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
	Albert_2007_PMID_17392789	Genome-wide study to map the occupancy of H2A.Z containing nucleosomes.
	Bernstein_2000_PMID_11095743	Genomic expression study of histone deacetylation.
	Buhler_2007_PMID_18076285	Genome-wide study to map single-strand DNA-associated double strand breaks (DSBs).
	Cavalieri_2000_PMID_11035792	Genomic expression study in a vineyard isolate.
	Chervitz_1998_PMID_9851918	Entire protein datasets used for the comparisons between S. cerevisiae and C. elegans.
	Costanzo_2010_PMID_20093466	Large-scale genetic interaction study.
	David_2006_PMID_16569694	Genome-wide transcriptome study.
	Deutschbauer_2005_PMID_15716499	Large-scale phenotypic study.
	Duan_2010_PMID_20436457	Genome-wide study identifying chromosomal interactions.
	Dudley_2006_PMID_16729036	Large-scale phenotypic study.
	Eaton_2010_PMID_20351051	Genome-wide study on replication origins.
	Field_2008_PMID_18989395	Genome-wide study to map nucleosome occupancy.
	Ghavi-Helm_2008_PMID_18628399	Genome-wide study to map the location of elongation factor TFIIS, RNA Pol II and III.
	Granovskaia_2010_PMID_20193063	Transcriptome study.
	Guillemette_2005_PMID_16248679	Genome-wide study to map the histone variant H2A.Z.
	Guillemette_2011_PMID_21483810	Genome-wide study to map histone H3 lysine 4 acetylation (H3K4ac) marks.
	He_2003_PMID_14690598	Genomic expression study.
	Hesselberth_2009_PMID_19305407	Genome-wide study mapping DNase I cleavage protected footprints across the budding yeast genome.
	Hsiang_2005_PMID_15883882	Computational biology study.
	Huh_Ghaemmaghami_2003_PMID_14562095_14562106	A large-scale protein localization and abundance studies.
	Ingolia_2009_PMID_19213877	Genome-wide translation study.
	Johnson_2011_PMID_21947206	Genome-wide study to examine the role of mRNA export factor Yra1 in 3'end processing.
	Kaplan_2009_PMID_19092803	Genome-wide study to map the occupancy of nucleosomes in vitro and in vivo.
	Kastenmayer_2006_PMID_16510898	Large-scale phenotypic study.
	Kertesz_2010_PMID_20811459	Genome-wide RNA secondary structure study.
	Kim_2006_PMID_16847258	Membrane proteomic study.
	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.
	Kirmizis_2007_PMID_17898715	Genome-wide study to map the distribution of histone H3 lysine 4 and H3 arginine 2 methlyation modifications.
	Kraeva_2007_PMID_17356699	Study on thermodynamic stability of nucleic acid sequences.
	Lardenois_2011_PMID_21149693	Genome-wide study of the expression program underlying vegetative and reproductive phases of the yeast life cycle.
	Lee_2004_PMID_15567862	Computational biology study.
	Lee_2007_PMID_17873876	Genome-wide study to map nucleosome occupancy using tiling arrays.
	Lesage_2004_PMID_15166135	Large-scale genetic interaction study.
	Lesage_2005_PMID_15715908	Large-scale phenotypic and genetic interaction study.
	Lisnic_2005_PMID_15776233	Study on palindromic sequences.
	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.
	MacIsaac_2006_PMID_16522208	Transcriptional regulator mapping study.
	Mancera_2008_PMID_18615017	Study on genome-wide crossover and non-crossover gene conversions.
	Mavrich_2008_PMID_18550805	Genome-wide study of nucleosome organization.
	Mayer_2010_PMID_20818391	Study to map the genome-wide occupancy of RNA polymerase II, its phosphorylated forms and transcription factors in growing yeast.
	Miura_2006_PMID_17101987	Large-scale transcriptome study.
	Myers_2004_PMID_16420673	Computational biology study.
	Nagalakshmi_2008_PMID_18451266	Genome-wide transcriptome study.
	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.
	Nieduszynski_2006_PMID_16847347	Study to identify replication origins.
	Osterberg_2006_PMID_16847257	Large-scale phenotypic study.
	Ozsolak_2010_PMID_21145465	Genome-wide study identifying polyadenylation events in the budding yeast genome using Direct RNA Sequencing technology.
	Pan_2011_PMID_21376234	Genome-wide map of the distribution of double strand breaks in the budding yeast genome.
	Pena-Castillo_2007_PMID_17435240	Study on uncharacterized genes.
	Pokholok_2005_PMID_16122420	Genome-wide study to map the distribution of methylated and acetylated histones in modified nucleosomes.
	Qi_2009_PMID_19832984	Study on meiotic crossovers and gene conversion.
	Reinders_2006_PMID_16823961	Mitochondrial localization study.
	Rhee_2011_PMID_22153082	Genome-wide map of binding locations of Gal4, Rap1, Reb1 & Phd1, a proof-of-concept study by ChIP-exo.
	Rhee_2012_PMID_22258509	Genome-wide study to map structural and positional organization of pre-initiation complexes.
	Riles_1993_PMID_8514151	Physical restriction map data.
	Roberts_2006_PMID_16741729	Genomic expression study.
	Rowicka_2007_PMID_17827275	Computational biology study.
	Schacherer_2007_PMID_17389913	SNP study.
	Schulze_2011_PMID_22056669	Genome-wide study mapping targets of deubiquitinases Ubp8 and Upb10.
	Segal_2006_PMID_16862119	Genome-wide nucleosome positioning study.
	Sickmann_2003_PMID_14576278	Mitochondrial localization study.
	Steinmetz_2002_PMID_12134146	Large-scale phenotypic study.
	Steinmetz_2006_PMID_17157256	Study on RNAP II occupancy.
	Tachibana_2005_PMID_15743812	Transcriptome study.
	Townsend_2003_PMID_12716989	Genomic expression study.
	Troyanskaya_2003_PMID_12826619	Computational biology study.
	van_Dijk_2011_PMID_21697827	Genome-wide study identifying 1658 Xrn1-sensitive unstable transcripts (XUTs) in the budding yeast genome.
	Velculescu_1997_PMID_9008165	Genomic expression study that utilized SAGE tags (includes the tags and their current genomic locations).
	Venters_2011_PMID_21329885	Genome-wide study to map the binding sites of transcription-related proteins using ChIP-chip.
	Vogtle_2009_PMID_19837041	Mitochondrial proteome study.
	Waern_2013_PMID_23390610	Differential expression RNA-seq across 17 experiment conditions.
	Xie_2005_PMID_15883373	Large-scale phenotypic study.
	Xu_2006_PMID_17067396	Genome-wide study on replication origins.
	Xu_2009_PMID_19169243	Transcriptome study.
	Yassour_2009_PMID_19208812	Transcriptome study.
	Yassour_2010_PMID_20796282	Genome-wide study identifying 1,103 putative antisense transcripts from sequencing a strand-specific cDNA library by RNA-seq.
	Zhang_2005_PMID_15905473	Study on transcription start sites.
	Zhang_2007_PMID_17351133	Study to identify spliced introns.
	archive	Old data archived for historical purposes.
	intergenic_positions.xls	Intergenic primer set designed by Vishy Iyer and Jason Lieb while in Pat Brown's lab.
	pgmap.xls	Information useful for comparison of the S. cerevisiae genetic and physical maps.