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Programmable mRNA Therapeutics for Controlled Epigenomic Modulation of Single and Multiplexed Gene Expression in Diverse Diseases (human data)

GSE290866 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2025/03/04 Platform GPL30173Platform GPL15520Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
20 samples: 9 conditions, mostly in duplicateGroups 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
Programmable mRNA therapeutics for controlled epigenomic modulation of single and multiplexed gene expression in diverse diseasesNature communications · 2025
Summary (written by the submitters)
Pathogenic gene dysregulation can be attributed to chromatin state change that pre-transcriptionally regulates expression. Recent breakthroughs elucidating the rules governing this DNA control layer, an epigenetic code, unlock a new modality in precision medicine to target gene dysregulation across myriad diseases. Leveraging these natural mechanisms, we developed a modular platform to design programmable mRNA therapeutics, Epigenomic Controllers (EC), that control gene expression through directed epigenetic change.
Read the full summary ↓
ECs tune expression levels of one or multiple genes with durable effect of weeks-to-months in vivo following a single dose. We characterized ECs across multiple targets and designed an EC effectively inhibiting the cancer- and inflammatory-disorder-associated multi-gene cluster CXCL1-8. With precision targeting of NF-kB signaling and novel identification of homologous murine surrogates, ECs significantly reduced neutrophil migration in vivo during acute lung inflammation. A platform approach to EC design for epigenomic modulation opens new treatment frontiers for diverse gene targets, including those considered "undruggable."
Published in
Programmable mRNA therapeutics for controlled epigenomic modulation of single and multiplexed gene expression in diverse diseases
O'Donnell CW, Farelli JD, Belaghzal H et al. · Nature communications 2025 · PMID 40082450 · doi:10.1038/s41467-025-57920-5
This dataset
Open GSE290866 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 GSE290866_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 PRJNA1047162. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40082450) ↗
Study design
9 conditions, mostly in duplicate
CHIPSEQ_HA_CXCL-EC1 ×2 CHIPSEQ_HA_CXCL-EC2 ×2 CHIPSEQ_H3K9ME3_CXCL-EC2 ×2 CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC2 ×2 CHIPSEQ_H3K9ME3_CXCL-EC1 ×2 CHIPSEQ_H3K9ME3_BASELINE_CXCL-EC1 ×2 CHIPSEQ_P65_CXCL-EC1_E1 ×2 CHIPSEQ_P65_Stimulated_CXCL-EC1 ×2 +3 more

Supports a case/control comparison: 4 samples read as cases, 6 as controls.

How we read this: 9 replicated groups read from 20 sample titles; they account for 18 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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