Cytotoxic NK cells impede response to checkpoint immunotherapy in melanoma with an immune-excluded phenotype
RNA-seq (gene expression) · mouse · 10 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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
- Cytotoxic NK Cells Impede Response to Checkpoint Immunotherapy in Melanoma with an Immune-Excluded PhenotypeCancer discovery · 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 GSE292854_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1241755 and SRA study SRP572961. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 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.
- GSM8867432 sc_YUMM_5_2_aPD1
- GSM8867433 sc_YUMM_5_2_aNK1_1
- GSM8867434 sc_YUMM_5_2_control
- GSM8867435 sc_YUMM_5_2_aPD1_aNK_1_1
- GSM8867436 sc_NRAS_control
- GSM8867437 sc_NRAS_aPD1
- GSM8867438 sc_NRAS_aNK_1_1
- GSM8867439 sc_NRAS_aPD1_aNK_1_1
- GSM8867440 CITE_NRAS_control
- GSM8867441 CITE_NRAS_aPD1
- GSE215963 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma. 1497 samples shares immunotherapy, melanoma
- GSE291447 Targeting CD11b+ regulatory B cells via RAS/RAF/PI3K pathway inhibition augments response to immune checkpoint blockade or CD40 agonism in metastatic melanoma 60 samples shares checkpoint, melanoma
- GSE290434 A stress response axis in tumor-associated macrophages dictates phenotype heterogeneity and immunotherapy evasion 21 samples shares immunotherapy, phenotype
- GSE263625 Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases 19 samples shares immunotherapy, melanoma
- GSE253092 Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy [bulk RNA-seq] 12 samples shares checkpoint, melanoma
- GSE207029 Blockade of avb8 integrin synergizes with checkpoint inhibition to enhance anti-tumor immunity through Cxcl9-dependent augmentation of CD8+ T cell cytotoxicity 12 samples shares checkpoint, cytotoxic
- GSE334497 TROP2/claudin program mediates immune exclusion to impede checkpoint blockade in breast cancer 10 samples shares checkpoint, impede
- GSE337208 scRNA seq. of PDAC models treated with Kras inhibitors in combination with checkpoint immunotherapy 9 samples shares immunotherapy, checkpoint
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.