GEO series

Synthetic RIG-I agonist-mediated cancer immunotherapy synergizes with MAP-Kinase inhibition against BRAF mutated melanoma

GSE268982 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2024/07/26 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 15 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: Homo sapiens (human)
Topic: MelanomaThis series is part of our curated briefing on it.
Samples: 15 samples: 15 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.

Summary (written by the submitters)

The implementations of targeted molecular therapies and immunotherapy in melanoma vastly improved the therapeutic outcome in patients with limited efficacy of surgical intervention. Nevertheless, a large fraction of melanoma patients still remains refractory or acquires resistance to these new forms of treatment, illustrating a need for improvement.

Read the full summary ↓

Here we report that the clinically relevant combination of MAP kinase inhibitors Dabrafenib and Trametinib synergizes with RIG-I agonist-induced immunotherapy to kill BRAF-mutated human and mouse melanoma cells. Kinase inhibition did not compromise the agonist-induced innate immune response of the RIG-I pathway in host immune cells. In a melanoma transplantation mouse model, the triple therapy outperformed the individual therapies. Our study suggests that targeted activation of RIG-I with its synthetic ligand 3pRNA could vastly improve tumor control in a substantial fraction of melanoma patients receiving MAP kinase inhibitors.

This dataset

Open GSE268982 in finder → Find more human RNA-seq datasets → Melanoma landscape →

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 GSE268982_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 PRJNA1119558 and SRA study SRP511470. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 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

GSM8304055 Melanoma human, no stimulation, no inhibitor, 24h, rep1
GSM8304056 Melanoma human, transfection control, no inhibitor, 24h, rep1
GSM8304057 Melanoma human, 3pRNA, no inhibitor, 24h, rep1
GSM8304058 Melanoma human, no stimulation, dabrafenib, 24h, rep1
GSM8304059 Melanoma human, transfection control, dabrafenib, 24h, rep1
GSM8304060 Melanoma human, 3pRNA, dabrafenib, 24h, rep1
GSM8304061 Melanoma human, no stimulation, trametinib, 24h, rep1
GSM8304062 Melanoma human, transfection control, trametinib, 24h, rep1
GSM8304063 Melanoma human, 3pRNA, trametinib, 24h, rep1
GSM8304064 Melanoma human, no stimulation, vehicle, 24h, rep1
GSM8304065 Melanoma human, transfection control, vehicle, 24h, rep1
GSM8304066 Melanoma human, 3pRNA, vehicle, 24h, rep1
GSM8304067 Melanoma human, no stimulation, dabrafenib+trametinib, 24h, rep1
GSM8304068 Melanoma human, transfection control, dabrafenib+trametinib, 24h, rep1
GSM8304069 Melanoma human, 3pRNA, dabrafenib+trametinib, 24h, rep1

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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.