Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [snATAC-seq]

ABSTRACT: To explore the mechanistic basis of the different phases of pre- and postnatal muscle development and the contraction-dependent control of muscle gene expression , we generated a multi-omics single nucleus RNAseq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) atlas of normal muscle and paralyzed muscle from mice lacking Cacna1s.

ORGANISM(S): Mus musculus

PROVIDER: GSE211542 | GEO | 2023/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [snRNA-seq]

Project description:To explore the mechanistic basis of the different phases of pre- and postnatal muscle development and the contraction-dependent control of muscle gene expression , we generated a multi-omics single nucleus RNAseq (snRNA-seq) and single nucleus ATAC-seq (snATAC-seq) atlas of normal muscle and paralyzed muscle from mice lacking Cacna1s.

2023-05-31 | GSE211543 | GEO

Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [snATAC-seq]

Project description:Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [snATAC-seq]

| PRJNA870875 | ENA

Reprogramming of Cis-regulatory networks during skeletal muscle atrophy [snATAC-seq]

Project description:Current atlas of regulatory sequences controlling skeletal muscle atrophy are still incomplete and lack cell type resolution. We applied single-cell chromatin accessibility assays (snATAC) to normal and denervated skeletal muscle from mice. We integrated these snATAC datasets with our single-nucleus RNA-sequence dataset to reveal the status of open chromatin. Using these datasets, we delineated chromatin accessibility maps in both normal and atrophic muscles and identified cis-regulatory elements (CREs) in all type of cell in skeletal muscle that may regulating muscle protein metabolism, energy metabolism and transcription activities, thus, provided a rich resource for understanding gene regulatory programs in skeletal muscle and related disorders.

2023-09-06 | GSE217575 | GEO

Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snATAC-seq]

Project description:Focal cortical dysplasia (FCD) is a heterogeneous group of cortical developmental malformations that constitute a common cause of medically intractable epilepsy. Multiomic integration was conducted via single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assays for transposase-accessible chromatin sequencing (snATAC-seq) to analyse cell type-specific alterations in chromatin accessibility and correlate them with gene expression changes in the epileptogenic cortex of FCD type IIIa (FCD IIIa).

2024-10-30 | GSE266303 | GEO

Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snATAC-seq]

Project description:Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (~3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.

2021-06-23 | GSE178733 | GEO

Reprogramming of Cis-regulatory networks during skeletal muscle atrophy [snATAC-seq]

Project description:Reprogramming of Cis-regulatory networks during skeletal muscle atrophy [snATAC-seq]

| PRJNA899568 | ENA

snATAC-seq of the developing mouse cerebellum across eleven stages

Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).

2021-09-07 | E-MTAB-9765 | biostudies-arrayexpress

A molecular pathway for cancer cachexia-induced muscle atrophy revealed at single nucleus resolution [snATAC]

Project description:A molecular pathway for cancer cachexia-induced muscle atrophy revealed at single nucleus resolution [snATAC]

| PRJNA1135089 | ENA

Human and rat skeletal muscle multi-omic profiling

| EGAS00001005730 | EGA

Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [ChIP-seq]

Project description:During the maturation of myofibers, the expression and activity of the basic leucine zipper TF Maf are increased compared to developmental stages. To determine the gene program regulated by this TF, we performed ChIP-seq against Maf and H3K27ac in adult gastrocnemius and quadriceps skeletal muscles.

2023-05-31 | GSE211541 | 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