Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ATAC-seq of control and Irx3-KO mouse beige ME3 cells on days 0, 1, and 7 of adipogenic differentiation

ABSTRACT: A map of open chromatin in control and Irx3-KO beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation. Cells were differentiated for indicated number of days, pelleted and snap-frozen in liquid nitrogen. After thawing, cells were treated with DNase to remove exogenous DNA released from cells that died prior to freezing. Remaining cells were lysed in ATAC-seq lysis buffer from the ATAC-seq. Crude nuclear extracts was isolated by centrifugation and resuspended in Tagmentation buffer. Nuclear integrety was verified under microscope, and 50,000 nuclei were transferred for tagmentation. Tagmentation and indexing was performed according to the instructions of the ATAC-seq Kit (Active Motif Catalog No. 53150). Library QC was performed on a Bioanalyzer, and the library was sequenced on a HiSeq4000 Illumina platform using 75 bp paired end sequencing. Reads were filtered to remove low quality mappings, duplicates and mitochondrial mappings. Peaks were called by Macs2 and ENCODE blacklisted regions were excluded. Differentially open chromatin was identified by featurecounts and DESeq2.

INSTRUMENT(S): NA, Illumina HiSeq 4000, ATAC-seq kit (Catalog No. 53150, Active Motif)

ORGANISM(S): Mus musculus

SUBMITTER: Jan-Inge Bjune

PROVIDER: E-MTAB-13525 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ATAC-seq of control and Irx3-KO mouse beige ME3 cells on days 0, 1, and 7 of adipogenic differentiation

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