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Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [MAPK inhibitors]

GSE232709 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/05/08 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 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
Homo sapiens (human)
Samples
12 samples: 3 × A375_MAPKi-0D vs 3 × A375_MAPKi-2D vs 3 × A375_MAPKi-9D vs 3 × A375_DMSO-0DGroups 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
Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repairNAR cancer · 2024
Summary (written by the submitters)
The translation-dependent effect of amino acid bioavailability on the nature of proteins that cells express could have major consequences on their phenotype. We report that the intracellular concentration decrease of amino acids like aspartate and glutamate in a melanoma cell line exposed to anti-cancer MAPK inhibitors (MAPKi) triggers ribosomal peaks in mRNA regions enriched in codons corresponding to these amino acids and in the translation-dependent degradation of mRNAs encoding proteins enriched in these amino acids.
Read the full summary ↓
Since aspartate- and glutamate-rich proteins are involved in cell proliferation and DNA repair, we propose that MAPKi surviving cells degrade aspartate and glutamate to generate energy which simultaneously decreases their needs through the downregulation of gene products involved in cell proliferation. Moreover, the expression level decrease of aspartate- and glutamate-rich proteins involved in DNA repair increases as a side effect the probability of DNA damages and consequently the emergence of mutated cells in response to MAPKi.
Published in
Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair
Aubé F, Fontrodona N, Guiguettaz L et al. · NAR cancer 2024 · PMID 38690580 · doi:10.1093/narcan/zcae019
This dataset
Open GSE232709 in finder → Find more human 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 GSE232709_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 PRJNA973618 and SRA study SRP438226. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38690580) ↗
Study design
3 × A375_MAPKi-0D vs 3 × A375_MAPKi-2D vs 3 × A375_MAPKi-9D vs 3 × A375_DMSO-0D

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. 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
Datasets on a similar topic

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