GEO series
Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19
GSE339365
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
120 samples
Submitted 2026/08/05
Platform GPL21697
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 120 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
- 120 samples: 116 distinct titles, 4 of them repeatedGroups 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)
Severe COVID-19 is associated with innate immune dysregulation resembling sepsis-induced immunoparalysis. Epigenetic mechanisms, particularly changes in H3K4me3 enrichment at gene promoters, have been observed in immune tolerance and monocyte dysfunction in sepsis. Whether comparable H3K4me3 alterations occur during acute critical COVID-19 illness has not been investigated.
Read the full summary ↓
Among 706 differentially bound consensus peaks with promoter association between ICU and non-ICU groups, 704 showed increased H3K4me3 occupancy in ICU patients, predominantly at neutrophil effector gene loci, supported by pathway enrichment of neutrophil degranulation and innate immune activation. Monocyte HLA-DR expression and ex vivo TLR-stimulated IL-6 secretion were persistently reduced throughout the first week of ICU treatment. Longitudinal profiling in the ICU group revealed a shift from an interferon-driven chromatin signature at admission toward sustained innate immune activation and ECM remodelling at day seven. This study provides the first genome-wide H3K4me3 characterization of circulating immune cells during acute critical COVID-19, demonstrating that epigenetic reprogramming is an active and dynamic process that mirrors the functional immune dysregulation observed in these patients.
This dataset
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.
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 GSE339365_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1498531 and SRA study SRP719950. Searching any of these in the dataset finder brings you back here.
Study design
116 distinct titles, 4 of them repeated
ICU patient #11, timepoint 1, ChIP with H3Pan… ×2
ICU patient #12, timepoint 1, ChIP with H3Pan… ×2
ICU patient #24, timepoint 1, ChIP with H3K4m… ×2
Non-ICU patient #7, timepoint 1, ChIP with H3… ×2
How we read this: Read from 120 sample titles: 116 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
- GSM9894260 ICU patient #1, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894261 ICU patient #1, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894262 ICU patient #2, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894263 ICU patient #2, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894264 ICU patient #2, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894265 ICU patient #2, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894266 ICU patient #3, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894267 ICU patient #3, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894268 ICU patient #3, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894269 ICU patient #3, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894270 ICU patient #4, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894271 ICU patient #4, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894272 ICU patient #5, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894273 ICU patient #5, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894274 ICU patient #5, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894275 ICU patient #5, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894276 ICU patient #6, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894277 ICU patient #6, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894278 ICU patient #6, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894279 ICU patient #6, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894280 ICU patient #7, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894281 ICU patient #7, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894282 ICU patient #8, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894283 ICU patient #8, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894284 ICU patient #9, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894285 ICU patient #9, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894286 ICU patient #9, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894287 ICU patient #9, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894288 ICU patient #10, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894289 ICU patient #10, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894290 ICU patient #10, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894291 ICU patient #10, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894292 ICU patient #11, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894293 ICU patient #11, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894294 ICU patient #11, timepoint 1, ChIP with H3Pan antibody (Input), Lane002
- GSM9894295 ICU patient #11, timepoint 2, ChIP with H3K4me3 antibody, Lane001
- GSM9894296 ICU patient #11, timepoint 2, ChIP with H3Pan antibody (Input), Lane001
- GSM9894297 ICU patient #12, timepoint 1, ChIP with H3K4me3 antibody, Lane001
- GSM9894298 ICU patient #12, timepoint 1, ChIP with H3Pan antibody (Input), Lane001
- GSM9894299 ICU patient #12, timepoint 1, ChIP with H3Pan antibody (Input), Lane002
+ 80 more — browse all 120 samples with per-sample file links →
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