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Single-cell sequencing across radiation treatment timepoints in head and neck cancer

GSE280982 Homo sapiens (human) Single-cell RNA-seq 49 samples Submitted 2025/04/23 Platform GPL34284Platform GPL24676
At a glance

Single-cell RNA-seq · human · 49 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Topic
Head and neck cancerThis series is part of our curated briefing on it.
Samples
49 samples: 49 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
Radiation therapy results in preferential tumor antigen-specific lymphodepletion in head and neck cancerNature communications · 2025
Summary (written by the submitters)
We performed single cell sequencing across treatment timepoints to evaluate the immunological impact of radiation in head and neck cancer.
Published in
Radiation therapy results in preferential tumor antigen-specific lymphodepletion in head and neck cancer
Zenga J, Awan MJ, Frei A et al. · Nature communications 2025 · PMID 40593620 · doi:10.1038/s41467-025-60827-w
This dataset
Open GSE280982 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 GSE280982_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 PRJNA1181774 and SRA study SRP543002. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40593620) ↗
Study design
49 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 49 sample titles: 49 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.

Samples in this study

+ 9 more — browse all 49 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.