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Gene expression profile at single cell level for human metastatic melanoma samples

GSE269936 Homo sapiens (human) Single-cell RNA-seq 38 samples Submitted 2025/06/24 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 38 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
MelanomaThis series is part of our curated briefing on it.
Samples
38 samples: 6 conditions, mostly in triplicateGroups 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.
Paper
Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanomaNature communications · 2025
Summary (written by the submitters)
There exists great intra- and inter-tumor heterogeneity for metastatic melanomas. We used single cell RNA sequencing (scRNA-seq) to analyze cell type heterogeneity of metastatic melanoma and cell type specific responses to different treatments.
Published in
Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma
Yang J, Wang C, Fu D et al. · Nature communications 2025 · PMID 40890106 · doi:10.1038/s41467-025-62878-5
This dataset
Open GSE269936 in finder → Find more human RNA-seq datasets → Melanoma landscape →
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 GSE269936_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 PRJNA1124138 and SRA study SRP514118. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40890106) ↗
Study design
6 conditions, mostly in triplicate
1098 ×5 406 ×4 1224 ×3 1063 ×3 509 ×2 620 ×2 926 ×1 1232 ×1 +17 more

Supports a between-group comparison across 19 samples.

How we read this: 6 replicated groups read from 38 sample titles; they account for 19 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
More Melanoma datasets

Search all human RNA-seq datasets in GEO →

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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.