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Pathogenic PPP2R5D variants alters the transcriptome of patient iPSC-derived glutamatergic neurons

GSE266958 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/05/19 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 6 × E198K_patient, DIV 14 neurons vs 6 × E198K_corrected, DIV14 neurons vs 3 × E420K_corrected, DIV14 neurons vs 3 × E420K_patient, DIV 14 neuronsGroups 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
Pathogenic PPP2R5D variants disrupt neuronal development and neurite outgrowth in patient-derived neurons that are reversed by allele-specific knockdownHGG advances · 2025
Summary (written by the submitters)
The pathogenic PPP2R5D E198K and E420K variant alters the transcriptome of patient iPSC-derived cortical neurons
Published in
Pathogenic PPP2R5D variants disrupt neuronal development and neurite outgrowth in patient-derived neurons that are reversed by allele-specific knockdown
Young RE, Zuccaro MV, LeDuc CA et al. · HGG advances 2025 · PMID 40340253 · doi:10.1016/j.xhgg.2025.100450
This dataset
Open GSE266958 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 GSE266958_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 PRJNA1108776 and SRA study SRP506210. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40340253) ↗
Study design
6 × E198K_patient, DIV 14 neurons vs 6 × E198K_corrected, DIV14 neurons vs 3 × E420K_corrected, DIV14 neurons vs 3 × E420K_patient, DIV 14 neurons

Supports a between-group comparison across 18 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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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