GEO series

Effect of HDAC1 deficiency on in vitro Th2 and pathogenic Th2 differentiated murine CD4+ T cells

GSE235803 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/01/23 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × WT Th2 # vs 3 × KO Th2 # vs 3 × pathogenic WT Th2 # vs 3 × pathogenic KO Th2 #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: Single-cell and chromatin accessibility profiling reveals regulatory programs of pathogenic Th2 cells in allergic asthmaNature communications · 2025

Summary (written by the submitters)

The differentiation of naïve CD4+ T cells into distinct effector T helper (Th) subsets is controlled by the chromatin state of the cells which in turn is regulated by various epigenetic mechanisms such as reversible lysine acetylation mediated by histone acetyltransferases and histone deacetylases (HDACs). In addition, Th2 cells can aquire pathogenic features, secreting pro-inflammatory factors and high levels of the cytokine IL-5.

Read the full summary ↓

By using HDAC1 deficient naïve CD4+ T cells and establishing a protocol for differentiation of pathogenic Th2 cells, we could establish a critical role for HDAC1 in regulating the differentiation and pathogenicity of in vitro generated pathogenic Th2 cells

Published in

Single-cell and chromatin accessibility profiling reveals regulatory programs of pathogenic Th2 cells in allergic asthma

Khan M, Alteneder M, Reiter W et al. · Nature communications 2025 · PMID 40089475 · doi:10.1038/s41467-025-57590-3

This dataset

Open GSE235803 in finder → Find more mouse 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 GSE235803_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 PRJNA987658 and SRA study SRP445966. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40089475) ↗

Study design

3 × WT Th2 # vs 3 × KO Th2 # vs 3 × pathogenic WT Th2 # vs 3 × pathogenic KO Th2 #

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7509798 WT Th2 #1 WT Th2 #
GSM7509799 WT Th2 #2 WT Th2 #
GSM7509800 WT Th2 #3 WT Th2 #
GSM7509801 KO Th2 #1 KO Th2 #
GSM7509802 KO Th2 #2 KO Th2 #
GSM7509803 KO Th2 #3 KO Th2 #
GSM7509804 pathogenic WT Th2 #1 pathogenic WT Th2 #
GSM7509805 pathogenic WT Th2 #2 pathogenic WT Th2 #
GSM7509806 pathogenic WT Th2 #3 pathogenic WT Th2 #
GSM7509807 pathogenic KO Th2 #1 pathogenic KO Th2 #
GSM7509808 pathogenic KO Th2 #2 pathogenic KO Th2 #
GSM7509809 pathogenic KO Th2 #3 pathogenic KO Th2 #

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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.