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