Unraveling cetuximab response in head and neck cancer with APHRODYTHE, a multi-omics patient-derived xenograft platform
RNA-seq (gene expression) · human · 114 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
- 114 samples: 114 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.
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 GSE317901_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 PRJNA1415770. 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 114 sample titles: 114 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.
- GSM9481405 Patient HNC0002, PDX sample, Biological Replicate A
- GSM9481406 Patient HNC0002, PDX sample, Biological Replicate B
- GSM9481407 Patient HNC0005, PDX sample
- GSM9481408 Patient HNC0007, PDX sample
- GSM9481409 Patient HNC0008, PDX sample, Biological Replicate A
- GSM9481410 Patient HNC0008, PDX sample, Biological Replicate B
- GSM9481411 Patient HNC0009, PDX sample, Biological Replicate A
- GSM9481412 Patient HNC0009, PDX sample, Biological Replicate B
- GSM9481413 Patient HNC0012, PDX sample, Biological Replicate A
- GSM9481414 Patient HNC0012, PDX sample, Biological Replicate B
- GSM9481415 Patient HNC0015, PDX sample, Biological Replicate A
- GSM9481416 Patient HNC0015, PDX sample, Biological Replicate B
- GSM9481417 Patient HNC0027, PDX sample, Biological Replicate A
- GSM9481418 Patient HNC0027, PDX sample, Biological Replicate B
- GSM9481419 Patient HNC0028, PDX sample, Merged Technical Replicate
- GSM9481420 Patient HNC0032, PDX sample, Biological Replicate A
- GSM9481421 Patient HNC0032, PDX sample, Biological Replicate B
- GSM9481422 Patient HNC0034, PDX sample
- GSM9481423 Patient HNC0035, PDX sample
- GSM9481424 Patient HNC0039, PDX sample, Biological Replicate A
- GSM9481425 Patient HNC0039, PDX sample, Biological Replicate B
- GSM9481426 Patient HNC0041, PDX sample, Merged Technical Replicate
- GSM9481427 Patient HNC0050, PDX sample
- GSM9481428 Patient HNC0052, PDX sample
- GSM9481429 Patient HNC0063, PDX sample
- GSM9481430 Patient HNC0070, PDX sample, Biological Replicate A
- GSM9481431 Patient HNC0070, PDX sample, Biological Replicate B
- GSM9481432 Patient HNC0077, PDX sample
- GSM9481433 Patient HNC0080, PDX sample
- GSM9481434 Patient HNC0081, PDX sample
- GSM9481435 Patient HNC0083, PDX sample
- GSM9481436 Patient HNC0086, PDX sample
- GSM9481437 Patient HNC0087, PDX sample
- GSM9481438 Patient HNC0089, PDX sample
- GSM9481439 Patient HNC0092, PDX sample, Biological Replicate A
- GSM9481440 Patient HNC0092, PDX sample, Biological Replicate B
- GSM9481441 Patient HNC0098, PDX sample
- GSM9481442 Patient HNC0104, PDX sample
- GSM9481443 Patient HNC0107, PDX sample, Biological Replicate A
- GSM9481444 Patient HNC0107, PDX sample, Biological Replicate B
+ 74 more — browse all 114 samples with per-sample file links →
- GSE132627 RNA-seq analysis of CD276-high/EpCAM+ cells from HNSCC patient-derived-xenograft 2 samples same disease briefing · shares patient-derived, xenograft
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares head
- GSE139324 Immune landscape of viral- and carcinogen-drived head and neck cancer 63 samples same disease briefing · shares head
- 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
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares head
- 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 cetuximab
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares head
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares head
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.