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Nfkb1 removal from proximal tubule cells improves renal tubular outcomes following ischemia reperfusion injury

GSE294923 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2025/06/15 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
14 samples: 3 × Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC, vs 3 × Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX, vs 2 × Multiome, Nfkb1c/c, ATAC, vs 2 × Multiome, Nfkb1c/c, GEX,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.
Paper
Nfkb1 Removal from Proximal Tubule Cells Improves Renal Tubular Outcomes Following Ischemia Reperfusion InjuryKidney360 · 2025
Summary (written by the submitters)
Chronic kidney disease (CKD) is a significant global health burden. Acute kidney injury (AKI) is a risk factor for progression to CKD. Recent studies have linked a failure in proximal tubule repair as a potential contributing factor to CKD in mouse and human studies. Failed repair proximal tubule cells (FR-PTCs), initially present at the site of maximal sensitivity to ischemia reperfusion injury and spreading to more cortical regions over time, adopt a senescence-associated secretory phenotype (SASP) linked to activation of the NF-kB pathway.
Read the full summary ↓
Several transcriptional regulatory factors mediate NF-kB pathway action. Of these, Nfkb1 is prominent within FR-PTCs and chromatin studies predict Nfkb1 interactions with pathology-associated gene targets. To examine the role of NF-kB in nephron injury outcomes, we removed Nfkb1 activity within the nephron lineage of the mouse kidney and examined the kidney’s response to bilateral ischemia reperfusion injury (Bi-IRI).
Published in
Nfkb1 Removal from Proximal Tubule Cells Improves Renal Tubular Outcomes Following Ischemia Reperfusion Injury
Cheng SY, Koppitch K, Guo J et al. · Kidney360 2025 · PMID 40465395 · doi:10.34067/KID.0000000868
This dataset
Open GSE294923 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 GSE294923_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 PRJNA1252043 and SRA study SRP579460. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40465395) ↗
Study design
3 × Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC, vs 3 × Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX, vs 2 × Multiome, Nfkb1c/c, ATAC, vs 2 × Multiome, Nfkb1c/c, GEX,

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 10 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
Datasets on a similar topic

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