Interlocking core regulatory circuits enable viral hijacking in Merkel cell carcinoma
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 43 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)
- Topic
- Merkel cell carcinomaThis series is part of our curated briefing on it.
- Samples
- 43 samples: 37 distinct titles, 6 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.
- Paper
- Interlocking host and viral cis-regulatory networks drive Merkel cell carcinomaThe Journal of clinical investigation · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE261681_RAW.tar (it can run to tens of gigabytes).
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 PRJNA1088415 and SRA study SRP495419. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 43 sample titles: 37 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.
- GSM8148703 Sample_MCC13 DNase
- GSM8148704 Sample_MCC26 DNase rep1
- GSM8148705 Sample_MCC26 DNase rep2
- GSM8148706 Sample_MKL1 DNase rep1
- GSM8148707 Sample_MKL1 DNase rep2
- GSM8148708 Sample_MKL2 DNase rep1
- GSM8148709 Sample_MKL2 DNase rep2
- GSM8148710 Sample_MS1 DNase rep1
- GSM8148711 Sample_MS1 DNase rep2
- GSM8148712 Sample_UISO DNase rep1
- GSM8148713 Sample_UISO DNase rep2
- GSM8148714 Sample_Waga DNase rep1
- GSM8148715 Sample_Waga DNase rep2
- GSM8148716 Sample_MCC13 H3K27ac
- GSM8148717 Sample_MCC26 H3K27ac
- GSM8148718 Sample_MKL1 H3K27ac
- GSM8148719 Sample_MKL2 H3K27ac
- GSM8148720 Sample_MS1 H3K27ac
- GSM8148721 Sample_UISO H3K27ac
- GSM8148722 Sample_Waga H3K27ac
- GSM8148723 Sample_MCC13 input
- GSM8148724 Sample_MCC26 input
- GSM8148725 Sample_MKL1 input
- GSM8148726 Sample_MKL2 input
- GSM8148727 Sample_MS1 input
- GSM8148728 Sample_UISO input
- GSM8148729 Sample_Waga input
- GSM8148730 Sample_MKL1 ATOH1
- GSM8148731 Sample_MKL2 ATOH1
- GSM8148732 Sample_MKL1 INSM1
- GSM8148733 Sample_MKL2 INSM1
- GSM8148734 Sample_MKL1 ISL1
- GSM8148735 Sample_MKL2 ISL1
- GSM8148736 Sample_MKL1 LXH3
- GSM8148737 Sample_MKL2 LXH3
- GSM8148738 Sample_MKL1 POU4F3
- GSM8148739 Sample_MKL2 POU4F3
- GSM8148740 Sample_MKL1 SOX2
- GSM8148741 Sample_MKL2 SOX2
- GSM8148742 Sample_MKL1 DMSO H3K27ac HiChIP
+ 3 more — browse all 43 samples with per-sample file links →
- GSE235093 Pre-existing skin-resident CD8 and γδ T cell circuits mediate immune response in Merkel cell carcinoma and Predict immunotherapy efficacy 333 samples same disease briefing · shares circuits, merkel
- GSE39612 Distinct gene expression profiles of viral- and non-viral associated Merkel cell carcinoma revealed by transcriptome analysis 138 samples same disease briefing · shares merkel, viral
- GSE305197 Targeting an essential viral oncoprotein with an IL-7-enhanced mRNA vaccine induces durable immunity to Merkel cell carcinoma 3 samples same disease briefing · shares merkel, viral
- GSE281260 Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment 146 samples same disease briefing · shares merkel
- GSE292992 MDM2 degradation overcomes feedback regulation of p53 signaling in Merkel cell carcinoma 66 samples same disease briefing · shares merkel
- GSE317774 ATR inhibition induces NF-κB-dependent immunogenicity in Merkel cell carcinoma independent of cGAS-STING 48 samples same disease briefing · shares merkel
- GSE154938 Glucose-6-Phosphate Dehydrogenase as a Prognostic Predictor Correlates with the Tumor Immune Activity Including Programmed Death Ligand-1 Expression in Merkel Cell Carcinoma 41 samples same disease briefing · shares merkel
- GSE214948 The significance of PAX5 in Merkel cell carcinoma 39 samples same disease briefing · shares merkel
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.