GEO DataSets

(Submitter supplied) Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

3 Samples

Download data: BW

(Submitter supplied) We report here differences in MNase digestibility comparing murine embryonic fibroblasts (MEFs) with and without Lsh. In the first set of samples we compare primary MEFs derived from Lsh+/+ (pMEF_WT5) or Lsh-/- (pMEF_KO6) day 13.5 gestation embryos. In a second set we compare MEFs form conditional Lsh knockout mice before (GC-OHT-NC) or after 48 hours of tamoxifen inducible cre-recombinase expression (GC-OHT-2D). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

9 Samples

Download data: BW

(Submitter supplied) A central question in biology is how enhancers are made accessible. The Drosophila embryo is a good model system to study this question as the gene regulatory networks regulating early developmental events have been well characterized. Zelda (Zld) is a uniformly distributed transcription factor (TF) integral to these networks, acting prior to and in collaboration with the patterning TFs to regulate target enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11203 GPL13304 GPL17275

32 Samples

Download data: BW, TXT

(Submitter supplied) Nucleosome positioning is critical to chromatin accessibility, and is associated with gene expression programs in cells. Previous nucleosome mapping methods assemble profiles from cell populations and reveal a cell-averaged pattern: nucleosomes are positioned and form a phased array surrounding the transcription start sites (TSSs ) of active genes and DNase I hypersensitive sites (DHSs). However, cells exhibit remarkable expression heterogeneity in response to active signaling even in a homogenous population of cells, which may be related to the heterogeneity in chromatin accessibility. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

586 Samples

Download data: BED

(Submitter supplied) Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that are activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL13304 GPL17275

64 Samples

Download data: BEDGRAPH

(Submitter supplied) Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL21306

9 Samples

Download data: BW

(Submitter supplied) Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

96 Samples

Download data: TSV

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

Organism:

Drosophila sechellia; Drosophila simulans; Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila ananassae; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni; Drosophila persimilis; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

15 related Platforms

175 Samples

Download data: BW

(Submitter supplied) Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. more...

Organism:

Drosophila persimilis; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila yakuba; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni; Drosophila ananassae; Drosophila sechellia; Drosophila simulans

Type:

Genome binding/occupancy profiling by high throughput sequencing

12 related Platforms

24 Samples

Download data: BW

(Submitter supplied) Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13304 GPL19132

46 Samples

Download data: BW, TSV

(Submitter supplied) Though the in vitro structural and in vivo spatial characteristics of transcription factor (TF) binding are well defined, TF interactions with chromatin and other companion TFs during development are poorly understood. To analyze such interactions in vivo, we profiled several TFs across a time course of human embryonic stem cell differentiation via CUT&RUN epigenome profiling, and studied their interactions with nucleosomes and co-occurring TFs by Enhanced Chromatin Occupancy (EChO), a computational strategy for classifying TF binding characteristics across time and space. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

109 Samples

Download data: BED, DOCX, PDF, RTF

(Submitter supplied) [1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells. HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA. [2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells. We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL9185 GPL6246

17 Samples

Download data: CEL, GFF, TXT

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

Organism:

Drosophila melanogaster; unidentified plasmid

Type:

Other

Platforms:

GPL19132 GPL21376

19 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL19132

18 Samples

Download data: TXT, XLS

(Submitter supplied) Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

Organism:

unidentified plasmid

Type:

Other

Platform:

GPL21376

1 Sample

Download data: FASTA, TSV, TXT

(Submitter supplied) Here we show how chromatin structure is involved in glucocorticoid receptor (GR) binding in a mouse mammary cell line. We show that GR binds to accessible chromatin sites that are either nucleosome-free or contain a nucleosome.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TDF

(Submitter supplied) Glucocorticoid hormone plays a major role in metabolism and many related diseases. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. GR-responsive enhancers have an accessible chromatin structure prior to hormone treatment (“pre-programmed”), whereas unresponsive enhancers specific to other cell types are inaccessible and inactive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TDF

(Submitter supplied) Here we have used a combination of advanced proteomics and genomics approaches to investigate the extent and mechanisms of transcription factor cross-talk at genomic hotspots. We identify ~12,000 transcription factor hotspots in the early phase of adipogenesis, and we find evidence of both simultaneous and sequential binding of transcription factors at these regions. We demonstrate for the first time that hotspots are highly enriched in large super-enhancer regions and that these drive the early adipogenic reprogramming of gene expression. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL11002 GPL18480

32 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: BW

(Submitter supplied) Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal status of such open chromatin, e.g., at active enhancers, is not clear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: BW