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NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid

GSE295743 Homo sapiens (human) RNA-seq (gene expression) 78 samples Submitted 2025/10/31 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 78 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
78 samples: 20 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.
Paper
NF-κB-dependent GR cistrome redistribution recruits GR to inflammatory genes but correlates with lesser glucocorticoid-mediated repressioniScience · 2025
Summary (written by the submitters)
While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization.
Read the full summary ↓
Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR_x0002_RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide_x0002_upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid_x0002_induced repression.
Published in
NF-κB-dependent GR cistrome redistribution recruits GR to inflammatory genes but correlates with lesser glucocorticoid-mediated repression
Mostafa MM, Necker-Brown A, Gao A et al. · iScience 2025 · PMID 41488369 · doi:10.1016/j.isci.2025.114206
This dataset
Open GSE295743 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 GSE295743_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1256284 and SRA study SRP581871. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41488369) ↗
Study design
20 conditions, mostly with about 4 replicates each
A549 cells, NS, 1h, ×4 A549 cells, NS, 2h, ×4 A549 cells, NS, 12h, ×4 A549 cells, NS, 24h, ×4 A549 cells, IL1B, 1h, ×4 A549 cells, IL1B, 2h, ×4 A549 cells, IL1B, 6h, ×4 A549 cells, IL1B, 12h, ×4 +12 more

Supports a between-group comparison across 78 samples.

How we read this: 20 replicated groups read from 78 sample titles; they account for 78 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

+ 38 more — browse all 78 samples with per-sample file links →

Datasets on a similar topic

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