GEO series

SETD1A Regulates Psychiatric Gene Networks Involved in Genomic Stability and Synaptic Function in Rare and Sporadic Schizophrenia [bulk RNA-seq]

GSE293155 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/09/15 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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: SETD1A regulates psychiatric gene networks involved in genomic stability and synaptic function in rare and sporadic schizophreniaNature communications · 2025

Summary (written by the submitters)

Rare loss-of-function (LoF) mutations in SETD1A are associated with schizophrenia (SCZ). However, how SETD1A haploinsufficiency leads to SCZ-associated phenotypes and its relevance to patients without these rare mutations is unknown. Here, we identify SETD1A bound loci and regulated genes in human prenatal cortex and isogenic pluripotent stem cell-derived neuronal models engineered with SETD1A LoF variants, including the most common patient mutation.

Read the full summary ↓

SETD1A preferentially binds the promoters of SCZ and Bipolar risk loci that regulate chromatin remodeling, DNA repair, and synaptic function. Additionally, SETD1A binds to DNA damage prone sites in neural progenitor cells and postmitotic neurons. SETD1A haploinsufficiency causes accelerated neurogenesis, reduced neuronal complexity, and DNA damage accumulation in postmitotic neurons that is rescued by inhibiting the H3K4me2/3 demethylase KDM5. In postmortem SCZ cortical tissue, individuals who lack SETD1A mutations exhibit reduced SETD1A expression, associated with downregulation of SETD1A-regulated genes, implicating SETD1A-H3K4me dysfunction in sporadic SCZ cases. Therefore, restoring the SETD1A-H3K4me epigenetic imbalance may benefit individuals with SETD1A haploinsufficiency as well as a broader psychiatric population without SETD1A mutations.

Published in

SETD1A regulates psychiatric gene networks involved in genomic stability and synaptic function in rare and sporadic schizophrenia

Sawada T, Feltrin AS, Wang Y et al. · Nature communications 2025 · PMID 41422157 · doi:10.1038/s41467-025-67154-0

This dataset

Open GSE293155 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 GSE293155_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 PRJNA1242963 and SRA study SRP573713. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41422157) ↗

Study design

24 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. 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

GSM8877576 LIBD2c1_CM130_24_NPC
GSM8877577 LIBD7c6_CA137_109_NPC
GSM8877578 LIBD7c6_CM130_78_NPC
GSM8877579 LIBD2c1_CA137_11_NPC
GSM8877580 LIBD2c1_CM130_9_NPC
GSM8877581 LIBD7c6_CA137_37_NPC
GSM8877582 LIBD7c6_CA137_69_NPC
GSM8877583 LIBD7c6_CM130_30_NPC
GSM8877584 LIBD2c1_CM130_11_NPC
GSM8877585 LIBD2c1_CM130_51_NPC
GSM8877586 LIBD7c6_CA137_43_NPC
GSM8877587 LIBD7c6_CA137_52_NPC
GSM8877588 LIBD2c1_CM130_24_Neuron_4wks
GSM8877589 LIBD7c6_CA137_109_Neuron_4wks
GSM8877590 LIBD7c6_CM130_78_Neuron_4wks
GSM8877591 LIBD2c1_CA137_11_Neuron_4wks
GSM8877592 LIBD2c1_CM130_9_Neuron_4wks
GSM8877593 LIBD7c6_CA137_37_Neuron_4wks
GSM8877594 LIBD7c6_CA137_69_Neuron_4wks
GSM8877595 LIBD7c6_CM130_30_Neuron_4wks
GSM8877596 LIBD2c1_CM130_11_Neuron_4wks
GSM8877597 LIBD2c1_CM130_51_Neuron_4wks
GSM8877598 LIBD7c6_CA137_43_Neuron_4wks
GSM8877599 LIBD7c6_CA137_52_Neuron_4wks

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GSE304368 Schizophrenia risk gene ZNF536 modulates retinoic acid response and neuronal gene networks in SH-SY5Y cells 18 samples shares schizophrenia, networks
GSE282552 Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ] 18 samples shares schizophrenia, synaptic
GSE258789 BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A (RNA-seq) 20 samples shares setd1a
GSE273826 Non-catalytic role of SETD1A promotes gastric cancer cell proliferation through the E2F4-TAF6 axis in the cell cycle 30 samples shares setd1a
GSE273824 Non-catalytic role of SETD1A promotes gastric cancer cell proliferation through the E2F4-TAF6 axis in the cell cycle (ChIP-seq) 24 samples shares setd1a

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