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Series GSE40173 Query DataSets for GSE40173
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
Genome binding/occupancy profiling by high throughput sequencing
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.
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
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
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (19)
GSM987800 pre-pro-B, H3K4me2 ChIP seq
GSM987801 pre-pro-B, CTCF ChIP seq
GSM987802 pre-pro-B, Rad21 ChIP seq
SRA SRP014892
BioProject PRJNA173552

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Supplementary file Size Download File type/resource
GSE40173_RAW.tar 1.8 Gb (http)(custom) TAR (of BED, BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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