New & Noteworthy

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

January 24, 2019


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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

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