Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy [bulk RNA-seq]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 12 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
- Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapyNature communications · 2024
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 GSE253092_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 PRJNA1064026 and SRA study SRP483341. 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 12 sample titles: 12 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.
- GSM8013631 17983x1 5526wt
- GSM8013632 17983x2 5527wt
- GSM8013633 17983x3 5548wt
- GSM8013634 17983x4 7657wt
- GSM8013635 17983x5 20681wt
- GSM8013636 17983x6 5588wt
- GSM8013637 17983x19 19836Arf6null
- GSM8013638 17983x20 19837Arf6null
- GSM8013639 17983x21 19846Arf6null
- GSM8013640 17983x22 19959Arf6null
- GSM8013641 17983x23 20001Arf6null
- GSM8013642 17983x24 20570Arf6null
- GSE298273 Tumor-derived RAC1A159V mutation promotes an immunosuppressive tumor microenvironment that represses response to immune checkpoint inhibitor [RNA-Seq] 12 samples shares immunosuppressive, microenvironment, checkpoint
- GSE310501 Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models 31 samples shares microenvironment, checkpoint
- GSE242272 Prostaglandin E2-EP4 signaling shapes immunosuppressive tumor microenvironment in human tumors by suppressing bioenergetics and ribosome biogenesis in infiltrating immune cells [RNA-seq] 18 samples shares immunosuppressive, microenvironment
- GSE275681 MHC II-restricted neoantigen vaccine reverses immune microenvironment and overcomes resistance to immune checkpoint inhibitors in cold tumors. 13 samples shares microenvironment, checkpoint
- GSE301138 Combining p53 mRNA nanotherapy with immune checkpoint blockade reprograms the immune microenvironment for effective cancer therapy 11 samples shares microenvironment, checkpoint
- GSE235598 Systemically inducing trained immunity overcomes solid tumors’ immunosuppressive microenvironment 12 samples shares immunosuppressive, microenvironment
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment
- GSE218173 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [acid] 150 samples shares microenvironment
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.