Single cell RNA-seq analysis of head and neck cancer
Single-cell RNA-seq · human · 5901 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
- 5901 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
- Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck CancerCell · 2017
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 GSE103322_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 PRJNA401654. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 5901 more — browse all 5901 samples with per-sample file links →
- 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
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 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
- GSE159067 Immunologically hot phenotype is associated with response to PD-1/PD-L1 inhibitors in patients with advanced head and neck squamous cell carcinoma. 102 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
- GSE156554 Liquid Biopsy: Examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for molecular tumor markers 15 samples same disease briefing · shares head, neck
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.