RNA-seq profiling of post-hypoxic head and neck cancer cell lines
RNA-seq (gene expression) · human · 18 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
- 18 samples: 5 × FADU-hfm HPV-negative post-hypoxic vs 5 × SCC154-hfm HPV-positive non-hypoxic vs 4 × FADU-hfm HPV-negative non-hypoxic vs 4 × SCC154-hfm HPV-positive post-hypoxicGroups 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
- Hypoxia Induces a Mitotic Survival Advantage After Radiotherapy in Head and Neck Cancer CellsInternational journal of cancer · 2026
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 GSE319374_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: 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 PRJNA1423175 and SRA study SRP676756. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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.
- GSM9516811 FADU-hfm HPV-negative non-hypoxic replicate 1 FADU-hfm HPV-negative n…
- GSM9516812 FADU-hfm HPV-negative post-hypoxic replicate 1 FADU-hfm HPV-negative p…
- GSM9516813 SCC154-hfm HPV-positive non-hypoxic replicate 1 SCC154-hfm HPV-positive…
- GSM9516814 FADU-hfm HPV-negative non-hypoxic replicate 2 FADU-hfm HPV-negative n…
- GSM9516815 FADU-hfm HPV-negative post-hypoxic replicate 2 FADU-hfm HPV-negative p…
- GSM9516816 SCC154-hfm HPV-positive non-hypoxic replicate 2 SCC154-hfm HPV-positive…
- GSM9516817 SCC154-hfm HPV-positive post-hypoxic replicate 2 SCC154-hfm HPV-positive…
- GSM9516818 FADU-hfm HPV-negative non-hypoxic replicate 3 FADU-hfm HPV-negative n…
- GSM9516819 FADU-hfm HPV-negative post-hypoxic replicate 3 FADU-hfm HPV-negative p…
- GSM9516820 SCC154-hfm HPV-positive non-hypoxic replicate 3 SCC154-hfm HPV-positive…
- GSM9516821 SCC154-hfm HPV-positive post-hypoxic replicate 3 SCC154-hfm HPV-positive…
- GSM9516822 FADU-hfm HPV-negative non-hypoxic replicate 4 FADU-hfm HPV-negative n…
- GSM9516823 FADU-hfm HPV-negative post-hypoxic replicate 4 FADU-hfm HPV-negative p…
- GSM9516824 SCC154-hfm HPV-positive non-hypoxic replicate 4 SCC154-hfm HPV-positive…
- GSM9516825 SCC154-hfm HPV-positive post-hypoxic replicate 4 SCC154-hfm HPV-positive…
- GSM9516826 FADU-hfm HPV-negative post-hypoxic replicate 5 FADU-hfm HPV-negative p…
- GSM9516827 SCC154-hfm HPV-positive non-hypoxic replicate 5 SCC154-hfm HPV-positive…
- GSM9516828 SCC154-hfm HPV-positive post-hypoxic replicate 5 SCC154-hfm HPV-positive…
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares rna-seq, head, neck
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares head, neck
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing · shares head, neck
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares head, neck
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares head, neck
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares head, neck
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares head, neck
- 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 · shares lines
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.