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NF-κB transcriptionally perturbs p53 dynamics hampering DNA2repair.

GSE320287 Homo sapiens (human) Single-cell RNA-seq 56 samples Submitted 2026/02/28 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 56 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
56 samples: 14 conditions, mostly with about 4 replicates eachGroups 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)
Cells integrate multiple, often concurrent signals through intertwined genetic circuits whose dynamics14shape transcriptional programs and cell fate decisions. Among these, the tumor suppressor p53 and15the inflammatory transcription factor NF-κB are central regulators of stress responses and cancer16biology, yet their dynamic crosstalk under co-activation remains poorly characterized.
Read the full summary ↓
Here, we combine17genetic engineering, single-cell live imaging, transcriptome analysis and mathematical modeling to18dissect the dynamic interplay between p53 and NF-κB. We find that co-activation of NF-κB by19inflammatory cytokines significantly enhances p53 accumulation and modulates the expression of p5320target genes, while leaving NF-κB dynamics largely unaltered. Mechanistically, we show that NF-κB21activation increasesTP53transcription, and mathematical modeling demonstrates that this22transcriptional upregulation is sufficient to account for the observed perturbation of p53 dynamics.23Functionally, NF-κB co-activation rewires p53-dependent transcriptional programs and impairs p53-24mediated DNA repair following genotoxic stress, an effect that is absent in NF-κB-deficient cells. Our25results uncover a transcriptionally mediated amplification of p53 signaling by NF-κB that results in26functional antagonism, highlighting how the dynamic crosstalk between stress-responsive transcription27factors shapes cellular outcomes in complex signaling environments.
This dataset
Open GSE320287 in finder → Find more human 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 GSE320287_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1427268 and SRA study SRP678869. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly with about 4 replicates each
MCF-7 NFκB-, 10Gy IR, 16h, ×4 MCF-7 NFκB-, 10Gy IR + TNF-ɑ, 16h, ×4 MCF-7 NFκB-, TNF-ɑ, 16h, ×4 MCF-7 NFκB-, 10Gy IR, 4h, ×4 MCF-7 NFκB-, 10Gy IR + TNF-ɑ, 4h, ×4 MCF-7 NFκB-, TNF-ɑ, 4h, ×4 MCF-7 NFκB-, Untreated, 0h, ×4 MCF-7 NFκB+, 10Gy IR, 16h, ×4 +6 more

Supports a between-group comparison across 56 samples.

How we read this: 14 replicated groups read from 56 sample titles; they account for 56 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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