GEO series

Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ]

GSE282552 Homo sapiens (human) Single-nucleus RNA-seq 18 samples Submitted 2025/12/01 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 18 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 18 samples: 11 × humanDLPFC_Control vs 7 × humanDLPFC_SchizophreniaGroups 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)

Over the past 15+ years, genetic studies have been notably successful in revealing the architecture of multiple psychiatric disorders, including schizophrenia. It is now widely acknowledged that schizophrenia is highly polygenic, consisting of both common variants of unknown significance, identified through genome-wide association studies (GWAS), and rare CNVs and coding variants.

Read the full summary ↓

Despite these advances, the underlying mechanisms of specific genes implicated by GWAS are not well understood. Multiple lines of evidence implicate alternative splicing in the pathophysiology of schizophrenia. Single-nucleotide polymorphisms (SNPs) within implicated schizophrenia loci could alter isoform diversity and abundances which may not be reflected in a typical differential expression study. Hence, we generated a comprehensive isoform survey of postmortem human dorsolateral prefrontal cortex (DLPFC) from schizophrenia cases and neurotypical controls to identify case-control isoform-level differences. We developed an analysis pipeline that combines the strengths of PacBio SMRT long-read RNA sequencing in conducting a detailed isoform census with the capacity of short-read RNA sequencing for the quantification of isoform abundances. From several hundred thousand discovered long-read isoforms we curated a transcriptome with tens of thousands of high confidence novel isoforms. We then identified differential isoform usage (DIU) genes using a combination of established and in-house pipelines that enables case-control comparisons. Many of these novel isoforms are differentially expressed in schizophrenia DLPFC vs neurotypical controls. Differentially expressed genes are enriched in gene sets related to synaptic structure and function, RNA binding and splicing, as well as cell types previously implicated in schizophrenia, including cortical excitatory neurons, medium spiny neurons, and pyramidal CA1 neurons. Publicly available splicing data, genotyping, proteomics, and single nucleus sequencing results verify and support our results.

This dataset

Open GSE282552 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 GSE282552_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1189123 and SRA study SRP546823. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

11 × humanDLPFC_Control vs 7 × humanDLPFC_Schizophrenia

Supports a between-group comparison across 18 samples.

How we read this: 2 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

GSM8645902 humanDLPFC_Control_1 humanDLPFC_Control
GSM8645903 humanDLPFC_Control_2 humanDLPFC_Control
GSM8645904 humanDLPFC_Control_3 humanDLPFC_Control
GSM8645905 humanDLPFC_Control_4 humanDLPFC_Control
GSM8645906 humanDLPFC_Control_5 humanDLPFC_Control
GSM8645907 humanDLPFC_Control_6 humanDLPFC_Control
GSM8645908 humanDLPFC_Control_7 humanDLPFC_Control
GSM8645909 humanDLPFC_Control_8 humanDLPFC_Control
GSM8645910 humanDLPFC_Control_9 humanDLPFC_Control
GSM8645911 humanDLPFC_Control_10 humanDLPFC_Control
GSM8645912 humanDLPFC_Control_11 humanDLPFC_Control
GSM8645913 humanDLPFC_Schizophrenia_1 humanDLPFC_Schizophrenia
GSM8645914 humanDLPFC_Schizophrenia_2 humanDLPFC_Schizophrenia
GSM8645915 humanDLPFC_Schizophrenia_3 humanDLPFC_Schizophrenia
GSM8645916 humanDLPFC_Schizophrenia_4 humanDLPFC_Schizophrenia
GSM8645917 humanDLPFC_Schizophrenia_5 humanDLPFC_Schizophrenia
GSM8645918 humanDLPFC_Schizophrenia_6 humanDLPFC_Schizophrenia
GSM8645919 humanDLPFC_Schizophrenia_7 humanDLPFC_Schizophrenia

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GSE310131 Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms 15 samples shares long-read, isoform
GSE311240 Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms. 15 samples shares long-read, isoform
GSE271384 The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [ATAC-seq] 20 samples shares differential, isoform

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