GEO DataSets

(Submitter supplied) We profiled the epigenetic landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using single nuclei processed with 10X Genomics's Single Cell ATAC platform.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

3 Samples

Download data: CSV, H5, TSV

(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

Platforms:

GPL30172 GPL21626

12 Samples

Download data: CSV, JPG, PNG, TSV

(Submitter supplied) We profiled the gene expression landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using fresh frozed tissue sections processed with 10X Genomics's Visium platform.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL21626

3 Samples

Download data: CSV, H5, JPG, PNG

(Submitter supplied) We profiled the epigenetic landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using fresh frozen tissue sections processed with 10X Genomics's OMNI ATAC, which allows to record regions of open chromatin while retaining spatial resolution.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

6 Samples

Download data: CSV, H5, JPG, TSV

(Submitter supplied) Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. In the popular ATAC-seq method, Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

143 Samples

Download data: BED, BEDGRAPH, PDF

(Submitter supplied) We recently introduced CUT&Tag, an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei, and then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds DNA sequencing adapters (“tagmentation”) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses exposure artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves signal-to-noise over current chromatin profiling methods. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

44 Samples

Download data: BED, PDF

(Submitter supplied) Understanding the spatial choreography of the acessible genome in the intact nucleus

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

8 Samples

Download data: BED

(Submitter supplied) In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

22 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL15520

8711 Samples

Download data

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

4208 Samples

Download data: TXT

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520

4207 Samples

Download data: TXT

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

288 Samples

Download data: TXT

(Submitter supplied) Here we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by Assay of Transposase-accessible Chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ~3,700 single cells, encompassing more than 75 unique genotype-phenotype relationships.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) The imprecision of linking intergenic mutations to target genes has limited molecular understanding of diverse human diseases. Here, we show H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naïve T cells to either T helper 17 cells or regulatory T cells create subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. more...

Organism:

Homo sapiens; Mus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL23787 GPL20301 GPL18573

58 Samples

Download data: BED, TXT

(Submitter supplied) An updated protocol for ATAC-seq, including wet-lab library preparation and guidelines about sequencing and data analysis.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL20301

23 Samples

Download data: BW

(Submitter supplied) We present spatially resolved chromatin accessibility profiling of tissue sections via next-generation sequencing by combining in situ ATAC-seq chemistry and microfluidic deterministic barcoding. Mouse and human tissues were profiled by spatial-ATAC-seq.

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301 GPL24247

10 Samples

Download data: TAR, TSV

(Submitter supplied) We optimzed ATAC-seq library preparation for use with Drosophila melanogaster. The protocol addresses factors specific to fruit flies, such as the insect exoskeleton and smaller genome size. The optimized protocol provides guidelines for sample input, nuclei isolation, and enzymatic reaction times. The data included here were generated using our optimized library preparation workflow.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

5 Samples

Download data: BW, CSV, NARROWPEAK

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility, due to its simplicity, speed, and low input material requirements. However, it can be difficult to evaluate data quality, particularly when processing many samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing ATAC-seq quality control results. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

62 Samples

Download data: BED, BEDGRAPH, BROADPEAK

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

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

9 Samples

Download data: NARROWPEAK

(Submitter supplied) The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasing popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: NARROWPEAK