GEO series

Phenotypic complexities of rare heterozygous neurexin-1 deletions

GSE288964 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/02/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 10 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: 10 samples: 10 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: Phenotypic complexities of rare heterozygous neurexin-1 deletionsNature · 2025

Summary (written by the submitters)

Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain.

Read the full summary ↓

Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1+/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. For NRXN1 deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration of NRXN1 isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.

Published in

Phenotypic complexities of rare heterozygous neurexin-1 deletions

Fernando MB, Fan Y, Zhang Y et al. · Nature 2025 · PMID 40205044 · doi:10.1038/s41586-025-08864-9

This dataset

Open GSE288964 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 GSE288964_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 PRJNA1220127 and SRA study SRP562084. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40205044) ↗

Study design

10 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 10 sample titles: 10 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

GSM8779930 2607-hCS-6mo
GSM8779931 2607-hSS-6mo
GSM8779932 581-hCS-6mo
GSM8779933 581-hSS-6mo
GSM8779934 641-hCS-6mo
GSM8779935 641-hSS-6mo
GSM8779936 972-hCS-6mo
GSM8779937 972-hSS-6mo
GSM8779938 973-hCS-6mo
GSM8779939 973-hSS-6mo

Datasets on a similar topic

GSE288881 Phenotypic complexities of rare heterozygous neurexin-1 deletions [shNEG_ASO_rnaseq] 54 samples shares neurexin-1, complexities, heterozygous, phenotypic, deletions, rare
GSE288880 Phenotypic complexities of rare heterozygous neurexin-1 deletions [nrxn1_bulk_rnaseq] 53 samples shares neurexin-1, complexities, heterozygous, phenotypic, deletions, rare
GSE291060 Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma [RNA-seq] 164 samples shares phenotypic
GSE273114 Phenotypic and transcriptomic characterisation of the human B cell response to a novel Ebola vaccine regimen (Ad26.ZEBOV, MVA-BN-Filo) 126 samples shares phenotypic
GSE289466 Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [RNA-seq] 98 samples shares phenotypic
GSE297342 Assessing the Effects of Silver Nanoparticles on ARPE-19 Cells via High-Throughput Phenotypic Profiling with the Cell Painting Assay. 88 samples shares phenotypic
GSE233236 Pan-Cancer Single-Cell Dissection Reveals Phenotypically Distinct B Cell Subtypes 78 samples shares phenotypic
GSE267243 Scalable, compressed phenotypic screening using pooled perturbations (PDAC screens) 54 samples shares phenotypic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.