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

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

PROVIDER: PRJNA932714 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23371702_1.fastq.gz	Fastqsanger.gz
	SRR23371702_2.fastq.gz	Fastqsanger.gz
	SRR23371703_1.fastq.gz	Fastqsanger.gz
	SRR23371703_2.fastq.gz	Fastqsanger.gz
	SRR23371704_1.fastq.gz	Fastqsanger.gz

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Genome-wide maps of chromatin architecture in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GLU) 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 | GSE224777 | GEO

scRNA-seq from abdominal and gluteofemoral subcutaneous adipose tissue derived stem cells (ADSC)

Project description:Recent studies using single cell (sc) RNAseq, identified subpopulations of adipose derived stem cells (ADSCs) within the stroma vascular fraction of human adipose tissue, potentially leading to functionally distinct adipocyte populations. We aimed to extend this analysis by exploring the heterogeneity of the ADSCs within abdominal (ABD) vs gluteofemoral (GF) subcutaneous fat depots of apple and pear shaped pre-menopausal women. Using full-length SMART-seq scRNAseq technology and a panel of known stem cell and preadipocyte markers for identification, we detected 7 subpopulations of cells in both ABD and GF-ADSCs. Two ADSC subpopulations enriched the GF depot were characterized by increased expression of genes involved in cholesterol and fatty acid metabolism. Two subpopulations enriched in the ABD depot had gene expression signatures associated with inflammation and fibrosis. The body shape comparison revealed that apple-shaped women have a unique fibrotic ADSC subpopulation in their ABD depot and a high proportion of predicted highly proliferative preadipocytes in their GF depot. We propose that these depot and body shape specific ADSC populations could contribute to the metabolic complications associated with the differential fat distribution.

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Human Subcutaneous ABD/GLU/Thi adipose tissue RNAseq - NYC sample

Project description:Human Subcutaneous ABD/GLU/Thi adipose tissue RNAseq - NYC sample

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

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

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

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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

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scRNA-seq from abdominal and gluteofemoral subcutaneous adipose tissue derived stem cells (ADSC)

Project description:scRNA-seq from abdominal and gluteofemoral subcutaneous adipose tissue derived stem cells (ADSC)

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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

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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.

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Identification of HOTAIR target genes using RNA-seq after overexpression (OE) and downregulation (si) of HOTAIR in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

Project description:Identification of HOTAIR target genes using RNA-seq after overexpression (OE) and downregulation (si) of HOTAIR in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue

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