GEO series
Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19
GSE339365
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
120 samples
Submitted 2026/08/05
Platform GPL21697
Summary
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. 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
Direct links to NCBI, no account and no request form: the whole study as GSE339365_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 120 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1498531 and SRA study SRP719950. Searching any of these in the dataset finder brings you back here.
Study design
38 conditions, each sampled once — no replicated groups
ICU patient #11, timepoint 1, ChIP with H3Pan… ×2
ICU patient #12, timepoint 1, ChIP with H3Pan… ×2
Read from the first 40 of 120 sample titles: 38 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- 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 →
Similar datasets
- GSE339049 Severe long-COVID is driven by monocyte reprogramming and broad immune dysregulation linked to herpesvirus activation 48 samples
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples
- GSE280574 mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer 576 samples
- GSE304074 RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair 118 samples
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples
- GSE280280 Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory circuits During Response to MAPK Inhibition in BRAF-mutant colorectal cancer 36 samples
- GSE319092 Integrated Multi-Omics and Interactome Analysis of CDK8 Inhibition Reveals Erythroid Differentiation Programs and BET Synergy in AML Stem-like Cells 135 samples
- GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples
Share this dataset
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.