Exploration of tumor associated macrophages in patients with metastatic uveal melanoma by single cell RNAseq
Single-cell RNA-seq · human · 12 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
- Uveal melanomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 10 distinct titles, 2 of them repeatedGroups 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
- Tebentafusp, a T cell engager, promotes macrophage reprogramming and in combination with IL-2 overcomes macrophage immunosuppression in cancerNature communications · 2025
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 GSE287090_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 PRJNA1211112 and SRA study SRP557603. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 12 sample titles: 10 distinct titles with little repetition. 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.
- GSM8738435 Patient 1 Sample 1
- GSM8738436 Patient 2 Sample 2
- GSM8738437 Patient 3 Sample 3
- GSM8738438 Patient 4 Sample 4
- GSM8738439 Patient 5 Sample 5
- GSM8738440 Patient 6 Sample 6
- GSM8738441 Patient 7 Sample 8
- GSM8738442 Patient 7 Sample 7
- GSM8738443 Patient 8 Sample 10
- GSM8738444 Patient 8 Sample 9
- GSM8738445 Patient 8 Post-treatment
- GSM8738446 Patient 8 Post-treatment_CD45_enriched
- GSE182942 ARL4C remarkably promotes the tumorigenesis of Uveal Melanoma and may represent a potential therapeutic target 6 samples same disease briefing · shares melanoma, uveal
- GSE285583 NELFCD: A Crucial Factor in Uveal Melanoma Cell Proliferation and Tumorigenesis 6 samples same disease briefing · shares melanoma, uveal
- GSE259383 Tebentafusp elicits on-target cutaneous immune responses driven by cytotoxic T cells in uveal melanoma patients 6 samples same disease briefing · shares melanoma, uveal
- GSE294950 Epigenetic library screen reveals novel targets for uveal melanoma 24 samples same disease briefing · shares melanoma, uveal
- GSE317536 Matched sampling reveals uncoupled phenotypic plasticity during metastasis formation in uveal melanoma 23 samples same disease briefing · shares melanoma, uveal
- GSE196624 The role of EHMT2 in Uveal melanoma progression [EHMT2_Inhibitors] 18 samples same disease briefing · shares melanoma, uveal
- GSE231395 PRAME induces genomic instability in uveal melanoma [RNA-seq] 15 samples same disease briefing · shares melanoma, uveal
- GSE317502 ATR Is a Critical Dependency Gene Supporting Uveal Melanoma Cell Survival 12 samples same disease briefing · shares melanoma, uveal
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.