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NEMO lysine mutant mice reveal ROS-RelA signaling required for optimal CD40-induced humoral immunity [NEMODK_CUTTAG]

GSE325580 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 60 samples Submitted 2026/06/09 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 60 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
60 samples: 20 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)
Oxidative and genotoxic stresses activate NF-κB signaling through intracellular pathways distinct from those initiated by membrane receptors, but their physiological roles remain incompletely defined. We created the NEMODK mouse model with germline arginine substitutions at NEMO (NF-κB essential modulator) lysines 270 and 302, key sites for post-translational modifications selectively induced by these intracellular stresses to enable NF-κB signaling in vitro.
Read the full summary ↓
NEMODK mice exhibited B cell-intrinsic defects in the generation of germinal center B cells and humoral responses. Mechanistically, NEMODK B cells displayed a CD40-specific NF-κB signaling defect, unrelated to acute canonical and delayed noncanonical NF-κB activity, which was accompanied by the lack of sustained NEMO monoubiquitination downstream of mitochondrial reactive oxygen species generation without relying on nuclear DNA damage. This specifically reduced persistent RelA activity and a failure to mount transcriptomic and epigenetic changes critical for homotypic B cell aggregation, cell proliferation, class switch recombination and antibody secreting cell generation. Thus, CD40 induces a uniquely sustained NEMO modification and persistent RelA transcriptional activity to efficiently generate class-switched antibodies.
This dataset
Open GSE325580 in finder → Find more mouse 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 GSE325580_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 PRJNA1440503 and SRA study SRP685548. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 conditions, mostly in triplicate
NEMODK, Stimulated, 2 days, IgG, ×3 WT, Stimulated, 2 days, IgG, ×3 WT, Unstimulated, 2 days, IgG, ×3 NEMODK, Stimulated, 2 days, RelA, ×3 WT, Stimulated, 2 days, RelA, ×3 WT, Unstimulated, 2 days, RelA, ×3 NEMODK, Stimulated, 2 days, H3K4me3, ×3 WT, Stimulated, 2 days, H3K4me3, ×3 +17 more

Supports a between-group comparison across 55 samples.

How we read this: 20 replicated groups read from 60 sample titles; they account for 55 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

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