New & Noteworthy

Proteome-wide abundance data

March 11, 2019

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. The original datasets were initially obtained using different methodologies (mass spectrometry, fluorescence microscopy, flow cytometry, and TAP-immunoblot), allowing Ho et al. to evaluate the strengths and weaknesses of these methods in addition to providing the community with a comprehensive reference map of the yeast proteome.

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

Special thanks to Brandon Ho and Grant Brown for generating this comprehensive reference map of protein abundance, and for their help in making this data available to the larger community.

Categories: New Data

Apply Now for the 2019 Yeast Genetics and Genomics Course

March 05, 2019

yeast_course_panorama

For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists. The application deadline is April 1st, so don’t miss your chance! Find all the details and application form here. This year’s instructors – Grant Brown, Greg Lang, and Elçin Ünal – have designed a course (July 23 – August 12) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:

  • Finding and Analyzing Yeast Information Using SGD
  • Isolation and Characterization of Mutants
  • Yeast Transformation, Gene Replacement by PCR, and Construction and Analysis of Gene Fusions
  • Tetrad Analysis
  • Genome-scale Screens Using Synthetic Genetic Array (SGA) Methodology    
  • Deep Sequencing Applied to SNP Mapping and Deep Mutational Scanning
  • Exploring Synthetic Biology with CRISPR/Cas9-directed Engineering of Biosynthetic Pathways
  • Computational Methods for Data Analysis
  • Modern Cytological Approaches Including Epitope Tagging and Imaging Yeast Cells Using Fluorescence Microscopy

Techniques have been summarized in a completely updated course manual, which was recently published by CSHL Press.

IMG_2185

There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).

Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.

Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!

The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!

Categories: Announcements

Register for the 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)

January 24, 2019


icygmb logo

The 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) will be held at the the Swedish Exhibition & Congress Centre, Gothenburg, Sweden, from August 18-22, 2019.

The ICYGMB brings together scientists from all around the globe to present and discuss cutting-edge research on yeast. Described as the “most important event in yeast research“, the conference facilitates an environment where the international yeast community can freely exchange information, strike collaborations, and build new projects and alliances.

The 2019 meeting is enriched with over 50 speakers and a program that aims to provide an up-to-date overview of the most exciting topics in yeast research. The program includes lectures and workshops that discuss topics such as cell signaling, evolutionary genetics, aging and disease models, yeast biotechnology, and more.

Registration and abstract submission are now open. The early registration deadline is April 1. The abstract submission deadline for oral presentations is May 15, whereas July 31 is the deadline for abstracts that will be included in the Conference Abstract book.

Categories: Conferences

New Data Tracks added to JBrowse

January 15, 2019


SGD has updated our JBrowse genome browser with 157 new data tracks related to genome-wide experiments and omics data for you to explore. You can easily access these new tracks, which visualize data from the twenty publications listed below, by entering JBrowse and clicking on the left-hand “Select tracks” tab. Then, search for the PMID associated with the reference of interest.

Note that some references appear more than once, as they have multiple data tracks associated that belong to different categories in JBrowse.

For more information on using JBrowse, be sure to check out our playlist of JBrowse video tutorials on YouTube. If you have any questions or feedback about the new tracks or about our genome browser, please don’t hesitate to contact us.

Transcription & Transcriptional Regulation

Reference PMID Description in JBrowse
Baptista et al. (2017) 28918903 ChEC-seq to map the genome-wide binding of the SAGA coactivator complex in budding yeast.
Castelnuovo et al. (2014) 24497191 Genome-wide measurement of whole transcriptome versus histone modified mutants
El Hage et al. (2014) 25357144 Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes retrotransposons and mitochondria.
Freeberg et al. (2013) 23409723 Mapped regions of untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs)
Kang et al. (2015) 25213602 Genome-wide transcript profiling by paired-end ditag sequencing
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Park et al. (2014) 24413663 Simultaneous mapping of RNA ends by sequencing (SMORE-seq) to identify the strongest transcription start sites and polyadenylation sites genome-wide
Rossbach et al. (2017) 28924058 Authors utilized the Calling Cards Ty5 retrotransposon insertion method to identify binding sites of cdc7kd, cdc7kdΔcterm and Gal4 transcription factor within the yeast genome.
Schaughnency et al. (2014) 25299594 Genome-wide identification of transcription termination sites; pA pathway and non-polyadenylation pathway in strains missing Sen1p or Nrd1p

Histone Modification

Reference PMID Description in JBrowse
Castelnuovo et al. (2014) 24497191 Genome-wide measurement of whole transcriptome versus histone modified mutants
Hu J. et al. (2015) 26628362 ChIP-seq and MNase-seq to determine how histone modifications and chromatin structure directly regulate meiotic recombination. Identified acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification
Joo et al. (2017) 29203645 Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) compared with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae
Kniewel et al. (2017) 28986445 ChIP-seq to determine the whole-genome enrichment of Mek1 targeted histone H3 threonine 11 phosphorylation (H3 T11ph) during Saccharomyces cerevisiae meiosis.
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Weiner et al. (2018) 25801168 Examining chromatin dynamics through genome-wide mapping of 26 histone modifications at 0 4 8 15 30 and 60 minutes after diamide addition using MNase-ChIP

Chromatin Organization

Reference PMID Description in JBrowse
Chereji et al. (2014) 29426353 Genome binding/occupancy profiling of single nucleosomes and linkers by high throughput sequencing
Gutierrez et al. (2017) 29212533 Authors sought to correct sequence bias of MNase-Seq with a method based on the digestion of naked DNA and the use of the bioinformatic tool DANPOS
Hu Z. et al. (2014) 24532716 Genome-wide measurement of nucleosome occupancy during cell aging
Hu J. et al. (2015) 26628362 ChIP-seq and MNase-seq to determine how histone modifications and chromatin structure directly regulate meiotic recombination. Identified acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification
Joo et al. (2017) 29203645 Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) compared with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.

RNA Catabolism

Reference PMID Description in JBrowse
Geisberg et al. (2014) 24529382 Half-lives of 21,248 mRNA 3_ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.
Smith et al. (2014) 24931603 Identification of genome-wide transcripts; looking at nonsense-mediated RNA decay pathway

Transposons

Reference PMID Description in JBrowse
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Michel et al. (2017) 28481201 Genome-wide examination of protein function by using transposons for targeted gene disruption
Rossbach et al. (2017) 28924058 Authors utilized the Calling Cards Ty5 retrotransposon insertion method to identify binding sites of cdc7kd, cdc7kdΔcterm and Gal4 transcription factor within the yeast genome.

DNA Replication, Recombination, and Repair

Reference PMID Description in JBrowse
Mao et al. (2017) 28912372 Map of N-methylpurine (NMP) lesion alkalation damage across the yeast genome

 

Categories: New Data

Next