Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Single-cell analysis of chromatin accessibility in adult mouse brain

PROVIDER: PRJNA1033582 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26585900_1.fastq.gz	Fastqsanger.gz
	SRR26585900_2.fastq.gz	Fastqsanger.gz
	SRR26586000_1.fastq.gz	Fastqsanger.gz
	SRR26586000_2.fastq.gz	Fastqsanger.gz
	SRR26585901_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 457

Similar Datasets

Analysis of chromatin accessibility in adult mouse pituitary using single-cell ATAC-seq

Project description:Analysis of chromatin accessibility in adult mouse pituitary using single-cell ATAC-seq

| PRJNA663883 | ENA

Analysis of chromatin accessibility in adult mouse pituitary using single-cell ATAC-seq

Project description:To gain insight into patterns of chromatin accessibility in distinct cell subtypes of mouse pituitary, pituitaries from two adult mice were collected and subjected to single-cell ATAC-seq analysis using 10X Genomics platform

2021-02-03 | GSE158070 | GEO

Single nuclei ATAC-seq (10X Genomics Chromium) of FACS enriched cortical and hippocampal interneurons from P30 mouse brains

Project description:While epigenetic modifications are critical for cell state changes throughout development, a detailed characterization of chromatin accessibility during neurogenesis has not been explored. We collected single-cell chromatin accessibility profiles of ~40,000 cells from 4 distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many of which were restricted to distinct progenitor cell types or brain regions. By integrating snATAC-Seq and transcriptome data, we characterized changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance throughout neurodevelopment. Integrating our chromatin accessibility profiles from embryonic and adult interneurons with the iPSYCH2012 GWAS dataset revealed several disease-associated polymorphisms overlapped accessible regions in embryonic cells and MGE-derived mature interneurons. These findings highlight the coordination between chromatin accessibility and gene expression as neural progenitors mature during embryogenesis, and open the door for future studies to define critical enhancer-promoter interactions that direct cell fate decisions.

2021-12-31 | GSE167048 | GEO

Decoding gene regulation in the fly brain

Project description:The Drosophila brain is a work horse in neuroscience. Single-cell transcriptome analysis, 3D morphological classification, and detailed mapping of the connectome have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly. The developmental trajectories of each of these cell types, from neuroblast to mature neuron or glial cell, as well as their maintenance and plasticity in the adult brain, are controlled by gene regulatory networks (GRNs) In this study, we profiled chromatin accessibility of 240,000 single cells, spanning nine developmental time points from larval, pupal, and adult brains, and integrated this data with single-cell transcriptomes. This atlas reveals the regulatory connections between genomic enhancers and the single-cell transcriptomes for more than 80 cell types in the fly brain. Each cell type is characterized by a unique chromatin accessibility landscape, with thousands of specific regulatory regions, summing to a total of 95,931 regulatory regions that are used in the brain. Exploiting this resource, we find that the combination of expressed transcription factors is reflected by their respective motif architecture within cell type-specific enhancers.

2021-08-10 | GSE163697 | GEO

Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus

Project description:Here we describe SNARE-seq, a droplet-based method to simultaneously profile gene expression and chromatin accessibility in each of thousands of single nuclei. Employing this method, we profiled 1047 nuclei from human cell line mixture, 5081 and 10309 nuclei from neonatal and adult mouse brain.

2019-02-05 | GSE126074 | GEO

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

Project description:Chromatin accessibility and transcriptome profiling are the most critical tools in single-cell technologies. Here, we present Microwell-seq3, a high-throughput and easy-to-handle platform for high-sensitive single-nucleus chromatin accessibility or full-length gene expression profiling. The method combined pre-indexing and a dual-pass “chip-in-tube” strategy for nuclei loading and DNA amplification. Therefore, Microwell-seq3 does not require specialized equipment and is suitable for any molecular biology lab with simple consumables and thermal cycler. We applied Microwell-seq3 to profile the chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in about 50,000 nuclei from multiple adult mouse tissues. Joint analysis of cell-type specific regulatory elements and total RNA uncovered cell type heterogeneity and differentially expressed genes in brain compared with previous polyadenylated transcripts capturing methods. Gene regulatory networks based on full-length transcriptome and chromatin accessibility provided improved cell-cell communications in neurons and glia. Finally, we applied Microwell-seq3 to comprehensively characterize malignant cells in spontaneous tumors from aging mouse.

2024-01-03 | GSE225133 | GEO

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

2024-01-03 | GSE225132 | GEO

a42f9d07-b3e4-4117-baee-e8e7443522e0 - samples

Project description:Single cell multiomics from 2 donor controls, expression and chromatin accessibility. Samples belong to gray matter tissue from the brain.

| EGAD00001008457 | EGA

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]

Project description:High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]

| PRJNA509254 | ENA

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Project description:We applied a combinatorial indexing assay, sci-ATAC-seq, to profile genome-wide chromatin accessibility in ~100,000 single cells from 13 adult mouse tissues. We identify 85 distinct patterns of chromatin accessibility, most of which can be assigned to cell types, and ~400,000 differentially accessible elements. We use these data to link regulatory elements to their target genes, to define the transcription factor grammar specifying each cell type, and to discover in vivo correlates of heterogeneity in accessibility within cell types. We develop a technique for mapping single cell gene expression data to single-cell chromatin accessibility data, facilitating the comparison of atlases. By intersecting mouse chromatin accessibility with human genome-wide association summary statistics, we identify cell-type-specific enrichments of the heritability signal for hundreds of complex traits. These data define the in vivo landscape of the regulatory genome for common mammalian cell types at single-cell resolution.

2018-08-02 | GSE111586 | GEO

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