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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

ABSTRACT: 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

PROVIDER: PRJNA793018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17377100.fastq.gz	Fastqsanger.gz
	SRR17377101.fastq.gz	Fastqsanger.gz
	SRR17377102.fastq.gz	Fastqsanger.gz
	SRR17377103.fastq.gz	Fastqsanger.gz
	SRR17377104.fastq.gz	Fastqsanger.gz

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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:Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to overexpress and downregulate HOTAIR (respectively). RNA-seq was used to study the transcriptome of control and treated cells.

2022-05-31 | GSE192750 | 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: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

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 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

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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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HOTAIR interacts with PRC2 complex regulating the regional preadipocyte transcriptome and human fat distribution

Project description:Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA, HOTAIR (HOX transcript antisense RNA), is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 tri-methylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (oestrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass in 25,200 individuals). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.

2022-07-26 | GSE205350 | GEO

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

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

Abd-B-GFP_vMock_W3L_ChIP-seq

Project description:modENCODE_submission_4961 This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Abd-B-GFP; Developmental Stage: L3; Genotype: w; PBac{y[+]-attP-3B}VK00037; Sex: Unknown; Transgene: Abd-B genomic coding region with stop codon replaced with GFP; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene Abd-B; Strain Abd-B-GFP; Antibody GFP ab290 (target is Green Fluorescent Protein)

2013-08-28 | E-GEOD-50362 | biostudies-arrayexpress

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