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Identification of Transcription Factor Binding Sites using ATAC-seq

ABSTRACT: Dendritic cells (DC) are professional antigen presenting cells that comprise different subsets: classical DC type 1 and 2 (cDC1 and cDC2, respectively) and plasmacytoid DC (pDC). In this study cDC1 or pDC were obtained in a two-step in vitro culture system according to Felker et al., J. Immunol. 185, 5326-5335, 2010. Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differentiate into DC with Flt3 ligand. cDC1 are CD11c+ CD11b+ XCR1+ and pDC are CD11c+ CD11b- B220+ and thus cDC1 and pDC were obtained by FACS sorting and subjected to Omin-ATAC-seq analysis. As an example of practical application of HINT-ATAC, we performed Omin-ATAC-seq experiments of cDC and pDC cell populations and used HINT-ATAC to detect footprints within ATAC-seq peaks of each of these two cells. Next, we estimated changes in binding activity for all factors with a motif in JASPAR. Cell-specific TF activity is measured by the depth of footprints and number of reads flanking regions. Two known cDC factors, BATF3 and HES1, are detected. In summary, we demonstrated that HINT-ATAC is capable of identifying relevant factors for dendritic cell specification.

ORGANISM(S): Mus musculus

PROVIDER: GSE118221 | GEO | 2019/01/15

REPOSITORIES: GEO

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A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation

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2015-08-01 | E-GEOD-68399 | biostudies-arrayexpress

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Project description:Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CMP, cDC and pDC. Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC

2016-08-03 | E-GEOD-73143 | biostudies-arrayexpress

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2016-08-03 | GSE73143 | GEO

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