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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chromatin state dynamics during blood formation (ATAC-seq)

ABSTRACT: We develop a new ChIpseq method (iChIP) to profile chromatin states of low cell number samples. We use IChIP to profile the chromatin dynamics during hematopoiesis across 16 different cell types which include the principal hematopoietic progenitors Examination of 2 different histone modifications in 2 cell types.

ORGANISM(S): Mus musculus

SUBMITTER: Ido Amit

PROVIDER: E-GEOD-59992 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin state dynamics during blood formation (ATAC-seq)

Project description:We develop a new ChIpseq method (iChIP) to profile chromatin states of low cell number samples. We use IChIP to profile the chromatin dynamics during hematopoiesis across 16 different cell types which include the principal hematopoietic progenitors

2014-08-08 | GSE59992 | GEO

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A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (ATAC-Seq)

Project description:During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes. Here we profiled accessible chromatin of moDC and pDC using ATAC-seq assay, developed by Buenrostro et al. (2013)

2014-12-14 | E-GEOD-62703 | biostudies-arrayexpress

Transcriptional heterogeneity and lineage commitment in myeloid progenitors [ChIP-seq]

Project description:Within the bone marrow, hematopoietic stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with the in vivo potential or gene regulatory mechanisms. Here we comprehensively identify myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups showing unexpected transcriptional priming towards seven differentiation fates, but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting the process is tightly regulated. Histone maps and knockout assays are consistent with the transcriptional states while traditional transplantation experiments are only partially overlapping myeloid transcriptional priming. Our analyses uncover the function of the underlying regulatory mechanisms for several sub groups and establishes a general framework for dissecting hematopoiesis. Bone marrow common myeloid progenitor H3K4me2 profiles were generated by deep sequencing of iChIP libraries on an Illumina NextSeq

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Chromatin state dynamics during blood formation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Mapping the Chromatin State Dynamics in Myoblasts

Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the Pitx2-null mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile. Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimb tissues from Pitx2 null mice using the Illumina HiSeq 2000

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Enhancer Mapping in Chronic Lymphocytic Leukemia

Project description:<p>In this study we profile the epigenomic enhancer landscapes of CLL B cells (CD19+/CD5+) harvested from peripheral blood of patients from our Center. Included are results of ChIPseq profiling using chromatin immunoprecipitation of the enhancer histone mark H3K27ac (acetylated lysine 27 on histone H3), and open chromatin profiles using ATAC-seq (assay for transposase accessible chromatin). These profiles are used to define the global enhancer and super enhancer landscape of CLL B cells, and to derive active transcription factor networks associated with this disease. Also included are H3K27ac ChIP-seq and ATAC-seq datasets for non-CLL B cells obtained from the peripheral blood of normal adult donors.</p>

| phs001704 | dbGaP

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