Genomics

Dataset Information

142

ATAC-seq analysis of chromatin accessibility in Mbd3-null and control lymphoid progenitor cells


ABSTRACT: To determine the role of Mbd3/NuRD in lymphopoiesis, chromatin accessbility was analysed in purified populations of Mbd3-deleted and control lymphoid progenitor cells using the assay for transposase-accessible chromatin using sequencing (ATAC-seq). Overall design: Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow and thymus by flow cytometry, including all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs), pro-B cells and DN3b thymocytes. ATAC-seq was performed as previously described (Buenrostro et al (2013) Nat. Methods 10:1213) on two or three biologically independent samples of 500 cells. Chromatin accessibility scores were determined based on the density of reads across the genome.

INSTRUMENT(S): Illumina HiSeq 2500 (Mus musculus)

SUBMITTER: Stephen John Loughran  

PROVIDER: GSE101729 | GEO | 2017-07-22

SECONDARY ACCESSION(S): PRJNA395309

REPOSITORIES: GEO

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Publications

Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program.

Loughran Stephen J SJ   Comoglio Federico F   Hamey Fiona K FK   Giustacchini Alice A   Errami Youssef Y   Earp Eleanor E   Göttgens Berthold B   Jacobsen Sten Eirik W SEW   Mead Adam J AJ   Hendrich Brian B   Green Anthony R AR  

The Journal of experimental medicine 20170912 10


Differentiation of lineage-committed cells from multipotent progenitors requires the establishment of accessible chromatin at lineage-specific transcriptional enhancers and promoters, which is mediated by pioneer transcription factors that recruit activating chromatin remodeling complexes. Here we show that the Mbd3/nucleosome remodeling and deacetylation (NuRD) chromatin remodeling complex opposes this transcriptional pioneering during B cell programming of multipotent lymphoid progenitors by r  ...[more]

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