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Gene expression analysis on melanoma cell lines and effects of NIPBL depletion

GSE263454 Homo sapiens (human) RNA-seq (gene expression) 22 samples Submitted 2025/05/01 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 22 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)
Samples
22 samples: 10 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
Disruption of TAD hierarchy promotes LTR co-option in cancerNature genetics · 2025
Summary (written by the submitters)
Gene expression was studied in melanoma cell lines with (SKMEL-23 and SKMEL-1128) or without (A375 and CLOL800) ALKATI expression. Effects on gene expression was also analyzed after knockdown of NIPBL in melanoma cell lines 501mel, COLO800 and A375
Published in
Disruption of TAD hierarchy promotes LTR co-option in cancer
Wong EWP, Sahin M, Yang R et al. · Nature genetics 2025 · PMID 40588507 · doi:10.1038/s41588-025-02239-6
This dataset
Open GSE263454 in finder → Find more human 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 GSE263454_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 PRJNA1097571 and SRA study SRP525129. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40588507) ↗
Study design
10 conditions, mostly in duplicate
RNAseq_SKMEL ×2 RNAseq_501mel shLuc 6D ×2 RNAseq_501mel shNIPBL_#1 6D ×2 RNAseq_501mel shNIPBL_#2 6D ×2 RNAseq_COLO800 shLuc 6D ×2 RNAseq_COLO800 shNIPBL_#1 6D ×2 RNAseq_COLO800 shNIPBL_#2 6D ×2 RNAseq_A375 shLuc 6D ×2 +4 more

Supports a between-group comparison across 20 samples.

How we read this: 10 replicated groups read from 22 sample titles; they account for 20 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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