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| Status |
Public on Oct 09, 2012 |
| Title |
Global changes in the nuclear positioning of chromatin domains and genomic interactions that orchestrate B cell fate |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The genome is folded into domains that are located in either transcriptionally inert or permissive compartments. Here we used genome-wide strategies to characterize domains during B cell development. Structured Interaction Matrix Analysis revealed that CTCF occupancy was primarily associated with intra-domain interactions, whereas p300, E2A, Pax5 and PU.1 were involved with intra- and inter-domain interactions that are developmentally regulated. We identified a spectrum of genes that switched nuclear location during early B cell development. In progenitors the transcriptionally inactive Ebf1 locus was sequestered at the nuclear lamina, thereby preserving multipotency, however upon development into the pro-B cell stage Ebf1 and other genes switched compartments to establish de novo intra- and inter-domain interactions that were associated with B lineage specific transcription signatures.
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| Overall design |
Performed Hi-C, GRO-seq, and ChIP-seq to pinpoint the underlying molecular mechanisms that link transcriptional regulation to genomic structure and architecture in lymphocyte development
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| Contributor(s) |
Lin YC, Benner C, Mansson R, Heinz S, Miyazaki K, Miyazaki M, Chandra V, Bossen C, Glass CK, Murre C |
| Citation(s) |
23064439 |
| Submission date |
Aug 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Benner |
| E-mail(s) |
cbenner@ucsd.edu
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| Organization name |
University of California, San Diego (UCSD)
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| Department |
Medicine
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| Street address |
9500 Gilman Dr. MC 0640
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0640 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (19)
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| GSM987803 |
pre-pro-B, H3K36me3 ChIP seq |
| GSM987804 |
pro-B, H3K4me2 ChIP seq |
| GSM987805 |
pro-B, CTCF ChIP seq |
| GSM987806 |
pro-B, Rad21 ChIP seq |
| GSM987807 |
pro-B, H3K36me3 ChIP seq |
| GSM987808 |
pro-B, p300 ChIP seq |
| GSM987809 |
pro-B, H3K27me3 ChIP seq |
| GSM987810 |
pro-B, c-Myc ChIP seq |
| GSM987811 |
pre-pro-B, Input |
| GSM987812 |
pro-B, Input FA |
| GSM987813 |
pro-B, Input EGS |
| GSM987814 |
pre-pro-B, GRO seq |
| GSM987815 |
pro-B, GRO seq |
| GSM987816 |
pre-proB, Hi-C EGS |
| GSM987817 |
pro-B, Hi-C FA |
| GSM987818 |
pro-B, Hi-C EGS |
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| Relations |
| SRA |
SRP014892 |
| BioProject |
PRJNA173552 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40173_RAW.tar |
1.8 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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