GEO DataSets

(Submitter supplied) The complexity of the brain and the links entailed to its functional diversity remain a major challenge of biology to understand. Distinct anatomical areas regulate a vast array of processes including organismal homeostasis, cognitive functions and susceptibility to neurological pathologies, many of which define our species. Distal enhancers have emerged as key regulatory elements that acquire epigenetic modifications in a cell-type specific manner, thus enforcing cell- and species-specific gene expression programs. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16288 GPL11154

151 Samples

Download data: BED, BEDGRAPH, BW, TXT

(Submitter supplied) The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4559 GPL1454

124 Samples

Download data: GPR, PAIR

(Submitter supplied) Eukaryotic gene regulatory information is contained within the DNA sequences of cis-regulatory elements and the epigenetic features of the chromatin surrounding these elements. Recent investigations in yeast, fly, and mammalian systems have made significant contributions toward our understanding of the relationship between gene activation and chromatin architecture at transcriptional promoters, but much work remains to improve our knowledge of this relationship at human promoters and other transcriptional regulatory elements, such as enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4558 GPL4559 GPL1454

64 Samples

Download data

(Submitter supplied) Gene regulation in mammals involves a complex interplay between promoter and distal regulatory elements that function in concert to drive precise spatio-temporal gene expression programs. However, the dynamics of distal gene regulatory elements and its function in transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here we use a combinatorial analysis of genomewide datasets for chromatin accessibility (FAIRE-Seq) and enhancer mark H3K27ac to reveal a highly dynamic nature of chromatin accessibility during neurogenesis that gets restricted to certain genomic regions as neurons acquire a post-mitotic, terminally differentiated state. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

20 Samples

Download data: TXT

(Submitter supplied) Characterisation of different histone modifications is crucial to understand gene regulation. In order to study the most predictive histone modification for active enhancers we created unbiased set of enhancers and used machine learning approach. Our approach revealed an unconventional histone modification H2BK20ac as most efficient marker of active enhancers. H2BK20ac also showed superior coverage of tissue specific active enhancers in complex invivo samples. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL9115 GPL9250 GPL13112

23 Samples

Download data: TXT, WIG

(Submitter supplied) We examined the histone modification H3K4 dimethylation (H3K4me2) in the prefrontal cortex of individual Rhesus macaques at different ages by chromatin immunoprecipitation, followed by deep sequencing (ChIP-seq) at the whole genome level

Organism:

Macaca mulatta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9160

5 Samples

Download data: BED, TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL9250 GPL9185 GPL6887

42 Samples

Download data: WIG

(Submitter supplied) The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL9185

31 Samples

Download data: WIG

(Submitter supplied) We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

11 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

Platform:

GPL21697

11 Samples

Download data: BIGWIG, BROADPEAK

(Submitter supplied) Enhancers are non-coding genomic features that regulate the transcriptional output of their target genes. Their dysregulation has been associated with various diseases including cancer. However, identification and characterisation of non-coding mutations that are relevant for tumorigenesis and prognosis remain a major challenge. Here we present the detection and characterisation of enhancer mutations in a genome-wide analysis of three lung cancer subtypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: BIGWIG, BROADPEAK

(Submitter supplied) Enhancers are non-coding genomic features that regulate the transcriptional output of their target genes. Their dysregulation has been associated with various diseases including cancer. However, identification and characterisation of non-coding mutations that are relevant for tumorigenesis and prognosis remain a major challenge. Here we present the detection and characterisation of enhancer mutations in a genome-wide analysis of three lung cancer subtypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

5 Samples

Download data: BIGWIG, BROADPEAK

(Submitter supplied) Here we used epigenomic profiling for H3K27ac, a mark of active enhancers to examine the genome-wide in vivo utilization of enhancers in three different mouse tissues across seven developmental stages, ranging from mid-gestation through adulthood. The majority of the ~90,000 enhancers identified exhibited tightly temporally restricted activity windows and were associated with stage-specific biological functions and regulatory pathways in individual tissues. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

48 Samples

Download data: BED, WIG, XLSX

(Submitter supplied) Allelic differences between the two sets of chromosomes can affect the propensity of inheritance in humans, but the extent of such differences in the human genome has yet to be fully explored. Here, we delineate allelic chromatin modifications and transcriptomes amongst a broad set of human tissues, enabled by a chromosome-span haplotype reconstruction strategy1. The resulting haplotype-resolved epigenomic maps reveal extensive allele bias in the transcription of human genes as well as chromatin state, allowing us to infer cis-regulatory relationships between genes and their control sequences. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

4 Samples

Download data: VCF

(Submitter supplied) We report transcriptome analysis of human embryonic stem cells and in vitro differentiated neural stem cells, comparing wild type H9, UGP2 homozygous knock-out and UGP2 mutant cells harboring a homozygous A>G nucleotide change affecting the start codon of UGP2 isoform 2 that was introduced by CRISPR-Cas9 engineering

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BW

(Submitter supplied) The aim of this data set is to measure the effect of rofecoxib and celecoxib on the transcription profile in an in vitro inflammation model. Transcription profiling was carried out using Affymetrix HG U-133A v2 microarrays.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

52 Samples

Download data: CEL