GEO DataSets

(Submitter supplied) Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. For a quantitative getic analysis of chromatin regulation, we generated open chromatin maps of 100 yeast samples including the parental strains (BY and RM, and two replicates for each) and their descendants by using the FAIRE-seq technique

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

96 Samples

Download data: BED

(Submitter supplied) Maps of open chromatin in three primary human blood cell types of the myeloid lineage (megakaryocytes, erythroblasts and monocytes) using the formaldehyde-assisted isolation of regulatory elements method followed by next-generation sequencing (FAIRE-seq). We also generated FAIRE-seq data in the megakaryocytic cell line CHRF-288-11. In addition to our data sets, we retrieved FAIRE-seq data for the erythroblastoid cell line K562 (ENCODE Project Consortium 2012) and pancreatic islets (Gaulton et al. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154 GPL9115

6 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae SK1

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platforms:

GPL4131 GPL4414

39 Samples

Download data: GPR

(Submitter supplied) To investigate the dynamics of the meiotic transcriptome and to ensure meiotic synchrony of our samples, we measured RNA abundance in vegetative cells, respiratory (pre-meiotic) cells and in synchronously sporulating cells at various times after transfer to sporulation media (SM).

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae SK1

Type:

Expression profiling by array

Platform:

GPL4414

27 Samples

Download data: GPR

(Submitter supplied) To investigate the relationship between chromatin organization and meiotic processes, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae SK1

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4131

12 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9134 GPL9825

222 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

174 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

48 Samples

Download data: TXT

(Submitter supplied) Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae x Saccharomyces paradoxus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL17601

20 Samples

Download data: BED

(Submitter supplied) High-throughput sequencing of genomic regions isolated using FAIRE (Formaldehyde-assisted isolation of regulatory elements) from three purified pancreatic islet samples For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL9115 GPL3514

5 Samples

Download data: BED, PAIR, WIG

(Submitter supplied) An eQTL analysis show that mutations in PDR8 gene in 59A strain versus S288c could trigger expressions variations of QDR2. In order to confirm this result and highlight other gene expression variations associated to PDR8 allelic variation, we performed an allele switch of PDR8 in 59A background (59A PDR8-S288c) and compared the transcriptomic profile of this strain to 59A. The analysis was performed in wine alcoholic fermentation conditions in stationary phase during nitrogen starvation and in alcoholic stress. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16012

6 Samples

Download data: GPR

(Submitter supplied) We performed here the transcriptomic profile of 44 segregants from a cross between S288c and 59A (a spore of EC1118 strain). The analysis was performed in wine fermentation condition in stationary phase during nitrogen starvation and in alcoholic stress. These data, associated with an individual genotyping by Affymetrix array allow us to highlight genetic variations involved in perturbation of regulatory network and fermentative behavior.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16012

56 Samples

Download data: GPR

(Submitter supplied) Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol. To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs). Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

960 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (?eQTLs?) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

60 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL4133 GPL8887 GPL6104

748 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL8887

224 Samples

Download data: TXT

(Submitter supplied) Most loci identified in genome wide association studies (GWAS) of complex traits reside in non-coding DNA and may contribute to phenotype via changes in gene regulation. The discovery of expression quantitative trait loci (‘eQTLs’) can thus be used to more precisely identify modest but real disease associations and provide insights into their underlying molecular mechanisms. This is particularly true for analyses of expression in non-transformed cells from tissues relevant to the complex traits of interest. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

464 Samples

Download data: TXT

(Submitter supplied) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

89 Samples

Download data: BED, TXT

(Submitter supplied) The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq to map “open chromatin”. Over 870,000 DNaseI or FAIRE sites, which correspond largely to nucleosome depleted regions (NDRs), were identified across the seven cell lines, covering nearly 9% of the genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

33 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq to map “open chromatin”. Over 870,000 DNaseI or FAIRE sites, which correspond largely to nucleosome depleted regions (NDRs), were identified across the seven cell lines, covering nearly 9% of the genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

16 Samples

Download data: BED, NARROWPEAK