Published Datasets

This directory contains files from published work. Some of these files are not regularly updated. Please note the date associated with the files and see the accompanying README documents for more information.

Name Description README
[DIR] Adhikari_2014_PMID_25356552 Comparative RNA-seq analysis of the cellular response to HOG and filamentous growth pathway inducers [TXT]
[DIR] Albert_2007_PMID_17392789 Genome-wide study to map the occupancy of H2A.Z containing nucleosomes. [TXT]
[DIR] Arribere_2013_PMID_23580730 TL-seq and TATL-seq study of 5' UTRs. [TXT]
[DIR] Buhler_2007_PMID_18076285 Genome-wide study to map single-strand DNA-associated double strand breaks (DSBs). [TXT]
[DIR] Cavalieri_2000_PMID_11035792 Genomic expression study in a vineyard isolate. [TXT]
[DIR] Chervitz_1998_PMID_9851918 Entire protein datasets used for the comparisons between S. cerevisiae and C. elegans. [TXT]
[DIR] Chong_2015_PMID_26046442 Large-scale protein abundance and localization data. [TXT]
[DIR] Costanzo_2010_PMID_20093466 Large-scale genetic interaction study. [TXT]
[DIR] David_2006_PMID_16569694 Genome-wide transcriptome study. [TXT]
[DIR] Deutschbauer_2005_PMID_15716499 Large-scale phenotypic study.
[DIR] Duan_2010_PMID_20436457 Genome-wide study identifying chromosomal interactions. [TXT]
[DIR] Dudley_2006_PMID_16729036 Large-scale phenotypic study.
[DIR] Eaton_2010_PMID_20351051 Genome-wide study on replication origins. [TXT]
[DIR] Field_2008_PMID_18989395 Genome-wide study to map nucleosome occupancy. [TXT]
[DIR] Ghaemmaghami_2003_PMID_14562106 Large-scale protein localization and abundance study. [TXT]
[DIR] Ghavi-Helm_2008_PMID_18628399 Genome-wide study to map the location of elongation factor TFIIS, RNA Pol II and III. [TXT]
[DIR] Granovskaia_2010_PMID_20193063 Transcriptome study. [TXT]
[DIR] Grant_2011_PMID_21330290 PWM-predicted binding site matches in the S. cerevisiae S288C reference genome, as determined by FIMO. [TXT]
[DIR] Guillemette_2005_PMID_16248679 Genome-wide study to map the histone variant H2A.Z. [TXT]
[DIR] Guillemette_2011_PMID_21483810 Genome-wide study to map histone H3 lysine 4 acetylation (H3K4ac) marks. [TXT]
[DIR] He_2003_PMID_14690598 Genomic expression study. [TXT]
[DIR] Hesselberth_2009_PMID_19305407 Genome-wide study mapping DNase I cleavage protected footprints across the budding yeast genome. [TXT]
[DIR] Hsiang_2005_PMID_15883882 Computational biology study. [TXT]
[DIR] Huh_2003_PMID_14562095 A large-scale protein localization and abundance studies. [TXT]
[DIR] Ingolia_2009_PMID_19213877 Genome-wide translation study. [TXT]
[DIR] Johnson_2011_PMID_21947206 Genome-wide study to examine the role of mRNA export factor Yra1 in 3'end processing. [TXT]
[DIR] Jubin_2014_PMID_24558267 Computational study of repetitive regions of the genome. [TXT]
[DIR] Kaplan_2009_PMID_19092803 Genome-wide study to map the occupancy of nucleosomes in vitro and in vivo. [TXT]
[DIR] Kastenmayer_2006_PMID_16510898 Large-scale phenotypic study. [TXT]
[DIR] Kertesz_2010_PMID_20811459 Genome-wide RNA secondary structure study. [TXT]
[DIR] Kim_2006_PMID_16847258 Membrane proteomic study. [TXT]
[DIR] Kim_2010_PMID_20835241 Genome-wide study to map the phosphorylation patterns of the CTD repeats of RNA Pol II and occupancy of CTD-associated factors. [TXT]
[DIR] Kirmizis_2007_PMID_17898715 Genome-wide study to map the distribution of histone H3 lysine 4 and H3 arginine 2 methlyation modifications. [TXT]
[DIR] Kraeva_2007_PMID_17356699 Study on thermodynamic stability of nucleic acid sequences. [TXT]
[DIR] Lardenois_2011_PMID_21149693 Genome-wide study of the expression program underlying vegetative and reproductive phases of the yeast life cycle. [TXT]
[DIR] Lee_2004_PMID_15567862 Computational biology study. [TXT]
[DIR] Lee_2007_PMID_17873876 Genome-wide study to map nucleosome occupancy using tiling arrays. [TXT]
[DIR] Lesage_2004_PMID_15166135 Large-scale genetic interaction study. [TXT]
[DIR] Lesage_2005_PMID_15715908 Large-scale phenotypic and genetic interaction study. [TXT]
[DIR] Lisnic_2005_PMID_15776233 Study on palindromic sequences. [TXT]
[DIR] Liu_2005_PMID_16122352 Study to map 12 different histone modification patterns on thousands of nucleosomes on chromosome 3 and 230 promoters on other chromosomes. [TXT]
[DIR] MacIsaac_2006_PMID_16522208 Transcriptional regulator mapping study. [TXT]
[DIR] Mancera_2008_PMID_18615017 Study on genome-wide crossover and non-crossover gene conversions. [TXT]
[DIR] Mavrich_2008_PMID_18550805 Genome-wide study of nucleosome organization. [TXT]
[DIR] Mayer_2010_PMID_20818391 Study to map the genome-wide occupancy of RNA polymerase II, its phosphorylated forms and transcription factors in growing yeast. [TXT]
[DIR] Miura_2006_PMID_17101987 Large-scale transcriptome study. [TXT]
[DIR] Myers_2004_PMID_16420673 Computational biology study. [TXT]
[DIR] Nagalakshmi_2008_PMID_18451266 Genome-wide transcriptome study. [TXT]
[DIR] Neil_2009_PMID_19169244 Study to map the genome-wide distribution of cryptic unstable transcripts (CUTs) in budding yeast using a 3'Long-SAGE strategy adapted for deep sequencing. [TXT]
[DIR] Nieduszynski_2006_PMID_16847347 Study to identify replication origins. [TXT]
[DIR] Osterberg_2006_PMID_16847257 Large-scale phenotypic study. [TXT]
[DIR] Ozsolak_2010_PMID_21145465 Genome-wide study identifying polyadenylation events in the budding yeast genome using Direct RNA Sequencing technology. [TXT]
[DIR] Pan_2011_PMID_21376234 Genome-wide map of the distribution of double strand breaks in the budding yeast genome. [TXT]
[DIR] Pena-Castillo_2007_PMID_17435240 Study on uncharacterized genes. [TXT]
[DIR] Pokholok_2005_PMID_16122420 Genome-wide study to map the distribution of methylated and acetylated histones in modified nucleosomes. [TXT]
[DIR] Qi_2009_PMID_19832984 Study on meiotic crossovers and gene conversion. [TXT]
[DIR] Reinders_2006_PMID_16823961 Mitochondrial localization study. [TXT]
[DIR] Rhee_2011_PMID_22153082 Genome-wide map of binding locations of Gal4, Rap1, Reb1 & Phd1, a proof-of-concept study by ChIP-exo. [TXT]
[DIR] Rhee_2012_PMID_22258509 Genome-wide study to map structural and positional organization of pre-initiation complexes. [TXT]
[DIR] Riles_1993_PMID_8514151 Physical restriction map data. [TXT]
[DIR] Rowicka_2007_PMID_17827275 Computational biology study. [TXT]
[DIR] Schacherer_2007_PMID_17389913 SNP study. [TXT]
[DIR] Schulze_2011_PMID_22056669 Genome-wide study mapping targets of deubiquitinases Ubp8 and Upb10. [TXT]
[DIR] Segal_2006_PMID_16862119 Genome-wide nucleosome positioning study. [TXT]
[DIR] Sickmann_2003_PMID_14576278 Mitochondrial localization study. [TXT]
[DIR] Song_2015_PMID_25781462 Pan-genome pipeline and analysis. [TXT]
[DIR] Steinmetz_2002_PMID_12134146 Large-scale phenotypic study. [TXT]
[DIR] Steinmetz_2006_PMID_17157256 Study on RNAP II occupancy. [TXT]
[DIR] Surma_2013_PMID_23891562 Quantitative genetic interaction map (E-MAP) for genes involved in lipid metabolism. [TXT]
[DIR] Tachibana_2005_PMID_15743812 Transcriptome study. [TXT]
[DIR] Townsend_2003_PMID_12716989 Genomic expression study. [TXT]
[DIR] Troyanskaya_2003_PMID_12826619 Computational biology study. [TXT]
[DIR] van_Dijk_2011_PMID_21697827 Genome-wide study identifying 1658 Xrn1-sensitive unstable transcripts (XUTs) in the budding yeast genome. [TXT]
[DIR] Velculescu_1997_PMID_9008165 Genomic expression study that utilized SAGE tags (includes the tags and their current genomic locations). [TXT]
[DIR] Venters_2011_PMID_21329885 Genome-wide study to map the binding sites of transcription-related proteins using ChIP-chip. [TXT]
[DIR] Vogtle_2009_PMID_19837041 Mitochondrial proteome study. [TXT]
[DIR] Waern_2013_PMID_23390610 Differential expression RNA-seq across 17 experiment conditions. [TXT]
[DIR] Xie_2005_PMID_15883373 Large-scale phenotypic study.
[DIR] Xu_2006_PMID_17067396 Genome-wide study on replication origins. [TXT]
[DIR] Xu_2009_PMID_19169243 Transcriptome study. [TXT]
[DIR] Yassour_2009_PMID_19208812 Transcriptome study. [TXT]
[DIR] Yassour_2010_PMID_20796282 Genome-wide study identifying 1,103 putative antisense transcripts from sequencing a strand-specific cDNA library by RNA-seq. [TXT]
[DIR] Zhang_2005_PMID_15905473 Study on transcription start sites. [TXT]
[DIR] Zhang_2007_PMID_17351133 Study to identify spliced introns. [TXT]
[DIR] archive Old data archived for historical purposes. [TXT]
[DIR] intergenic_positions.xls Intergenic primer set designed by Vishy Iyer and Jason Lieb while in Pat Brown's lab. [TXT]
[DIR] pgmap.xls Information useful for comparison of the S. cerevisiae genetic and physical maps. [TXT]