GEO series

Bronchial epithelial cells accessibility upon flagellin stimulation (ATAC-Seq)

GSE227259 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2025/08/10 Platform GPL18573

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: 15 samples, each with a distinct title — no replicated groupsGroups 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 epigenomic landscape of bronchial epithelial cells reveals the establishment of trained immunityGenes and immunity · 2025

Summary (written by the submitters)

Innate immune memory is a new concept describing ability of innate myeloid and lymphoid cells to gain memory characteristics after transient stimulation, resulting in an nonspecific modified response upon secondary challenge. In recent work, we demonstrated that bronchial epithelial cells, non immune cells, that are the first immune cells of the lower respiratory tract to encounter pathogens were capable of innate immune memory after pre-exposure to Pseudomonas aeruginosa flagellin.

Read the full summary ↓

In the present study we identified chromatin modifications induced by flagellin pre-exposure that sustain reprogramming of transcriptional patterns. We researched chromatin structure modifications responsible for the modulation of gene expression and thus of innate memory induced by the exposure of cells to flagellin.

Published in

The epigenomic landscape of bronchial epithelial cells reveals the establishment of trained immunity

Bigot J, Legendre R, Hamroune J et al. · Genes and immunity 2025 · PMID 40993329 · doi:10.1038/s41435-025-00357-z

This dataset

Open GSE227259 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 GSE227259_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 PRJNA944250 and SRA study SRP427115. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40993329) ↗

Study design

15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 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

GSM7093940 D0 rep 1 control
GSM7093941 D0 rep 2 control
GSM7093942 D0 rep 3 control
GSM7093943 D2 rep 1 with flagellin
GSM7093944 D2 rep 1 control
GSM7093945 D2 rep 2 with flagellin
GSM7093946 D2 rep 2 control
GSM7093947 D2 rep 3 with flagellin
GSM7093948 D2 rep 3 control
GSM7093949 D6 rep 1 with flagellin
GSM7093950 D6 rep1 control
GSM7093951 D6 rep 2 with flagellin
GSM7093952 D6 rep 2 control
GSM7093953 D6 rep 3 with flagellin
GSM7093954 D6 rep3 control

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.