GEO series
Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (ChIP-Seq)
GSE229439
Homo sapiens; Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
85 samples
Submitted 2025/02/24
Platform GPL24247Platform GPL18573Platform GPL24676
Summary
An integral part of human cellular homeostasis substantially relies on defense transcriptional responses tailored to fight microbial pathogens, including Viruses. However, a definitive anatomy of the “virus-responsive” fates of the non-coding genome was largely elusive. Here, we exhaustively assayed the human transcriptome and epigenome under naïve and antiviral cellular states and defined remarkable reprogramming to mark the exchange of cellular fates, involving previously unspecified, unsupervised, or overlooked non-coding entities endowed with thousands of novel virus-responsive enhancers, Super-enhancers (SEs), and Repetitive DNA enhancers. These functional determinants demonstrate superior chromatin architecture, stimulus-specificity, and transcriptional fitness, and neighbor, reside proximal, or entirely coincide with hundreds of the virus-stimulated genes, while a multitude of those is bound by the master antimicrobial TFs, IRF3 or/and NFκB, upon cell infection. A plethora of these DNA elements is traced within the repetitive fate of the human genome including Simple Tandem Repeats (STRs), Dispersed Repeats (DRs) such as retrotransposons and DNA transposons, and chimeras of those, enriched in HCTFBSs recognized by IRF3 or/and NFκB and exhibits pervasive imprints in the genomes of evolutionary recent, old and ancient species, including viruses. These findings emphasize the role of the architectural and functional compartmentalization of the human epigenome in naïve and infected cells on the perplexing natural conflicts and mechanistic dependencies that impose the frontage of defense gene expression in humans.
Published in
Koutsi MA, Pouliou M, Chatzopoulos D et al.
· Nucleic acids research 2025
· PMID 40131776
· doi:10.1093/nar/gkaf207
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE229439_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 85 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA954441 and SRA study SRP432078. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 85 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM7163567 IRF3-ChIP-seq_HL_SVI_0h_exp1_2023
- GSM7163568 IRF3-ChIP-seq_HL_SVI_3h_exp1_2023
- GSM7163569 IRF3-ChIP-seq_HL_SVI_6h_exp1_2023
- GSM7163570 IRF3-ChIP-seq_HL_SVI_0h_exp2_2023
- GSM7163571 IRF3-ChIP-seq_HL_SVI_3h_exp2_2023
- GSM7163572 IRF3-ChIP-seq_HL_SVI_6h_exp2_2023
- GSM7163573 IRF3-ChIP-seq_NM_SVI_0h_2023
- GSM7163574 IRF3-ChIP-seq_NM_SVI_3h_2023
- GSM7163575 IRF3-ChIP-seq_NM_SVI_6h_2023
- GSM7163576 p65-ChIP-seq_HL_SVI_0h_2023
- GSM7163577 p65-ChIP-seq_HL_SVI_3h_2023
- GSM7163578 p65-ChIP-seq_HL_SVI_6h_2023
- GSM7163579 p65-ChIP-seq_NM_SVI_0h_2023
- GSM7163580 p65-ChIP-seq_NM_SVI_3h_2023
- GSM7163581 p65-ChIP-seq_NM_SVI_6h_2023
- GSM7163582 CBP-ChIP-seq_HL_SVI_0h_2023
- GSM7163583 CBP-ChIP-seq_HL_SVI_3h_2023
- GSM7163584 CBP-ChIP-seq_HL_SVI_6h_2023
- GSM7163585 CBP-ChIP-seq_NM_SVI_0h_2023
- GSM7163586 CBP-ChIP-seq_NM_SVI_3h_2023
- GSM7163587 CBP-ChIP-seq_NM_SVI_6h_2023
- GSM7163588 MED1-ChIP-seq_HL_SVI_0h_exp1_2023
- GSM7163589 MED1-ChIP-seq_HL_SVI_3h_exp1_2023
- GSM7163590 MED1-ChIP-seq_HL_SVI_6h_exp1_2023
- GSM7163591 MED1-ChIP-seq_HL_SVI_0h_exp2_2023
- GSM7163592 MED1-ChIP-seq_HL_SVI_3h_exp2_2023
- GSM7163593 MED1-ChIP-seq_HL_SVI_6h_exp2_2023
- GSM7163594 MED1-ChIP-seq_NM_SVI_0h_2023
- GSM7163595 MED1-ChIP-seq_NM_SVI_3h_2023
- GSM7163596 MED1-ChIP-seq_NM_SVI_6h_2023
- GSM7163597 RNA_polII-ChIP-seq_HL_SVI_0h_2023
- GSM7163598 RNA_polII-ChIP-seq_HL_SVI_3h_2023
- GSM7163599 RNA_polII-ChIP-seq_HL_SVI_6h_2023
- GSM7163600 RNA_polII-ChIP-seq_NM_SVI_0h_2023
- GSM7163601 RNA_polII-ChIP-seq_NM_SVI_3h_2023
- GSM7163602 RNA_polII-ChIP-seq_NM_SVI_6h_2023
- GSM7163603 H3K4me3-ChIP-seq_HL_SVI_0h_exp1_2023
- GSM7163604 H3K4me3-ChIP-seq_HL_SVI_3h_exp1_2023
- GSM7163605 H3K4me3-ChIP-seq_HL_SVI_6h_exp1_2023
- GSM7163606 H3K4me3-ChIP-seq_HL_SVI_0h_exp2_2023
+ 45 more — browse all 85 samples with per-sample file links →
Similar datasets
- GSE288595 Tracing functional (epi)genomic imprints and their evolutionary origins in human defense antiviral cellular response (ChIP-seq III) 14 samples
- GSE294572 HNF4a controls growth, identity and response to KRAS inhibition in IMA [ChIP- seq] 38 samples
- GSE277367 The functional antagonism between SIRT2 and MOF regulates cell cycle progression and genome stability [ChIP-seq] 24 samples
- GSE245731 HNF4G and FOXA1 are context-specific drivers of pancreatic cancer progression [ChIP-seq] 172 samples
- GSE260742 DOT1L provides transcriptional memory through PRC1.1 antagonism [ChIP-Seq] 158 samples
- GSE292571 SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [ChIP-seq] 116 samples
- GSE279644 BCR::ABL1-induced enhancer reprogramming uncovers hypersensitivity of Ph+B-ALL cells to enhancer-targeting drugs [ChIP-Seq] 91 samples
- GSE298543 Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum [CUT&RUN] 88 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.