← BioTransfer GEO Dataset Finder
GEO series

Systematic multivariate analysis of chromatin complex dependencies reveals Set1C/COMPASS as a melanoma-enriched epigenetic vulnerability

GSE324132 Homo sapiens (human) Single-cell RNA-seq 24 samples Submitted 2026/07/18 Platform GPL30173
At a glance

Single-cell RNA-seq · human · 24 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
MelanomaThis series is part of our curated briefing on it.
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.
Summary (written by the submitters)
Melanoma exhibits lineage-specific transcriptional programs that may create selective epigenetic vulnerabilities. To identify melanoma-enriched chromatin dependencies, we analyzed large-scale CRISPR gene-dependency data from cancer cell lines together with curated epigenetic complex annotations. This analysis identified the H3K4 methyltransferase complex Set1C/COMPASS as a melanoma-enriched dependency, with CXXC1 emerging as a selectively required subunit in a subset of melanoma cell lines.
Read the full summary ↓
Functional validation using iterative indirect immunofluorescence imaging (4i) and quantitative single-cell analysis showed that siRNA-mediated depletion of CXXC1 reduced global H3K4me3 levels and impaired proliferation in CXXC1-dependent melanoma cell lines. To define the transcriptional consequences of Set1C/COMPASS perturbation, we performed bulk RNA sequencing (RNA-seq) following siRNA-mediated depletion of CXXC1. Four melanoma cell lines (UACC62, LOXIMVI, MALME3M, and SKMEL28) were transfected with siCXXC1 or a non-targeting control (siNTC), with three independent biological replicates per condition. RNA was harvested 96 hours post-transfection and sequenced to quantify genome-wide expression changes associated with CXXC1 depletion. Transcriptomic analysis revealed suppression of proliferation-associated gene expression programs, including MYC and E2F target signatures, in CXXC1-dependent melanoma cell lines.
This dataset
Open GSE324132 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 GSE324132_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1433494 and SRA study SRP681757. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
Cell line UACC62, nontargeting control siRNA, ×3 Cell line UACC62, CXXC1 siRNA, ×3 Cell line MALME3M, nontargeting control siRNA, ×3 Cell line MALME3M, CXXC1 siRNA, ×3 Cell line LOXIMVI, nontargeting control siRNA, ×3 Cell line LOXIMVI, CXXC1 siRNA, ×3 Cell line SKMEL28, nontargeting control siRNA, ×3 Cell line SKMEL28, CXXC1 siRNA, ×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
More Melanoma datasets

Search all human RNA-seq 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.