← BioTransfer GEO Dataset Finder
GEO series

Optimal CXCR5 Expression during Tfh Maturation Involves Bhlhe40-Pou2af1 Axis

GSE247137 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 44 samples Submitted 2025/09/21 Platform GPL21493
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 44 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
44 samples: 12 conditions, mostly in duplicateGroups 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.
Paper
Optimal CXCR5 expression during Tfh maturation involves the Bhlhe40-Pou2af1 axisCell reports · 2025
Summary (written by the submitters)
Bcl6/Blimp1 are well-known for Tfh cell determination, but they are dispensable in regulating the expression of CXCR5, which is critical for Tfh migration into germinal center (GC). In this study, we uncovered a novel pair of transcription factors, Bhlhe40/Pou2af1, that regulate Tfh maturation through regulation of CXCR5. Pou2af1 promotes Tfh generation by upregulating CXCR5, while Bhlhe40 represses Tfh differentiation by inhibiting Pou2af1.
Read the full summary ↓
Pou2af1 was further verified being essential for GC Tfh cell localization, whereas Bhlhe40 inhibits pre-Tfh cells import into GC. Such migration behavior change can be explained by an alteration in the MFI of CXCR5. RNA-Seq analysis confirmed Bhlhe40 inhibiting Pou2af1 and the requirement of Pou2af1 upregulation in optimal CXCR5 expression. Thus, our study filled a long-standing gap in the regulation of optimal CXCR5 expression by revealing a key transcriptional regulatory circuit involving Bhlhe40/Pou2af1, which operates downstream of the Bcl6/Blimp-1 circuit that determines Tfh cell fate. RNA-Seq analysis of gene expression in T cell subsets (Th1, Th2, Th17 and iTreg), which are primed and differentiated in vitro from WT mice or Bhlhe40f/f-CD4Cre mice. RNA-Seq analysis of gene expression in antigen-specific Tfh cells and non-Tfh cells, which were sorted from the indicated bone marrow chimera mice (WT, Pou2af1-/-, Bhlhe40-/-). ChIP-Seq analysis of binding sites by Bhlhe40 in Th1, Th2, Th17 and iTreg. ChIP-Seq analysis of binding sites by Pou2af1 in splenic B cells.
Published in
Optimal CXCR5 expression during Tfh maturation involves the Bhlhe40-Pou2af1 axis
Zhu X, Chen X, Cao Y et al. · Cell reports 2025 · PMID 41134666 · doi:10.1016/j.celrep.2025.116470
This dataset
Open GSE247137 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 GSE247137_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1036269 and SRA study SRP470418. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41134666) ↗
Study design
12 conditions, mostly in duplicate
RNA-seq_Bhlhe40_WT_iTreg ×2 RNA-seq_Bhlhe40_WT_Th1 ×2 RNA-seq_Bhlhe40_WT_Th17 ×2 RNA-seq_Bhlhe40_WT_Th2 ×2 RNA-seq_Bhlhe40_KO_iTreg ×2 RNA-seq_Bhlhe40_KO_Th1 ×2 RNA-seq_Bhlhe40_KO_Th17 ×2 RNA-seq_Bhlhe40_KO_Th2 ×2 +24 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 44 sample titles; they account for 24 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.