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Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN

GSE212250 Homo sapiens (human) Single-nucleus RNA-seq 3973 samples Submitted 2024/11/18 Platform GPL24676Platform GPL15520
At a glance

Single-nucleus RNA-seq · human · 3973 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Homo sapiens (human)
Topic
Head and neck cancerThis series is part of our curated briefing on it.
Samples
3973 samples: 10 conditions, mostly in triplicateGroups 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
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progressionGenome research · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
Womersley HJ, Muliaditan D, DasGupta R et al. · Genome research 2025 · PMID 39622638 · doi:10.1101/gr.279105.124
This dataset
Open GSE212250 in finder → Find more human RNA-seq datasets → Head and neck cancer landscape →
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.

Series matrix ↓
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 GSE212250_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
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.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA874747. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39622638) ↗
Study design
10 conditions, mostly in triplicate
HN120Pri, H3K4me3, Rep2, Cell ×184 HN120Pri, H3K4me3, Rep1, Cell ×92 HN120Met, H3K4me3, Rep1, Cell ×92 HN120Met, H3K4me3, Rep2, Cell ×14 HN120Pri, biol ×3 HN120Met, biol ×3 HN120PCR, biol ×3 HN137Pri, biol ×3 +2 more

Supports a between-group comparison across 400 samples.

How we read this: 10 replicated groups read from the first 400 of 3973 sample titles; they account for 400 of them. 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

+ 3933 more — browse all 3973 samples with per-sample file links →

More Head and neck cancer datasets

Search all human RNA-seq datasets in GEO →

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.