Venters_2011_PMID_21329885.README Last modified: 2016-07-07 Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C, Pugh BF (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41(4):480-92 PMID: 21329885 Venters et al. determined the genome-wide binding locations of 200 yeast transcription-related proteins under normal and acute heat-shock conditions by ChIP-chip. Micorarray probes targetting the upstream UAS, TSS and 3'end regions of ORFs and ncRNAs were used to interrogate binding. A short summary of the contents of each data file compiled by SGD can be found in the following section. More in depth details can be found within the file header of each file. Data files last modified: May 24, 2011 SGD has compiled the following data files from this publication for the following binding factors: Ada2, Ahc1, Aor1, Arp6, Asf1, Ash1, Bas1, Bdf1, Bdf2, Bre1, Bre2, Brf1, Brn1, Bur2, Bur6, Bye1, Caf130, Caf40, Ccr4, Cdc36, Cdc39, Cha4, Chd1, Chz1, Cin5, Ctk1, Ctr9, Cyc8, Dhh1, Dig1, Dot1, Dst1, Eaf3, Elp3, Epl1, Esa1, Ess1, Fcp1, Fhl1, Fkh1, Fkh2, Gal4, Gcn4, Gcn5, Gcr1, Gln3, Hda1, Hfi1, Hho1, Hht1, Hht2, Hif1, Hos1, Hos2, Hos3, Hpa3, Hpr1, Hta2, Htb1, Htb2, Htz1, Ifh1, Ino2, Ino4, Ino80, Ioc2, Ioc3, Ioc4, Irc20, Irr1, Isw1, Isw2, Itc1, Iws1, Jhd1, Jhd2, Kin28, Leu3, Med2, Med4, Med6, Mft1, Mot1, Msn2, Nap1, Ncb2, Nhp6a, Not3, Not5, Nut1, Otu1, Paf1, Pcf11, Pho2, Pob3, Pop2, Pta1, Put3, Rad3, Rad6, Rap1, Reb1, Rei1, Rfx1, Rgr1, Rlr1, Rna14, Rpb2, Rpb3, Rpb7, Rpd3, Rph1, Rpo21, Rpt1, Rpt6, Rsc1, Rsc2, Rsc4, Rsc8, Rsc9, Rtg2, Rtt103, Rtt109, Rvb1, Rvb2, Rxt1, Rxt2, Sas4, Set1, Set2, Sfp1, Sif2, Sin3, Sir2, Sir3, Skn7, Snf1, Snf2, Snf4, Snf5, Snf7, Spt16, Spt2, Spt20, Spt21, Spt23, Spt3, Spt6, Spt7, Spt8, Srb4, Srb5, Ssl1, Ssl2, Ste12, Stp1, Sua7, Swc1, Swi3, Swi4, Swi5, Swr1, Taf1, Taf10, Taf13, Taf14, Taf3, Taf4, Taf5, Taf8, Taf9, Tbp, Tfa1, Tfa2, Tfb1, Tfb3, Tfc6, Tfc7, Tfc8, Tfg1, Tfg2, Thp1, Toa2, Top1, Tup1, Ubp8, Uga3, Ume6, Ure2, Vps72, Wtm1, Wtm2, Xbp1, Yaf9, Yap1, Yap5, Yap6, Ycg1, Ycs4, Yng1, Zap1, Zms1 * Venters_2011_[binding factor]_25C_FDR5_log_ratios_V64.gff3 * Venters_2011_[binding factor]_25C_log_ratios_V64.gff3 * Venters_2011_[binding factor]_37C_FDR5_log_ratios_V64.gff3 * Venters_2011_[binding factor]_37C_log_ratios_V64.gff3 These data files were compiled from the following supplementary files accompanying the publication and represent the normalized log2 ChIP binding ratios for each TAP-tagged factor over background (untagged) at each assayed temperature. High-confidence interactions were determined using a 5% FDR threshold for each assayed factor by the authors. Additionally, the authors have performed ChIP-seq for 20 elongation factors to examine binding events at a finer level from -350 to +1000 from the TSS for each ORF in 25bp windows. The author- processed data files for these factors can be found on the SGD download site as well as under accession E-MTAB-440 at ArrayExpress. The elongation factors are as follows: Bye1, Bur2, Ccr4, Cdc39, Ctk1, Ctr9, Dhh1, Dst1, Fcp1, Ess1, Iws1, Pcf11, Not5, Not3, Pta1, Pop2, Pob3, Rpo21, Rpb7, Rpb3 The sequencing reads were originally mapped to the R53-1-1 (2006_04_14) build of the S. cerevisiae reference genome by the authors and lifted over to the latest version (SGD R64-1-1, February 2011) by SGD. The original R53 files are contained in: * Venters_2011_PMID_21329885_V53_gff3_files.tgz * Venters_2011_PMID_21329885_V53_FDR5_gff3_files.tgz Unmapped reads are contained in the files: * Venters_2011_PMID_21329885_V53toV64_FDR5_gff3_unmapped_files.tgz * Venters_2011_PMID_21329885_V53toV64_gff3_unmapped_files.tgz Supplementary data files from the authors website (http://atlas.bx.psu.edu/data/binding) are contained in: 21329885_supplementary_website_files.zip Additional supplementary information: ArrayExpress accession: E-MTAB-311 and E-MTAB-440 http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-311/ http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-440/