Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [CUT&RUN-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
- Head and neck cancerThis series is part of our curated briefing on it.
- Samples
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Virus-human chromatin interactions reorganise 3D genome and hijack KDM5B for promoting metastasis in nasopharyngeal carcinomaNature communications · 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 GSE278607_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 PRJNA1168075 and SRA study SRP536202. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM8551173 NP69, CUT&RUN-seq, H3K4me3
- GSM8551174 NP69, CUT&RUN-seq, CTCF
- GSM8551175 C17, CUT&RUN-seq, H3K4me3
- GSM8551176 C17, CUT&RUN-seq, CTCF
- GSM8551177 C17, CUT&RUN-seq, H3K27ac
- GSM8551178 C666, CUT&RUN-seq, H3K4me3
- GSM8551179 C666, CUT&RUN-seq, CTCF
- GSM8551180 C666, CUT&RUN-seq, H3K27ac
- GSM8551181 NPC43, CUT&RUN-seq, H3K4me3
- GSM8551182 NPC43, CUT&RUN-seq, CTCF
- GSM8551183 NPC43, CUT&RUN-seq, H3K27ac
- GSM9017742 NP69, CUT&RUN-seq, IgG
- GSM9017743 NP460, CUT&RUN-seq, H3K4me3
- GSM9017744 NP460, CUT&RUN-seq, CTCF
- GSM9017745 NP460, CUT&RUN-seq, IgG
- GSM9017746 C17, CUT&RUN-seq, IgG
- GSM9017747 C666, CUT&RUN-seq, IgG
- GSM9017748 NPC43, CUT&RUN-seq, IgG
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares interactions
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing
- GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing
- GSE114446 Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines 33 samples same disease briefing
- GSE172146 Aberrant translation regulation by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives HNSCC progression 28 samples same disease briefing
- GSE176077 RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma 28 samples same disease briefing
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.