GEO DataSets

(Submitter supplied) 96 scATAC-seq samples generated for the retinoic acid-induced mESC differentiation at day 4.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

96 Samples

Download data: XLSX

(Submitter supplied) HiChIP data generated for the retinoic acid-induced mESC differentiation at day 4.

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

17 Samples

Download data: BEDPE

(Submitter supplied) 464 scRNA-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

464 Samples

Download data: TXT

(Submitter supplied) We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. more...

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

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

4 related Platforms

20 Samples

Download data: BW, TAR, TSV

(Submitter supplied) Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volumes of data pose unique computational challenges. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: HDF5

(Submitter supplied) Profiles of single cell epigenomes, assayed using scATAC-seq, in K562 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

288 Samples

Download data: CSV

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL19132 GPL25244 GPL21306

429 Samples

Download data: BW, TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

1 Sample

Download data: TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

1 Sample

Download data: TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL25244

14 Samples

Download data: BW

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

384 Samples

Download data: BW, TSV

(Submitter supplied) Enhancers act as docking stations in the genome to which transcription factors bind, tightly regulating gene expression. Although single-cell technologies allow measuring chromatin accessibility or gene expression in each individual cell, exploiting both layers towards bona fide gene regulatory networks and enhancers is still a challenge. Here, we independently generate comprehensive single-cell transcriptome and epigenome atlases of the Drosophila eye-antennal disc and propose the spatial integration of single-cell RNA-seq and single-cell ATAC-seq data using a virtual latent space that mimics the spatial organization of the 2D tissue. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19132

29 Samples

Download data: BW, TSV

(Submitter supplied) We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

265 Samples

Download data: TXT

(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

Platform:

GPL19057

833 Samples

Download data

(Submitter supplied) We have developed a computational approach that uses self-organizing maps for integrative genomic analysis. We utilize this approach to identify the single-cell chromatin and transcriptomic profiles during mouse pre-B cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

568 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

543 Samples

Download data: TXT

(Submitter supplied) This dataset is related to our recent study "APEC: an accesson-based method for single-cell chromatin accessibility analysis". We adopted a fluorescent tagmentation-based single-cell ATAC-seq technique (ftATAC-seq) to investigated the per cell regulome dynamics of mouse thymocytes. Associated with ftATAC-seq, APEC revealed a detailed epigenomic heterogeneity of thymocytes, characterized the developmental trajectory and predicted the regulators that control the stages of maturation process.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

704 Samples

Download data: BED, CSV, MTX

(Submitter supplied) We propose a computational method for quantifying the open chromatin status of regulatory regions from single cell ATAC-seq experiments. scOpen, which is based on positive-unlabeled learning of matrices, is able to estimate the probability that a region is open at a given cell mitigating the sparsity of scATAC-seq matrices. We demonstrate that scOpen improves all down-stream analysis steps of scATAC-seq data as clustering, visualization, detection of transcription factors and chromatin conformation in several scATAC-seq data.

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL18573 GPL19057

12 Samples

Download data: BED, MTX, TSV

(Submitter supplied) We propose a computational method for single cell comparative regulatory analysis based on single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq) from two different conditions. Our software sc-compReg provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and construction of differential regulatory networks across two conditions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

4 Samples

Download data: BED, MTX, TSV

(Submitter supplied) The assay for transposase-accessible chromatin using sequencing (ATAC-seq) at single-cell level can provide different perspectives of regulatory patterns based on cell type-specific accessible regions. While human genomic elements have been well studied, understanding how nuclear acid sequence regulates the expression of target genes in a genome-wide level in other organisms remains a major challenge. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32518

2 Samples

Download data: BED