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Lysine-specific demethylase 1 target genes in brown adipocytes

ABSTRACT: Lysine-specific demethylase 1 target genes in brown adipocytes

OTHER RELATED OMICS DATASETS IN: GSE81557PXD004745

PROVIDER: PRJNA321978 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3539320_1.fastq.gz	Fastqsanger.gz
	SRR3539320_2.fastq.gz	Fastqsanger.gz
	SRR3539330_1.fastq.gz	Fastqsanger.gz
	SRR3539330_2.fastq.gz	Fastqsanger.gz
	SRR3539321_1.fastq.gz	Fastqsanger.gz

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Lysine-specific demethylase 1 targets in brown adipocytes [ChIP-seq]

Project description:The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes. Purpose: The aim of this study is to identify the Lsd1 genome binding profile in brown adipocytes. Methods: Libraries were prepared from Lsd1-immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2 (Langmead et al., 2009). Data were further analysed using the peak finding algorithm MACS 1.41 (Zhang et al., 2008) using input as control. All peaks with FDR greater than 0.3 % were excluded from further analysis. The uniquely mapped reads were used to generate the genome-wide intensity profiles, which were visualized using the IGV genome browser (Thorvaldsdottir et al., 2012). Results: HOMER (Heinz et al., 2010) was used to annotate peaks, to calculate overlaps between different peak files, and for motif searches. The genomic features (promoter, exon, intron, 3’ UTR, and intergenic regions) were defined and calculated using Refseq and HOMER. Genes annotated by HOMER were further used for a pathway analysis in WebGestalt (Heinz et al., 2010; Wang et al., 2013). ChIP-seq analysis revealed that Lsd1 was located at the promoter of 11735 genes.

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Project description:We have identified a population of adipocytes in fat tissue that arise from bone marrow-derived progenitor cells. We used microarrays to compare the global gene expression patterns of the bone marrow progenitor-derived adipocytes as well as conventional white and brown adipocytes to evaluate the relationship between these adipocyte subpopulations. Gonadal fat tissue (for white adipocytes) and intrascapular fat tissue (for brown adipocytes) was digested with collagenase and adipocytes were recovered by centrifugation/flotation. Bone marrow derived adipocytes were isolated from the adipocyte fraction of gonadal fat tissue from mice receiving bone marrow tranplants from donors expressing either green fluorescent protein (GFP) or beta-galactosidase (LacZ) by flow cytometry.

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Lysine-specific demethylase 1 target genes in brown adipocytes

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-10-27 | GSE81557 | GEO

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