GEO DataSets

(Submitter supplied) We previous identified enhancers that regulate MYC expression in K562 cells (Fulco et al. Science 2016). Here, we perturbed MYC enhancers with individual CRISPRi gRNAs and performed ChIP-seq to study the effects on chromatin state.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

54 Samples

Download data: TDF

(Submitter supplied) We generated ATAC-seq and H3K27ac ChIP-seq data in immortalized immune cancer cell lines to predict enhancer-gene regulation using the ABC model.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

67 Samples

Download data: TDF

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed ChIP-Exo for CTCF to map the insulator regions in ESC, TSC and XEN

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

5 Samples

Download data: BED, BW

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

Organism:

Mus musculus

Type:

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

4 related Platforms

75 Samples

Download data: BED, BW

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed HiChIP to profile putative enhancer interactions in TSC, ESC, XEN and EPISC cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: BEDPE

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed gene expression profiling in ESC, TSC, XEN and EPISC with RNA-seq technique.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: CSV

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed HiC to map large-scale 3D architectural rewiring in ESC, TSC and XEN

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

4 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed ChIP-seq for H3k27ac to map the putative active enhancers and promoters in ESC, TSC, XEN and EPISC

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

15 Samples

Download data: BED, BW

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed ATAC to map accessible regions (AR) in enhancer and promoter regions in ESC, TSC, XEN and EPISC

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

12 Samples

Download data: BED, BW

(Submitter supplied) To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed high-resolution in situ 4C-seq analysis around enhancers and promoters of cell-type specific genes (e.g. Sox17 for XEN and Nanog for ESC), which showed high concordance both with the virtual 4C of HiChIP and the called HiChIP contacts in the respective cell type

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

25 Samples

Download data: BW

(Submitter supplied) Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: TDF

(Submitter supplied) Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: TDF

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL17021

46 Samples

Download data: HIC, TDF, TXT

(Submitter supplied) Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

4 Samples

Download data: HIC

(Submitter supplied) Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TXT

(Submitter supplied) Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) A major goal of genetics research is to elucidate mechanisms explaining how genetic variation contributes to phenotypic variation. The genetic variants identified in genome-wide association studies (GWASs) generally explain only a small proportion of heritability of phenotypic traits, the so-called missing heritability problem. Recent evidence suggests that additional common variants beyond lead GWAS variants contribute to phenotypic variation; however, their mechanistic underpinnings generally remain unexplored. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

14 Samples

Download data: BED, CSV, MATRIX

(Submitter supplied) We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity.

Organism:

Escherichia coli; Homo sapiens

Type:

Other

Platforms:

GPL11154 GPL14548

6 Samples

Download data: TXT

(Submitter supplied) For Large White (LW) and Meishan (MS) skeletal muscle, we performed H3K27ac BL HiCHIP to establish enhancer-promoter interaction maps. We also performed GRID-seq which uses a bivalent linker to ligate RNA to DNA in situ.

Organism:

Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19176

12 Samples

Download data: BEDPE, MCOOL, TXT

(Submitter supplied) Although major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and ChIP-Seq analyses. more...

Organism:

Sus scrofa

Type:

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

Platform:

GPL22918

200 Samples

Download data: BED, BEDGRAPH, BIGWIG, NARROWPEAK