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Gene expression profile of antisense oligonucleotide-treated Neural Progenitors from controls and Schinzel-Giedion Syndrome cases

GSE315664 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2026/05/15 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 60 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
60 samples: 10 conditions, mostly with about 9 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
Prevention of hydrocephalus with a small oligonucleotideMolecular therapy : the journal of the American Society of Gene Therapy · 2026
Summary (written by the submitters)
Schinzel-Giedion Syndrome (SGS) is a severe multisystemic disorder caused by germline heterozygous missense mutations in a mutational hotspot found in SETBP1. Hotspot mutations affect the degron region of SETBP1, leading to an increase in SETBP1 protein levels. SGS has a range of neurological symptoms, including severe intellectual disability, frequent seizures, hydrocephalus, distorted neuronal layering, and delayed myelination, leading to early death in children.
Read the full summary ↓
To investigate the gene expression change induced by a gapmer antisense oligonucleotide designed for treatment of SGS, we performed transcriptome analysis of neural progenitor cells from SGS cases and controls treated with an ASO targetting the SETBP1 gene, Inotersen ASO, vehicle-treated cells and untreated cells.
Published in
Prevention of hydrocephalus with a small oligonucleotide
Antonyan L, Bossini L, Zhang X et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2026 · PMID 41612697 · doi:10.1016/j.ymthe.2026.01.034
This dataset
Open GSE315664 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 GSE315664_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 PRJNA1398645 and SRA study SRP659941. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41612697) ↗
Study design
10 conditions, mostly with about 9 replicates each
only_reagent_control ×9 Inotersen_30nM_control ×9 IGUANa-001_ASO_30nM_control ×9 IGUANa-001_ASO_50nM_control ×9 No_transfected_control ×9 only_reagent_patient ×3 Inotersen_30nM_patient ×3 IGUANa-001_ASO_30nM_patient ×3 +2 more

Supports a case/control comparison: 15 samples read as cases, 45 as controls.

How we read this: 10 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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