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GSE270594 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/09/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
MITF, TFEB, and TFE3 drive distinct adaptive gene expression programs and immune infiltration in melanomaCell reports · 2025
Summary (written by the submitters)
Unlike MITF-M, the melanocyte-specific isoform of MITF, TFEB, TFE3 and non-melanocyte MITF isoforms are regulated primarily by mTORC1-mediated phosphorylation at the lysosome that promotes their cytoplasmic retention. As low levels of glucose or amino acids trigger down-regulation of MITF, it is likely that on nutrient limitation some MITF functions are assumed by TFE3 and TFEB, enabling MITFLow melanoma cells to survive and proliferate. The role TFEB and TFE3 in melanoma biology and their impact on MITF-driven proliferation is poorly understood.
Published in
MITF, TFEB, and TFE3 drive distinct adaptive gene expression programs and immune infiltration in melanoma
Dias D, Oliveira E, Martí-Díaz R et al. · Cell reports 2025 · PMID 41275493 · doi:10.1016/j.celrep.2025.116499
This dataset
Open GSE270594 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 GSE270594_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 PRJNA1127539 and SRA study SRP515831. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41275493) ↗
Study design
8 conditions, mostly in triplicate
B16F10-luc2 ×3 B16F10-luc2_Mitf_sKO ×3 B16F10-luc2_Tfe3_sKO ×3 B16F10-luc2_Tfeb_sKO ×3 B16F10-luc2_Mitf_Tfe3_dKO ×3 B16F10-luc2_Mitf_Tfeb_dKO ×3 B16F10-luc2_Tfeb_Tfe3_dKO ×3 B16F10-luc2_Mitf_Tfeb_Tfe3_tKO ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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