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Series GSE147497 Query DataSets for GSE147497
Status Public on Dec 08, 2020
Title RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary During cellular differentiation, chromosome conformation is intricately remodelled to support the lineage-specific transcriptional programs required for initiating and maintaining lineage identity. When these changes occur in relation to cell cycle, division and time is unclear although it has been proposed they would occur during DNA synthesis 5 or after mitosis. Here we elucidate the chromosome conformational changes in B lymphocytes as they differentiate and massively expand from a naïve, quiescent state into antibody secreting plasma cells. Unexpectedly, we find dramatic gene-regulatory chromosome reorganization in late G1 phase prior to the first division, and that this configuration is remarkably stable as the cells massively 10 and rapidly clonally expansion. A second wave of conformational change occurs as cells terminally differentiate into plasma cells, coincident with increased time in G1 phase. In this study we stimulated naive B cells with LPS and harvested activated B cells or plasmablasts at different time points after stimulation. RNA-seq was used to profile gene expression and in situ Hi-C was used to profile DNA-DNA interactions at each time point.
Overall design Naive resting B-cells were purified from the bone marrow of C57BL/6 mice using flow cytometry sorting. Naive B cells were activated with LPS and harvested 3 hours, 10 hours or 33 hours after the LPS treatment. Expanded activated B cells (CD22+ CD138-) and plasmablasts (CD22- CD138+) were also harvested on day 4 post-stimulation. Two biological replicates from different mice were prepared of each cell population.
Contributor(s) Coughlan HD, Smyth GK
Citation(s) 33637722
Submission date Mar 24, 2020
Last update date Mar 02, 2021
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (20)
GSM4431512 B cell activation 3 hours 1
GSM4431513 B cell activation 3 hours 2
GSM4431514 B cell activation 10 hours 1
This SuperSeries is composed of the following SubSeries:
GSE147467 In situ HiC of primary mouse B cell progenitor populations after activation with LPS
GSE147496 RNA-seq of primary mouse B cell progenitor populations after activation with LPS
BioProject PRJNA614984

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Supplementary file Size Download File type/resource
GSE147497_RAW.tar 1.4 Gb (http)(custom) TAR (of MTX, TSV)
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