Tumor-resident T cells and dendritic cells form an in situ archetype for immunotherapy response in melanoma [bulk RNA-seq]
Single-cell RNA-seq · human · 29 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)
- Topic
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 29 samples: 29 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.
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 GSE294272_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 PRJNA1248920. 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 29 sample titles: 29 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.
- GSM8901585 HM002_RNA-seq
- GSM8901586 HM003-Large_RNA-seq
- GSM8901587 HM003-Small_RNA-seq
- GSM8901588 HM004_RNA-seq
- GSM8901589 HM005_RNA-seq
- GSM8901590 HM006_RNA-seq
- GSM8901591 HM007_RNA-seq
- GSM8901592 HM009_RNA-seq
- GSM8901593 HM012_RNA-seq
- GSM8901594 HM014_RNA-seq
- GSM8901595 HM015_RNA-seq
- GSM8901596 HM017_RNA-seq
- GSM8901597 HM019_RNA-seq
- GSM8901598 HM020_RNA-seq
- GSM8901599 HM025_RNA-seq
- GSM8901600 HM026_RNA-seq
- GSM8901601 HM028_RNA-seq
- GSM8901602 HM030_RNA-seq
- GSM8901603 HM032_RNA-seq
- GSM8901604 HM035_RNA-seq
- GSM8901605 HM036_RNA-seq
- GSM8901606 HM038_RNA-seq
- GSM8901607 HM041_RNA-seq
- GSM8901608 Mel-TIL-002_RNA-seq
- GSM8901609 Mel-TIL-011_RNA-seq
- GSM8901610 Mel-TIL-019_RNA-seq
- GSM8901611 Mel-TIL-022_RNA-seq
- GSM8901612 Mel-TIL-026_RNA-seq
- GSM8901613 Mel-TIL-030_RNA-seq
- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma, rna-seq
- GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
- GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
- GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares melanoma
- GSE12391 Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi 114 samples same disease briefing · shares melanoma
- GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma
- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
- GSE91061 Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy 109 samples same disease briefing
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.