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YAP1/TAZ knockdown in melanoma

GSE259388 Homo sapiens (human) RNA-seq (gene expression) 54 samples Submitted 2025/07/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 54 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
54 samples: 18 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
Targeting TAZ-TEAD in minimal residual disease enhances the duration of targeted therapy in melanoma modelsNature communications · 2025
Summary (written by the submitters)
Targeted therapies in cancer are limited by cells exhibiting drug tolerance. We aimed to target drug tolerance in order to delay the development of acquired resistance. In melanoma, tolerance to MAPK pathway inhibitors is associated with loss of SOX10 and an enhanced TEAD transcriptional program. We show that loss of SOX10 is sufficient to up-regulate TEAD targets with dependence on the co-activator, TAZ.
Read the full summary ↓
Active TAZ was sufficient to mediate tolerance to BRAF inhibitors and MEK inhibitors. We developed novel covalent inhibitors, OPN-9643 and OPN-9652, designed to target the central palmitate binding pocket of TEADs. In SOX10-deficient cells, OPN-9643 and OPN-9652 reduced TEAD-dependent reporter activity and expression of TEAD targets, CTGF and CYR61. OPN-9643 and OPN-9652 treatment enhanced the inhibitory effects of MAPK-targeted therapies in 2D and 3D growth assays and reversed tolerance mediated by active TAZ. In vivo, OPN-9652 delayed the onset of acquired resistance to BRAF inhibitors and MEK inhibitors from minimal residual disease. Thus, TAZ-TEAD activity plays an important role in melanoma drug tolerance and the development of acquired resistance.
Published in
Targeting TAZ-TEAD in minimal residual disease enhances the duration of targeted therapy in melanoma models
Ott CA, Purwin TJ, Chen PY et al. · Nature communications 2025 · PMID 41193428 · doi:10.1038/s41467-025-64682-7
This dataset
Open GSE259388 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 GSE259388_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 PRJNA1081396 and SRA study SRP492148. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41193428) ↗
Study design
18 conditions, mostly in triplicate
A375_nosiRNA ×3 A375_siCTRL ×3 A375_siTAZ1 ×3 A375_siTAZ2 ×3 A375_siYAP1 ×3 A375_siYAP2 ×3 218_nosiRNA ×3 218_siCTRL ×3 +10 more

Supports a between-group comparison across 54 samples.

How we read this: 18 replicated groups read from 54 sample titles; they account for 54 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

+ 14 more — browse all 54 samples with per-sample file links →

More Melanoma datasets

Search all human RNA-seq datasets in GEO →

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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.