Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

D0c374dd-52ba-473d-a7db-7fd4d6343f40 - samples

ABSTRACT: Human data for chromatin accessibility (scATAC-Seq) in CD34+ B cell precursors.

PROVIDER: EGAD00001010910 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Single-cell chromatin accessibility data using scATAC-seq

Project description:Single-cell chromatin accessibility data using scATAC-seq

| PRJNA274006 | ENA

9de3010e-4fe7-4952-a7cc-01182e507c23 - samples

Project description:Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

| EGAD00001010909 | EGA

bcbd0d10-02f5-46d3-902c-f563f699d047 - samples

Project description:Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

| EGAD00001010908 | EGA

Homo sapiens

Project description:Single-cell chromatin accessibility data from K562 cells using scATAC-seq

| PRJNA387476 | ENA

Single-cell chromatin accessibility data using scATAC-seq

Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.

2015-06-17 | E-GEOD-65360 | biostudies-arrayexpress

90a46c29-4ef0-43b5-9aa4-5f4ae95e8535 - samples

Project description:Human data for transcriptome (scRNA-Seq) in CD34+ B cell precursors.

| EGAD00001010907 | EGA

Human data for chromatin accessibility (ATAC-Seq and scATAC-Seq) and transcriptome (RNA-Seq and scRNA-Seq) in eight B-cell precursors, from HSC to Naive B cells

Project description:We generated paired transcriptomic (RNA-Seq) and chromatin accessibility (ATAC-Seq) profiles from 8 immune cell populations representing the early lymphoid hematopoietic differentiation stages along the B cell lineage: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+. Cell populations were isolated from healthy adult human bone marrow precursors and peripheral blood (n=13) following a predefined sorting strategy. For each donor, a subset of different cell type populations was obtained. Additionally, to explore the continuous dynamic of RNA and ATAC, we generated a single-cell sample of human CD34+ B cell precursors.

| EGAS00001007296 | EGA

Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing [scATAC-seq]

Project description:Dissecting transcriptional and chromatin accessibility heterogeneity of proliferating cone precursors in human retinoblastoma tumours by single cell sequencing [scATAC-seq]

| PRJNA699543 | ENA

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to benchmark scATAC-Seq analysis methods

Project description:Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics.

2024-01-10 | GSE223319 | GEO

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to validate long read RNA-Seq isoforms and benchmark scATAC-Seq analysis methods II

2023-09-14 | GSE224045 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data