New & Noteworthy
New data tracks added to GBrowse
April 23, 2012
SGD has added a new mix of data tracks to our GBrowse genome viewer from seven publications covering transcriptome exploration via tiling microarrays (David et al. 2006), genomic occupancy of RNA polymerase II and III and associated factors (Kim et al. 2010; Ghavi-Helm 2008), 3′ end processing (Johnson et al. 2011), histone H2BK123 monoubiquitination (Schulze et al. 2011) and high-resolution ChIP by a novel method called ChIP-exo (Rhee et al. 2011; Rhee et al. 2012). Download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse or directly from the SGD downloads page. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!
Tags: ChIP-exo > histone modifications > RNA polymerase II > RNA polymerase III > transcriptome
Expression Data and LiftOver Files Available for Download
February 14, 2012
RNA expression data that are included in SGD’s SPELL expression analysis tool are now available for download in the expression directory. Datasets have been grouped by publication and are in PCL format.
LiftOver files that allow conversion of chromosomal coordinates between different S. cerevisiae genome versions are also now available for download via the genome_releases link in the sequence directory.
New data tracks added to GBrowse
January 26, 2012
SGD has added a mélange of data tracks to our GBrowse genome viewer from six publications covering various applications of high-throughput sequencing, including genome-wide distributions of DNase I-protected genomic footprints (Hesselberth et al. 2009), recombination-associated double strand breakpoints (Pan et al. 2011), polyadenylation sites (Ozsolak et al. 2010), antisense ncRNAs (Yassour et al. 2010), cryptic unstable transcripts (CUTs) (Neil et al. 2009) and Xrn1-sensitive unstable transcripts (XUTs) (van Dijk et al. 2011). You can now also easily download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse. Please watch our video tutorial for more information on how to download data from GBrowse. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!
View Downloading GBrowse Data at SGD on Vimeo.
Updated Resource: YPL+
January 25, 2012
Links to YPL+ (the Yeast Protein LocalizationPlus Database) have been added to the “Protein Information” section of SGD Locus Summary pages. YPL+ is a recently upgraded version of the YPL image database, and has been expanded to include GFP-localization data for more than 3500 genes. Data in YPL+ are derived from a collection of GFP fusion constructs generated by C-terminal chromosomal tagging (Huh et al., 2003, Nature 425, 686-691) as well as a collection of proteins involved in lipid-metabolism, constructed by in vivo recombination (Natter et al., 2005, Mol. Cell. Proteomics 4(5), 662-672). Thanks to Sepp Kohlwein for help in setting up these links.
New Histone Modification and Variant Data Tracks Added to GBrowse
August 5, 2011
We have added new data tracks to our GBrowse genome viewer from six publications covering various histone acetylation and methlyation modifications (Guillemette et al. 2011; Kirmizis et al. 2007; Liu et al. 2005 and Pokholok et al. 2005) and the mapping of histone variant H2A.Z (Albert et al. 2007 and Guillemette et al. 2005). We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments.