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Translational control of germinal center response and plasma cell differentiation by Dhx29

GSE317659 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/05/06 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × B cells in iGCB culture,WT,RNA, vs 3 × B cells in iGCB culture,WT,Riboseq, vs 3 × B cells in iGCB culture,Dhx29 KO,RNA, vs 3 × B cells in iGCB culture,Dhx29 KO,Riboseq,Groups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
The roles of translational control in the immune system are poorly understood. In this study, we performed CRISPR/Cas9-mediated functional screening of RNA helicases in an in vitro system of plasma cell differentiation and identified Dhx29 as a critical regulator of this process. Mice with B cell-specific deletion of Dhx29 exhibited severely impaired germinal center B cell formation, plasma cell differentiation, and antibody production.
Read the full summary ↓
Mechanistically, Dhx29 promotes translation of Tcf3 and Tle3 via binding to 5’UTRs of those mRNAs. In the absence of Dhx29, B cells exhibit normal proliferation but fail to undergo class switch to IgG1 and differentiation into plasma cells, resulting in impaired antibody production. Ectopic expression of TCF3 and Tle3 largely restores plasma cell differentiation of Dhx29-deficient B cells. Therefore, this study unravels critical roles of Dhx29 in promoting translation of key transcription factors controlling germinal center response and plasma cell differentiation, discovers a previously unrecognized role of Tle3 in plasma cell differentiation, and illustrates the functional importance of translation control in the immune system.
This dataset
Open GSE317659 in finder → Find more mouse datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE317659_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1335761 and SRA study SRP629243. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × B cells in iGCB culture,WT,RNA, vs 3 × B cells in iGCB culture,WT,Riboseq, vs 3 × B cells in iGCB culture,Dhx29 KO,RNA, vs 3 × B cells in iGCB culture,Dhx29 KO,Riboseq,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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