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Series GSE43428 Query DataSets for GSE43428
Status Public on Dec 31, 2018
Title ChIP-seq analysis of hematopoetic progenitors
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Bivalent chromatin refers to the simultaneous occurrence of transcription activation (H3K4me3)- and repression (H3K27me3)-associated histone modifications at gene promoters. This mark was first identified in ES cells and proposed to maintain genes in a poised state for future resolution to fully-active (H3K4me3-only) or fully-repressed (H3K27me3-only) states. In this report we rigorously test the poising hypothesis using a well-established developmental paradigm of hematopoietic stem cell differentiation to T lymphoid lineage committed cells. We show that bivalent chromatin is generated and resolved at specific stages of hematopoiesis. The epigenetic states from which it is generated and the states to which it is resolved vary with developmental stage, suggesting that bivalency serves different functions at each stage. Moreover, singly-marked genes do not transition to the opposing univalent state via a bivalent intermediate.
 
Overall design Fresh ex vivo cells were used from mice to study dynamics of bivalent chromatin during hematopoietic differentiation to the T lymphoid lineage. Hematopoietic stem cells (HSC), lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP) were purified from bone marrow of C57BL/6J mice; early thymic precursors (ETP), double negative 2 (DN2) and double negative 3 (DN3) cells were purified from C57BL6 thymus. We analyzed at least two independent cell preparations for each subset, obtained from approximately 25 mice per preparation. Purified cells were subjected to micro-chromatin immunoprecipitation (micro-ChIP) using antibodies directed against H3K4me3 and H3K27me3. Immunoprecipitated DNA was sequenced using standard Illumina platform
 
Contributor(s) Ghosh A, De S, Bell J, Weber BN, Wood WH, Becker KG, Sen JM, Bhandoola A, Sen R
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Submission date Jan 10, 2013
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (19)
GSM1062343 Hematopoietic stem cells (HSC)-K4me3 micro-ChIP
GSM1062344 Lymphoid-primed multipotent progenitors (LMPP)-K4me3 micro-ChIP
GSM1062345 Common lymphoid progenitors (CLP)-K4me3 micro-ChIP
This SubSeries is part of SuperSeries:
GSE43461 Gene expression and ChIP-seq analysis of hematopoetic progenitors
Relations
BioProject PRJNA186450
SRA SRP017923

Download family Format
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MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE43428_INPUT.bed.gz 137.7 Mb (ftp)(http) BED
GSE43428_RAW.tar 1.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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