this page for a quick overview of the new transcriptome data tracks and how to access them. More information about these tracks and how SGD created them can also be found on our Genome Browser help page.

If you have any questions or feedback about the new Transcriptome data tracks or about our genome browser, please don’t hesitate to contact us.

Data tracks that visualize transcript isoforms that fully overlap a gene coding region:

Data Track Title Description
longest_full-ORF_transcripts_ypd This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media.
longest_full-ORF_transcripts_gal This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media.
most_abundant_full-ORF_transcripts_ypd This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media.
most_abundant_full-ORF_transcripts_gal This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media.
unfiltered_full-ORF_transcripts This track contains all transcripts that overlapped individual open reading frame (ORF) completely for WT cells grown in either glucose (ypd) or galactose (gal) media.

Data tracks that quantify the number of transcripts that cover a given nucleotide in the S288c genome:

Data Track Title Description
plus_strand_coverage_ypd For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the plus strand is represented in this track.
plus_strand_coverage_gal For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the plus strand is represented in this track.
minus_strand_coverage_ypd For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the minus strand is represented in this track.
minus_strand_coverage_gal For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the minus strand is represented in this track.

 

Categories: Tutorial, New Data

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