GEO DataSets

(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) We performed whole-genome gene expression profiling in Pik3cg-/- mice and subsequent gene ontology clustering of differentially expressed genes compared to wild type mice, in order to investigate the role of Pik3cg in platelet membrane biogenesis and blood coagulation. Pik3cg-deficient mice were obtained from sources previously described (T. Sasaki et al, 2000, Science 287, 1040-1046), backcrossed onto the C57BL/6J Jax genetic background for eight generations (B6J;129-Pik3cg-tm1Pngr) and then maintained as a closed colony by intercrossing from within the colony (C57BL/6J Jax contribution: 99.6%).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) Maps of open chromatin in a megakaryocytic (CHRF-288-11) and an erythroblastoid (K562) cell line using the formaldehyde-assisted isolation of regulatory elements (FAIRE) method. We profiled chromatin structure at 62 non-redundant genetic loci representing all known associations (as of November 2009, CEU population) with 11 cardiovascular traits: coronary artery disease (CAD), (early-onset) myocardial infarction (MI), mean platelet volume (MPV), platelet counts (PLT), platelet signaling (PLS), white blood cell counts (WBC), red blood cell counts (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), systolic blood pressure (SBP), diastolic blood pressure (DBP), hypertension (HYP).

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL11256

4 Samples

Download data: PAIR

(Submitter supplied) Annotation in this record is based on NCBI human build 36 (hg18) We profiled chromatin structure at 62 non-redundant genetic loci representing all known associations (as of November 2009, CEU population) with 11 cardiovascular traits: coronary artery disease (CAD), (early-onset) myocardial infarction (MI), mean platelet volume (MPV), platelet counts (PLT), platelet signaling (PLS), white blood cell counts (WBC), red blood cell counts (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), systolic blood pressure (SBP), diastolic blood pressure (DBP), hypertension (HYP). more...

Organism:

Homo sapiens

1 Series

4 Samples

Download data: NDF, POS

(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) 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) Incomplete annotation of cell-to-cell state variation and widespread linkage disequilibrium in the human genome represent significant challenges to elucidating mechanisms of trait-associated genetic variation. Here, using data from the UK Biobank, we perform genetic fine-mapping for 16 blood cell traits to quantify posterior probabilities of association while allowing for multiple independent signals per region. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: NARROWPEAK

(Submitter supplied) Background: Genome wide association studies (GWASs) have revealed many susceptibility loci for complex genetic diseases. For most loci the causal genes have not been identified. The identification of candidate genes is currently mainly based genes that localize close to or within the identified loci. We have recently shown that 92 of the 163 Inflammatory Bowel Disease (IBD)-loci co-localize with noncoding DNA regulatory elements (DRE). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

372 Samples

Download data: WIG

(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) We generated a genome-wide interaction map of regulatory elements in human cells (K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. For data usage terms and conditions, please refer to https://www.encodeproject.org/about/data-use-policy

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

7 Samples

Download data: BED, TXT

(Submitter supplied) Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single nucleotide polymorphisms (SNPs) associated with cancer risk lie in non protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs), and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

43 Samples

Download data: NARROWPEAK

(Submitter supplied) Deciphering the impact of genetic variation on gene regulation is fundamental to understanding common, complex human diseases. In this study, we obtained genome-wide RNA-Seq and ChIP-Seq (for H3K4me3 and H3K27ac histone modifications) data in the human liver. We mapped quantitative trait loci (QTLs) of gene expression levels and histone modification states. We integrated our findings with summary statistics of genome-wide association studies (GWAS) and identified candidate genes, gene regulatory regions, and variants in GWAS loci.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16791

1794 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL25201 GPL24676 GPL16791

60 Samples

Download data: BW, IDAT, NARROWPEAK

(Submitter supplied) Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL25201

20 Samples

Download data: IDAT

(Submitter supplied) Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: RDATA, TXT

(Submitter supplied) Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTL) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTL have been identified in a limited set of human tissues. Here we mapped caQTL in human liver tissue in 20 liver samples and identified 3,123 caQTL. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

20 Samples

Download data: BED, BW, NARROWPEAK, RDATA