GEO series

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

GSE317658 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/05/06 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 6 conditions, mostly in triplicateGroups 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 GSE317658 in finder → Find more mouse RNA-seq 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 GSE317658_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 PRJNA975663 and SRA study SRP439228. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

WT ipc0h ×3 WT ipc12h ×3 WT ipc24h ×3 KO ipc0h ×3 KO ipc12h ×3 KO ipc24h ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM9476103 WT ipc0h biological replicate 1 WT ipc0h
GSM9476104 WT ipc0h biological replicate 2 WT ipc0h
GSM9476105 WT ipc0h biological replicate 3 WT ipc0h
GSM9476106 WT ipc12h biological replicate 1 WT ipc12h
GSM9476107 WT ipc12h biological replicate 2 WT ipc12h
GSM9476108 WT ipc12h biological replicate 3 WT ipc12h
GSM9476109 WT ipc24h biological replicate 1 WT ipc24h
GSM9476110 WT ipc24h biological replicate 2 WT ipc24h
GSM9476111 WT ipc24h biological replicate 3 WT ipc24h
GSM9476112 KO ipc0h biological replicate 1 KO ipc0h
GSM9476113 KO ipc0h biological replicate 2 KO ipc0h
GSM9476114 KO ipc0h biological replicate 3 KO ipc0h
GSM9476115 KO ipc12h biological replicate 1 KO ipc12h
GSM9476116 KO ipc12h biological replicate 2 KO ipc12h
GSM9476117 KO ipc12h biological replicate 3 KO ipc12h
GSM9476118 KO ipc24h biological replicate 1 KO ipc24h
GSM9476119 KO ipc24h biological replicate 2 KO ipc24h
GSM9476120 KO ipc24h biological replicate 3 KO ipc24h

Datasets on a similar topic

GSE317659 Translational control of germinal center response and plasma cell differentiation by Dhx29 12 samples shares dhx29, translational, germinal, control, center, plasma
GSE275123 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) III 21 samples shares germinal, center, plasma
GSE275124 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 4 and Figure 5) 20 samples shares germinal, center, plasma
GSE275121 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) 1 13 samples shares germinal, center, plasma
GSE275122 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) II 12 samples shares germinal, center, plasma
GSE270908 Comparative transcriptomic analysis of pre-plasma germinal center B cells in wild type and Kdm6b B knockout models 12 samples shares germinal, center, plasma
GSE286974 RNA-Seq analysis of germinal center B cells from Tfr-depleted and control kidney transplant recipients 10 samples shares germinal, control, center
GSE312596 RNA-seq analysis of germinal center-derived splenic IgG1 or IgM plasma cells 10 samples shares germinal, center, plasma

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.