Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM_MI-ATAC_unstained]

ABSTRACT: A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).

ORGANISM(S): Homo sapiens

PROVIDER: GSE112195 | GEO | 2018/11/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [Tumor_stained_for_EpCam_HIF1a]

Project description:A novel scATAC-seq approach, Multi-Index single cell ATAC-seq (MI-ATAC), in which we not only index the accessible chromatin of individual cells, but also index their protein expression using index Fluorescence Activated Cell Sorting (FACS).

2018-11-09 | GSE112246 | GEO

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [Tumor_stained_for_EpCam_CD45]

2018-11-09 | GSE112245 | GEO

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM12878]

2018-11-09 | GSE112090 | GEO

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [K562_GATA2]

2018-11-09 | GSE112200 | GEO

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [GM_single_cell_unstimulated]

2018-11-09 | GSE112198 | GEO

Joint single-cell chromatin and protein profiling reveals environmental regulation of epigenomic heterogeneity [4T1-Splenocyte]

2018-11-09 | GSE112194 | GEO

Simultaneous epitope and epigenetic profile measurements with multi-index single-cell ATAC-sequencing [4T1]

2018-11-09 | GSE112089 | GEO

The epigenomic landscape of cognitive stimulation in the context of aging in mouse dorsal hippocampus - SWATH

Project description:Aging is a universal biological phenomenon linked to many diseases, such as cancer or neurodegeneration. However, the molecular mechanisms underlying aging, or how lifestyle interventions such as cognitive stimulation can ameliorate this process, are yet to be clarified. Here, we performed a multi-omic profiling, including RNA-seq, ATAC-seq, ChIP-seq, EM-seq, SWATH-MS and single cell Multiome scRNA and scATAC-seq, in the dorsal hippocampus of young and old mouse subjects which were subject to cognitive stimulation using the paradigm of environmental enrichment. In this study we were able to describe the epigenomic landscape of aging and cognitive stimulation.

2023-09-29 | PXD045567 | Pride

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.

Project description:Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. Pi-ATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1? protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells.

| S-EPMC6214962 | biostudies-literature

A simple and robust plate-based single-cell ATAC-seq on various tissues and cell lines

Project description:The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, only a few studies have been done at the single cell level (scATAC-seq) due to technical difficulties. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk tagmentation with single-nuclei sorting, to investigate open chromatin regions. We applied this method on mouse splenocytes and unbiasedly revealed key regulatory regions and transcription factors that define each cell (sub)type.

2018-10-10 | E-MTAB-6714 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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