← BioTransfer GEO Dataset Finder
GEO series

MY-COMP, an inhibitor of the transcriptional activity of YAP-B-MYB, identifies NEK2 as a novel mediator of YAP oncogenesis in uveal melanoma cells

GSE227974 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 29 samples Submitted 2024/03/06 Platform GPL18573Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 29 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
Uveal melanomaThis series is part of our curated briefing on it.
Samples
29 samples: 7 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
Inhibition of the YAP-MMB interaction and targeting NEK2 as potential therapeutic strategies for YAP-driven cancersOncogene · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Inhibition of the YAP-MMB interaction and targeting NEK2 as potential therapeutic strategies for YAP-driven cancers
Jessen M, Gertzmann D, Liss F et al. · Oncogene 2024 · PMID 38182898 · doi:10.1038/s41388-023-02926-w
This dataset
Open GSE227974 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Uveal 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 GSE227974_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 PRJNA947598 and SRA study SRP428755. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38182898) ↗
Study design
7 conditions, mostly in triplicate
RNAseq_92_1_siCtrl ×3 RNAseq_92_1_siYAP ×3 RNAseq_92_1_MY_COMP ×3 RNAseq_MCF10A_noDox_noOHT ×3 RNAseq_MCF10A_noDox_withOHT ×3 RNAseq_MCF10A_withDox_noOHT ×3 RNAseq_MCF10A_withDox_withOHT ×3 CnR3_IgG ×1 +7 more

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 29 sample titles; they account for 21 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
More Uveal 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.