single-cell spatial analysis reveals molecular mechanisms underlying immune cell organization and cancer cell heterogeneity in HPV-associated oropharyngeal carcinoma
Single-cell RNA-seq · human · 15 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
- 15 samples: 15 × scRNA-seq of HPV-OPSCC; NCIGroups 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 GSE290040_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 PRJNA1225949 and SRA study SRP565199. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 1 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8804247 scRNA-seq of HPV-OPSCC; NCI_3 scRNA-seq of HPV-OPSCC;…
- GSM8804248 scRNA-seq of HPV-OPSCC; NCI_4 scRNA-seq of HPV-OPSCC;…
- GSM8804249 scRNA-seq of HPV-OPSCC; NCI_5 scRNA-seq of HPV-OPSCC;…
- GSM8804250 scRNA-seq of HPV-OPSCC; NCI_6 scRNA-seq of HPV-OPSCC;…
- GSM8804251 scRNA-seq of HPV-OPSCC; NCI_7 scRNA-seq of HPV-OPSCC;…
- GSM8804252 scRNA-seq of HPV-OPSCC; NCI_8 scRNA-seq of HPV-OPSCC;…
- GSM8804253 scRNA-seq of HPV-OPSCC; NCI_9 scRNA-seq of HPV-OPSCC;…
- GSM8804254 scRNA-seq of HPV-OPSCC; NCI_10 scRNA-seq of HPV-OPSCC;…
- GSM8804255 scRNA-seq of HPV-OPSCC; NCI_11 scRNA-seq of HPV-OPSCC;…
- GSM8804256 scRNA-seq of HPV-OPSCC; NCI_12 scRNA-seq of HPV-OPSCC;…
- GSM8804257 scRNA-seq of HPV-OPSCC; NCI_13 scRNA-seq of HPV-OPSCC;…
- GSM8804258 scRNA-seq of HPV-OPSCC; NCI_14 scRNA-seq of HPV-OPSCC;…
- GSM8804259 scRNA-seq of HPV-OPSCC; NCI_15 scRNA-seq of HPV-OPSCC;…
- GSM8804260 scRNA-seq of HPV-OPSCC; NCI_21 scRNA-seq of HPV-OPSCC;…
- GSM8804261 scRNA-seq of HPV-OPSCC; NCI_22 scRNA-seq of HPV-OPSCC;…
- GSE182227 Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma 24 samples same disease briefing · shares heterogeneity, oropharyngeal
- 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 heterogeneity, single-cell
- GSE140042 Single-cell atlas of head and neck squamous cell carcinoma 18 samples same disease briefing · shares single-cell
- GSE173647 Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma 2 samples same disease briefing · shares single-cell
- GSE162738 Immune gene signatures in oropharyngeal cancers are associated with inverse prognosis by HPV-status 51 samples same disease briefing · shares oropharyngeal
- GSE164690 Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing 51 samples same disease briefing · shares single-cell
- GSE181919 Single-cell transcriptome profiling of the stepwise progression of head and neck cancer 37 samples same disease briefing · shares single-cell
- GSE103322 Single cell RNA-seq analysis of head and neck cancer 5901 samples same disease briefing
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.