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RNA sequencing of non-targetting ASOs on HEK293 and U2OS cells

GSE280432 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/05/19 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 9 conditions, mostly with about 4 replicates eachGroups 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
A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular anti-sense oligonucleotide activityNature communications · 2025
Summary (written by the submitters)
Non-targetting ASOs are commonly used as negative controls in vitro and in vivo. Here, we compare the transcriptomic profile of HEK293 and U2OS, following 3 days treatment with 3 different non-targetting ASOs. In those conditions, we did not find major transcriptomic changes following ASO treatment, confirming that they are appropriate negative controls.
Published in
A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular anti-sense oligonucleotide activity
Malong L, Roskosch J, Hager C et al. · Nature communications 2025 · PMID 40588516 · doi:10.1038/s41467-025-61039-y
This dataset
Open GSE280432 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 GSE280432_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 PRJNA1178585 and SRA study SRP541548. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40588516) ↗
Study design
9 conditions, mostly with about 4 replicates each
U2OS-CTRL1 ASO-3 days ×4 U2OS-CTRL2 ASO-3 days ×4 U2OS-CTRL3 ASO-3 days ×4 U2OS-SSO-3 days ×4 U2OS-untreated ×4 HEK293-CTRL1 ASO-3 days ×4 HEK293-CTRL2 ASO-3 days ×4 HEK293-CTRL3 ASO-3 days ×4 +1 more

Supports a between-group comparison across 36 samples.

How we read this: 9 replicated groups read from 36 sample titles; they account for 36 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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