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Splicing and gene expression changes in cell lines treated with splicing switching oligonucleotide targeting TRA2B

GSE231555 Homo sapiens (human) RNA-seq (gene expression) 46 samples Submitted 2024/12/20 Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 46 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
GlioblastomaThis series is part of our curated briefing on it.
Samples
46 samples: 14 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
Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effectsNature communications · 2025
Summary (written by the submitters)
RNA-sequencing data from MDA-MB231 breast cancer cells, U87MG glioblastoma cells, and mouse breast cancer PDX models treated with antisense oligonucleotides targeting exon 2 of TRA2B. Additionally, RNA-sequencing data from MDA-MB231 breast cancer cells and U87MG glioblastoma cells treated with siRNAs targeting TRA2B. RNA-sequencing data from MDA-MB231 breast cancer cells nad U87MG glioblastoma cells treated with antisense oligonucleotides targeting exon 2 of TRA2B.
Published in
Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects
Leclair NK, Brugiolo M, Park S et al. · Nature communications 2025 · PMID 39955311 · doi:10.1038/s41467-025-56913-8
This dataset
Open GSE231555 in finder → Find more human RNA-seq datasets → Glioblastoma 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 GSE231555_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 PRJNA966982 and SRA study SRP436109. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39955311) ↗
Study design
14 conditions, mostly in triplicate
ASOPDX_CTL ×5 ASOPDX_1570 ×5 MDA-MB231_ASO-CTL ×3 MDA-MB231_ASO-1570 ×3 U87MG_ASO-CTL ×3 U87MG_ASO-1570 ×3 MB231_50nM_CTL ×3 MB231_50nM_1570 ×3 +6 more

Supports a between-group comparison across 46 samples.

How we read this: 14 replicated groups read from 46 sample titles; they account for 46 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

+ 6 more — browse all 46 samples with per-sample file links →

More Glioblastoma 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.