Bulk RNA-seq profiling of human head and neck squamous cell carcinoma (HNSCC) with primary tumors and metastatic lymph nodes
Single-cell RNA-seq · human · 10 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Topic
- Head and neck cancerThis series is part of our curated briefing on it.
- Samples
- 10 samples: 6 × SCCGroups 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.
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 GSE286234_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: 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 PRJNA1208459 and SRA study SRP556269. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 1 replicated groups read from 10 sample titles; they account for 6 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.
- GSM8721430 SCC7233 SCC
- GSM8721431 SCC7238 SCC
- GSM8721432 SCC7240 SCC
- GSM8721433 SCC7267 SCC
- GSM8721434 SCC7268 SCC
- GSM8721435 SCC7275 SCC
- GSM8721436 SCC7233B
- GSM8721437 SCC7240B
- GSM8721438 SCC7267B
- GSM8721439 SCC7276B
- 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 hnscc, bulk
- GSE185965 Single cell RNA sequencing of head and neck squamous carcinoma (HNSCC) patient sample 3 samples same disease briefing · shares hnscc, squamous
- GSE132627 RNA-seq analysis of CD276-high/EpCAM+ cells from HNSCC patient-derived-xenograft 2 samples same disease briefing · shares hnscc, rna-seq
- GSE176077 RNA-seq profiling of salivary transcriptome reveals potential diagnostic RNAs and oral microbial dysbiosis in oral squamous cell carcinoma 28 samples same disease briefing · shares squamous, rna-seq
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing · shares rna-seq
- GSE172146 Aberrant translation regulation by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives HNSCC progression 28 samples same disease briefing · shares hnscc
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares squamous
- GSE173161 Comparative analysis of gene expression after Oct4 or Scrambled siRNA knockdown in HNSCC cell lines 18 samples same disease briefing · shares hnscc
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.