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| Status |
Public on Sep 21, 2018 |
| Title |
Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16 [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Multipotent progenitors confirm their T-lineage identity at the DN2a to DN2b pro-T cell transition, when expression of the essential transcription factor Bcl11b begins. This study defines the molecular basis of direct and indirect actions of Bcl11b in acquisition of T cell identity. In vivo and in vitro stage-specific deletions identify functional regulation targets genome-wide for mechanistic analysis. Bcl11b can associate with multiple co-factors and its direct action is needed to recruit these to selective target sites. Sites of Bcl11b-dependent cofactor recruitment are enriched at functionally regulated targets, and deletion of individual cofactors can relieve repression of many Bcl11b-repressed genes. In parallel, Bcl11b indirectly regulates a subset of its target genes by a gene network circuit via Id2 and Zbtb16, which are directly repressed by Bcl11b and control distinct alternative programs.
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| Overall design |
RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen). Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.
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| Contributor(s) |
Hosokawa H, Romero-Wolf M, Yui MA, Ungerbäck J, Matsumoto M, Nakayama KI, Tanaka T, Rothenberg EV |
| Citation(s) |
30374131 |
| |
| Submission date |
Feb 20, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Maile Romero-Wolf |
| E-mail(s) |
mwerner2@caltech.edu
|
| Phone |
6263954915
|
| Organization name |
California Institute of Technology
|
| Department |
BBE
|
| Lab |
Rothenberg
|
| Street address |
1200 E California Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91025 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (34)
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| This SubSeries is part of SuperSeries: |
| GSE115744 |
Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16 |
|
| Relations |
| BioProject |
PRJNA434730 |
| SRA |
SRP133169 |
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