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Series GSE182463 Query DataSets for GSE182463
Status Public on Jul 06, 2022
Title Biallelic PAX5 mutations cause hypogammaglobulinemia,sensorimotor deficits and autism spectrum disorder
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To investigate the molecular basis for the B cell developmental arrest in Pax5R31Q/– mice, we performed RNA-sequencing (RNA-seq) with ex vivo sorted Pax5+/+ and Pax5R31Q/– pro-B cells. We identified Pax5-activated and Pax5-repressed genes that were no longer properly regulated by the Pax5-R31Q protein in Pax5R31Q/– pro-B cells. Notably, these genes were only a subset of the activated and repressed genes identified by comparing Pax5+/+ and Pax5–/– pro-B cells, which raised the question whether binding of the Pax5-R31Q protein may be selectively lost at the subset of deregulated genes in Pax5R31Q/– pro-B cells. By using a Pax5 paired domain antibody for chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) of short-term cultured Pax5+/+ and Pax5R31Q/– pro-B cells, we identified all associated Pax5 binding sites. Common Pax5 peaks had a similar Pax5-binding density in contrast to the strong binding difference observed at the unique peaks present in Pax5+/+ pro-B cells. To investigate a correlation between the loss of Pax5 binding and gene expression, we focused our analysis on Pax5 peaks in the TSS region of activated genes. We systematically investigated the correlation between loss of Pax5 binding at the TSS and down-regulation of gene expression in Pax5R31Q/– pro-B cells. The ratio of Pax5 binding between Pax5R31Q/– and Pax5+/+ pro-B cells at the TSS of these activated genes was significantly reduced compared to that of expressed non-regulated genes. We next explored whether the Pax5-binding difference at the TSS also correlated with the magnitude of gene expression difference. The loss of Pax5 binding at the TSS also correlated with the degree of expression change in Pax5R31Q/– pro-B cells compared to Pax5+/+ pro-B cells. We conclude therefore that the selective DNA-binding of Pax5-R31Q is responsible for the observed gene expression differences in Pax5R31Q/– pro-B cells.
Overall design 8 RNA-Seq samples, 4 different conditions (A,B,C,D) two replicates each. A (wildtype): Pro-B cells Pax5(+/+) 111735 + 111736; B (R31Q mutant): Pro-B cells pax5(R31Q/-) 111739 + 111740; C (Pax5 knock out): Progenitor cells Pax5(fl/fl) VAV-cre 111726 + 111741; D (Pro-B cells Pax5 het): Pro-B cell Pax5(+/-) 111737 + 111738. 2 ChIP-Seq samples (65448 (wildtype) + 65449 (mutant)).
Contributor(s) Kaiser FM, Grünbacher S, Jaritz M, Busslinger M
Citation(s) 35947077
Submission date Aug 19, 2021
Last update date Aug 25, 2022
Contact name Meinrad Busslinger
Organization name IMP
Lab Busslinger
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code A-1030
Country Austria
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (10)
GSM5529816 111735: RNA-seq Pro-B cell Pax5(+/+)
GSM5529817 111736: RNA-seq Pro-B cell Pax5(+/+)
GSM5529818 111739: RNA-seq Pro-B cell Pax5(R31Q/-)
BioProject PRJNA759253
SRA SRP335064

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE182463_RAW.tar 1024.0 Mb (http)(custom) TAR (of BED, BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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