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SRX7802225: GSM4339448: BXD2-WT_#2_single_cell_VDJseq(BCR); Mus musculus; RNA-Seq
4 ILLUMINA (Illumina MiSeq) runs: 19.4M spots, 6G bases, 3Gb downloads

Submitted by: NCBI (GEO)
Study: IL-23 promotes a coordinated B-cell germinal center program for class-switch recombination to IgG2b in BXD2 mice
show Abstracthide Abstract
IL-23 promotes autoimmune disease including Th17 CD4 T-cell development and autoantibody (autoAb) production. Here, we show that a deficiency of the p19 component of IL-23 in autoimmune BXD2 (BXD2-p19-/-) mice leads to an imbalance of the follicular T-helper cell program with a shift from Tfh-IL-17 to Tfh-IFN-?. Although the germinal center (GC) size and number of GC B cells remained the same, BXD2-p19-/- mice exhibited a lower class-switch recombination (CSR) program in the GC B cells, leading to a lower serum levels of IgG2b. Single cell transcriptomics analysis revealed that while GC B cell expression of Ifngr1 and Il21r genes exhibited a synchronized expression pattern with plasma cell program genes, Il17ra exhibited a synchronized expression pattern with pre-plasmablast GC program genes. Down-regulation of Ighg2b in BXD2-p19-/- GC B cells was associated with decreased expression of CSR-related base excision repair genes that were otherwise predominantly expressed by Il17ra+ cells compared to Ifngr1+ GC B cells in BXD2 mice. Together, these results suggest that although IL-23 is dispensable for GC formation, it is essential for development of the Tfh-IL17 Tfh subpopulation, which drives CSR-related base excision repair genes during the pre-plasmablast GC stage of development. Overall design: We carried out single cell RNAseq and single-cell V(D)J seq for GC B cells derived from the spleens of BXD2 mice and IL-23-deficient BXD2 (BXD2-p19-/-)mice
Sample: BXD2-WT_#2_single_cell_VDJseq(BCR)
SAMN14207638 • SRS6216269 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina MiSeq
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Single cells and beads containing barcoded DNA oligos were captured into oil droplets by 10xChromium controller using 10xGenomics 5' VDJ reagent kits. Individual cells were lyzed immediately, mRNA were released, and reverse transcription was performed by plyT primers according to 10xGenomics 5' VDJ standard protocol. Single-stranded cDNA was then captured in the each oil droplet by the barcoded DNA oligos carried by the beads. Barcoded single cell cDNA were pooled and preamplified, 5' biased transcriptome libraries and BCR libraries were constructed according to the standard protocol of 10xGenomics 5' VDJ reagent kits.
Experiment attributes:
GEO Accession: GSM4339448
Links:
Runs: 4 runs, 19.4M spots, 6G bases, 3Gb
Run# of Spots# of BasesSizePublished
SRR111816305,033,0801.6G792.4Mb2020-05-15
SRR111816314,933,5871.5G769.9Mb2020-05-15
SRR111816324,605,0801.4G729.9Mb2020-05-15
SRR111816334,779,6081.5G753.7Mb2020-05-15

ID:
10205241

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