Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (abd) and gluteofemoral (glut) subcutaneous adipose tissue

ABSTRACT: Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (abd) and gluteofemoral (glut) subcutaneous adipose tissue

PROVIDER: PRJNA932442 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23363500.fastq.gz	Fastqsanger.gz
	SRR23363600.fastq.gz	Fastqsanger.gz
	SRR23363501.fastq.gz	Fastqsanger.gz
	SRR23363601.fastq.gz	Fastqsanger.gz
	SRR23363502.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 172

Similar Datasets

Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (abd) and gluteofemoral (glut) subcutaneous adipose tissue

Project description:Over the past two decades, studies have identified distinct transcriptional signatures between ABD and GF-adipose tissues and between both body shapes. Remarkably, a significant fraction of these depot specific gene expression patterns and more recently the differential chromatin structure profiles have been shown to be conserved during the culture and in vitro differentiation of the precursor cells into mature adipocytes. Our team and others have also shown distinct DNA methylation levels between ABD and GF-AT, that are preserved in isolated ADSCs cultured in vitro. Altogether, these data suggest that depot specific epigenomic profiles contribute significantly to the unique transcriptional profiles of ABD vs GF adipose tissues depots. To extend these earlier studies and to determine how the differential gene expression patterns in different adipose depots may be significantly influenced by chromatin landscape we performed H3K4me3, H3K4me2, H3K27me3, H3K9me3 and CTCF ChIP-seq and ATAC-seq on chromatin isolated from ABD and GF-ADSCs. We paired this with highly differentially expressed genes between ABD and GF-ADSCs. Then, to evaluate the potential role for long range chromatin interactions we utilized an H3K27Ac Hi-ChIP approach to capture putative regulatory loops with at least one anchor being marked by this enhancer associated histone mark. This in-depth analysis of the chromatin structure and organization of ABD and GF-ADSCs provides a better understanding of the intrinsic genomic regulatory features that help define the functionally distinct phenotypes of different subcutaneous adipose tissue depots and how they influence fat distribution in women.

2024-01-02 | GSE224770 | GEO

Genome-wide maps of chromatin architecture in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GLU) subcutaneous adipose tissue

2024-01-02 | GSE224777 | GEO

Genome-wide maps of chromatin architecture in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GLU) subcutaneous adipose tissue

Project description:Genome-wide maps of chromatin architecture in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GLU) subcutaneous adipose tissue

| PRJNA932714 | ENA

Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

Project description:Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

| PRJNA793019 | ENA

scRNA-Seq from stroma vascular fraction of abdominal and gluteofemoral subcutaneous white adipose tissue

Project description:scRNA-Seq from stroma vascular fraction of abdominal and gluteofemoral subcutaneous white adipose tissue

| PRJNA1077367 | ENA

scRNA-Seq from stroma vascular fraction of abdominal and gluteofemoral subcutaneous white adipose tissue

Project description:SVF was isolated from ABD and GF-adipose tissue biopsies by collagenase digestion and centrifugation, from 5 healthy women (38yo ±4.4; 31.8kg/m-2 ±3.12; WHR 0.86 ±0.05). After isolation, cells were counted with a Countess II automated cell counter (Thermofisher Scientific). Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. The method used was described in [6]. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene HiSeqX instrument.

2024-02-23 | GSE255996 | GEO

Gene expression signature of subcutaneous abdominal and subcutaneous gluteal adipose tissue

2013-11-15 | GSE47511 | GEO

Gene expression signature of subcutaneous abdominal and subcutaneous gluteal adipose tissue

Project description:To identify genes differentially expressed in abdominal and gluteal adipose tissue, we determined the mRNA transcription profile of 10 abdominal and 10 gluteal female adipose tissue sections using Agilent Whole Human Genome Microarrays. RNA of 10 subcutaneous abdominal and 10 subcutaneous gluteal fat depot samples was processed by Miltenyi Biotech GmbH (Bergisch Gladbach, Germany) and loaded on single-color Whole Human Genome 4x44K microarrays (G4112F) from Agilent Technologies.

2013-11-15 | E-GEOD-47511 | biostudies-arrayexpress

Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

Project description:Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to perform assess accessible chromatin regions by ATAC-seq, chromatin marks, CTCF and RNAPII identification by chIP-seq

2022-05-31 | GSE192749 | GEO

DNA methylation analysis of subcutaneous adipose tissue abdominal versus subcutenaous adipose tissue gluteal

Project description:In humans, adipose tissue is distributed in subcutaneous abdominal and subcutaneous gluteal depots that comprise a variety of functional differences. Whereas energy storage in gluteal adipose tissue has been shown to mediate a protective effect, an increase of abdominal adipose tissue is associated with metabolic disorders. However, the molecular basis of depot-specific characteristics is not completely understood yet. Using array-based analyses of transcription profiles, we identified a specific set of genes that was differentially expressed between subcutaneous abdominal and gluteal adipose tissue. To investigate the role of epigenetic regulation in depot-specific gene expression, we additionally analyzed genome-wide DNA methylation patterns in abdominal and gluteal depots. By combining both data sets, we identified a highly significant set of depot-specifically expressed genes that appear to be epigenetically regulated. Interestingly, the majority of these genes form part of the homeobox gene family. Moreover, genes involved in fatty acid metabolism were also differentially expressed. Therefore we suppose that changes in gene expression profiles might account for depot-specific differences in lipid composition. Indeed, triglycerides and fatty acids of abdominal adipose tissue were more saturated compared to triglycerides and fatty acids in gluteal adipose tissue. Taken together, our results uncover clear differences between abdominal and gluteal adipose tissue on the gene expression and DNA methylation level as well as in fatty acid composition. Therefore, a detailed molecular characterization of adipose tissue depots will be essential to develop new treatment strategies for metabolic syndrome associated complications. DNA methylation profiles of abdominal adipose tissue (6 samples) and gluteal adipose tissue (6 samples) were generated using Infinium methylation 450K BeadChips from Illumina (Illumina, San Diego, USA).

2013-11-15 | E-GEOD-47512 | 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