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Human papillomavirus (HPV) infected epithelial cells and FBLN1+ fibroreticular cells govern the immunogenic tumor microenvironment in HPV-associated oropharyngeal squamous cell carcinoma

GSE288786 Homo sapiens (human) Single-cell RNA-seq 10 samples Submitted 2026/04/30 Platform GPL18573
At a glance

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)
Samples
10 samples: 5 × Tonsil, HPV-positive, sample vs 3 × Tonsil, control, sample vs 2 × Tonsil, HPV-negative, sampleGroups 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.
Summary (written by the submitters)
OPSCC can occur through either the exposure to carcinogens such as alcohol and/or tobacco or high-risk human papillomavirus (HPV) infection. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenvironment (TME) of HPV-positive OPSCC exhibits distinctive features, with relevance to the interaction between cancer cells and adjacent stromal cells.
This dataset
Open GSE288786 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE288786_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1219405 and SRA study SRP561668. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Tonsil, HPV-positive, sample vs 3 × Tonsil, control, sample vs 2 × Tonsil, HPV-negative, sample

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.

Samples in this study
Datasets on a similar topic

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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.