GEO series

p52:ETS1: a transcriptional complex essential for germinal center formation [ChIP-seq]

GSE300334 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2025/07/26 Platform GPL34281

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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: Homo sapiens (human)
Samples: 15 samples: 14 distinct titles, 1 of them repeatedGroups 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: The transcription complex p52-ETS1 is essential for germinal center formationNature immunology · 2025

Summary (written by the submitters)

It is well-established that the five transcription factors of the NFκB family form homo/hetero dimers amongst themselves to regulate gene expression by binding DNA. Our study challenges this paradigm by showing that p52 activates transcription without directly binding DNA but as part of a hetero-tetrameric partnership with ETS1, a transcription factor outside the NFκB family.

Read the full summary ↓

By generating a knock-in mouse model (p52ki/ki) with three mutated residues on p52 required for its interactions with ETS1 but not with RelB, we demonstrate that the p52:ETS1 complex is the hitherto undiscovered regulator of transcription factors, OCT1 and OBF1, known to be critical for the germinal centre (GC) program. Consequently B cell-intrinsic expression of p52:ETS1 complex is indispensable for splenic GC B cell formation and T cell-dependent antibody responses. Functionally, loss of p52:ETS1 interaction led to diminished antigen-specific IgE thereby protecting mice from allergic responses. Collectively, our expand our current knowledge of NFkB signalling and provide new therapeutic targets for the treatment of allergic diseases.

Published in

The transcription complex p52-ETS1 is essential for germinal center formation

Morgan D, Zhang B, Fidan K et al. · Nature immunology 2025 · PMID 40715659 · doi:10.1038/s41590-025-02236-1

This dataset

Open GSE300334 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE300334_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 PRJNA1280107 and SRA study SRP593514. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40715659) ↗

Study design

14 distinct titles, 1 of them repeated

Ly3_ETS1 ×2

How we read this: Read from 15 sample titles: 14 distinct titles with little repetition. 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

GSM9058596 Ly3_ETS1 rep1
GSM9058597 Ly3_H3K27 rep1
GSM9058598 Ly3_IgG rep1
GSM9058599 Ly3_Input rep1
GSM9058600 Ly3_P52 rep1
GSM9058601 Ly3_RelB rep1
GSM9058602 Ly3_ETS1 rep2
GSM9058603 Ly3_H3K4Me3_IP rep1
GSM9058604 Ly3_H3K27Ac_IP rep2
GSM9058605 Ly3_H3K27Me_IP rep1
GSM9058606 Ly3_IgG_IP rep2
GSM9058607 Ly3_Input_DNA rep2
GSM9058608 Ly3_p52 rep2
GSM9058609 Ly3_PolII_IP rep1
GSM9058610 Ly3_Relb rep2

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