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Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.

GSE311240 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2026/07/07 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 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.
Summary (written by the submitters)
Reference annotations incompletely capture the transcript diversity of the human brain, obscuring the genetic architecture of neurodevelopmental disorders. Here, we integrated deep long-read RNA sequencing and proteomics in iPSC-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half novel) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences.
Read the full summary ↓
Crucially, population genetics demonstrate that novel splice sites are under strong negative selection, comparable to known missense mutations, confirming their functional importance. During neuronal maturation, we observe that ASD risk genes undergo dynamic isoform switching, including microexon usage and intron retention, that remodels key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between splicing and polyadenylation, revealing complex regulatory logic. Critically, our atlas enables variant reinterpretation in ASD, demonstrating that an isoform-centric view is essential for interpreting pathogenic variation in neurodevelopment.
This dataset
Open GSE311240 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 GSE311240_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 PRJNA1368846 and SRA study SRP648286. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly in triplicate
Induced pluripotent stem cells ×3 Intermediate cells replicate 1 derived from i… ×3 Intermediate cells replicate 2 derived from i… ×3 Neurons replicate 1 derived from iPSC ×3 Neurons replicate 2 derived from iPSC ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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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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.