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Transcriptional characterization of adjuvantly radio(chemo)therapy treated head and neck squamous cell carcinoma (HNSCC).

GSE235223 Homo sapiens (human) RNA-seq (gene expression) 134 samples Submitted 2024/05/16 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 134 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Head and neck cancerThis series is part of our curated briefing on it.
Samples
134 samples
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
Metabolic pathway-based subtypes associate glycan biosynthesis and treatment response in head and neck cancerNPJ precision oncology · 2024
Summary (written by the submitters)
We characterized n=134 HNSCC by Quantseq 3´-RNA-sequencing for their transcriptional profiles in order to analyze differential expression of clinically relevant subgroups, define transcriptionally defined molecular subgroups and to characterize the tumor microenvironment by gene expression devonvolution approaches.
Published in
Metabolic pathway-based subtypes associate glycan biosynthesis and treatment response in head and neck cancer
Dankó B, Hess J, Unger K et al. · NPJ precision oncology 2024 · PMID 38783045 · doi:10.1038/s41698-024-00602-0
This dataset
Open GSE235223 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 GSE235223_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA985582 and SRA study SRP444851. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38783045) ↗
Study design
A cohort of 134 individual samples

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

How we read this: Sample titles run HNSCC_LMU_KKG_Sample_034 … HNSCC_LMU_KKG_Sample_157 and carry no group information.

Samples in this study

+ 94 more — browse all 134 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.