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Melanoma plasticity is regulated by mTOR-mediated crosstalk between MITF and TFE3

GSE273815 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2025/03/20 Platform GPL34284Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Topic
MelanomaThis series is part of our curated briefing on it.
Samples
56 samples: 25 conditions, mostly in duplicateGroups 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
Antagonistic roles for MITF and TFE3 in melanoma plasticityCell reports · 2025
Summary (written by the submitters)
ATAC-seq performed to identify chromatin accessibility across the genome. CUT&RUN-seq was performed to identify and compare transcription factor and histone mark occupancy across genome of WT and MITF and TFE3 KO cells.
Published in
Antagonistic roles for MITF and TFE3 in melanoma plasticity
Chang J, Campbell-Hanson KR, Vanneste M et al. · Cell reports 2025 · PMID 40138313 · doi:10.1016/j.celrep.2025.115474
This dataset
Open GSE273815 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE273815_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1143400 and SRA study SRP523870. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40138313) ↗
Study design
25 conditions, mostly in duplicate
SKMEL28, wild type, ATAC seq, ×4 SKMEL28, Anti-MITF, CUT&RUN, biol ×4 SKMEL28, Anti-IgG, CUT&RUN, biol ×3 SKMEL28, MITFKO, ATAC seq, ×2 SKMEL28, Anti-TFE3, CUT&RUN, biol ×2 D2, Anti-MITF, CUT&RUN, biol ×2 D2, Anti-TFE3, CUT&RUN, biol ×2 D2, Anti-IgG, CUT&RUN, biol ×2 +18 more

Supports a between-group comparison across 55 samples.

How we read this: 25 replicated groups read from 56 sample titles; they account for 55 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

+ 16 more — browse all 56 samples with per-sample file links →

More Melanoma datasets

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.