A unique genetic signature for cancer-associated fibroblasts in Melanoma metastases
Single-cell RNA-seq · mouse · 21 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
- Mus musculus (mouse)
- Samples
- 21 samples: 5 conditions, mostly with about 5 replicates eachGroups 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
- A Unique Signature for Cancer-Associated Fibroblasts in Melanoma MetastasesPigment cell & melanoma research · 2025
Read the full summary ↓
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 GSE254072_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 PRJNA1065791 and SRA study SRP484452. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 5 replicated groups read from 21 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.
- GSM8033015 lung, unchallenged, rep1 lung, unchallenged,
- GSM8033016 lung, unchallenged, rep4 lung, unchallenged,
- GSM8033017 lung, unchallenged, rep5 lung, unchallenged,
- GSM8033018 lung, unchallenged, rep6 lung, unchallenged,
- GSM8033019 metastasis, TME, rep4 metastasis, TME,
- GSM8033020 metastasis, TME, rep5 metastasis, TME,
- GSM8033021 metastasis, TME, rep6 metastasis, TME,
- GSM8033022 metastasis, TME, rep7 metastasis, TME,
- GSM8033023 metastasis, TME, rep8 metastasis, TME,
- GSM8033024 metastasis, MM, rep4 metastasis, MM,
- GSM8033025 metastasis, MM, rep5 metastasis, MM,
- GSM8033026 metastasis, MM, rep6 metastasis, MM,
- GSM8033027 metastasis, TME, rep1-3
- GSM8033028 primary tumor, TME, rep1-3
- GSM8033029 primary tumor, TME, rep4 primary tumor, TME,
- GSM8033030 primary tumor, TME, rep5 primary tumor, TME,
- GSM8033031 primary tumor, TME, rep6 primary tumor, TME,
- GSM8033032 primary tumor, TME, rep7 primary tumor, TME,
- GSM8033033 primary tumor, TME, rep8 primary tumor, TME,
- GSM8033034 primary tumor, MM, rep4 primary tumor, MM,
- GSM8033035 primary tumor, MM, rep5 primary tumor, MM,
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- GSE300536 Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [2] 137 samples shares signature, genetic
- GSE263625 Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases 19 samples shares metastases, melanoma
- GSE243373 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq] 15 samples shares signature, unique
- GSE235242 Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma suppress CD8+ T cell activation and inhibit response to immune checkpoint therapy [Kras_p53] 14 samples shares cancer-associated, fibroblasts
- GSE271267 Tumoral Interferon Beta Induces an Immune-Stimulatory Phenotype in Tumor-Associated Macrophages in Melanoma Brain Metastases 12 samples shares metastases, melanoma
- GSE308848 Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1 [scRNA-Seq] 12 samples shares cancer-associated, fibroblasts
- GSE316731 Endothelial Cell-specific Activation of NOX1 Drives Obesity and Metabolic Syndrome via Skeletal Muscle Mitochondrial Dysfunction with Novel Genetic Signatures 12 samples shares signature, genetic
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.