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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
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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.
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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
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Contributor(s) |
Ghosh A, De S, Bell J, Weber BN, Wood WH, Becker KG, Sen JM, Bhandoola A, Sen R |
Citation missing |
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Submission date |
Jan 10, 2013 |
Last update date |
Jun 22, 2020 |
Contact name |
Supriyo De |
Organization name |
NIA-IRP, NIH
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Department |
Laboratory of Genetics and Genomics
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Lab |
Computational Biology & Genomics Core
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Street address |
251 Bayview Blvd
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City |
Baltimore |
State/province |
Maryland |
ZIP/Postal code |
21224 |
Country |
USA |
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Platforms (1) |
GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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Samples (19)
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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 |
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This SubSeries is part of SuperSeries: |
GSE43461 |
Gene expression and ChIP-seq analysis of hematopoetic progenitors |
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Relations |
BioProject |
PRJNA186450 |
SRA |
SRP017923 |