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ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (RNA-Seq)

GSE217803 Mus musculus (mouse) RNA-seq (gene expression) 46 samples Submitted 2024/04/06 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 46 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
46 samples: 44 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
ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunityCell · 2024
Summary (written by the submitters)
Clinical trials have identified ARID1A mutations as enriched among patients who respond favorably to Immune Checkpoint Blockade (ICB) in several solid tumor types independent of microsatellite instability. We show that ARID1A loss in murine models is sufficient to induce anti-tumor immune phenotypes observed in ARID1A mutant human cancers, including increased CD8+ T cell infiltration and cytolytic activity.
Read the full summary ↓
ARID1A deficient cancers upregulated an interferon (IFN) gene expression signature, the ARID1A-IFN signature, associated with increased R-loops and cytosolic single stranded DNA (ssDNA). Overexpression of the R-loop resolving enzyme, RNASEH2B, or cytosolic DNase, TREX1, in ARID1A deficient cells prevented cytosolic ssDNA accumulation and ARID1A-IFN gene upregulation. Further, the ARID1A-IFN signature and anti-tumor immunity were driven by STING dependent Type I IFN signaling, which was required for improved responsiveness of ARID1A mutant tumors to ICB treatment. These findings define a molecular mechanism underlying anti-tumor immunity in ARID1A mutant cancers.
Published in
ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity
Maxwell MB, Hom-Tedla MS, Yi J et al. · Cell 2024 · PMID 38754421 · doi:10.1016/j.cell.2024.04.025
This dataset
Open GSE217803 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE217803_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA900581 and SRA study SRP407497. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38754421) ↗
Study design
44 distinct titles, 2 of them repeated
Total_RNA_seq_sgScr_B16F10 ×2 Total_RNA_seq_sgArid1a_B16F10 ×2

Supports a case/control comparison: 4 samples read as cases, 8 as controls.

How we read this: Read from 46 sample titles: 44 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.

Samples in this study

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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