Single cell RNAseq data of human neurons, Bouwen et al Nat Comm 2025

Brain tumor patients often suffer from epilepsy, but the underlying neuronal changes leading to this neurological symptom are not well understood. This study examined the transcriptomic profiles of human cortical neurons collected from brain tumor patients with or without seizures. The goals of the study were to identify the molecular identities of the recorded neurons and confirm that they are layer 2/3 pyramidal neurons rather than neuron-like tumor cells; and to compare the differential gene expression profiles between patients with and without epilepsy. For each patient, cortical neurons were rapidly isolated from surgically resected tissue and prepared using the Smart-seq2 protocol. Samples from 12 patients were sequenced on an Illumina HiSeq 2500 platform to generate their transcriptomic profiles.

Type: Transcriptome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001979	These documents contain the patch seq data presented in the Bouwen et al Nat Comm 2025. Human brain samples were gathered during surgery, neurons were isolated using patch clamp glass pipette. Isolated cells were processed using Smartseq2 pipeline, and sequenced using an Illumina 2500. Files are formatted in fastq format. There are a total of 12 patient samples, each with 2 replication runs.	Illumina HiSeq 2500	12

Publications	Citations
Aberrant neural activity in the peritumoral cortex underlies the progression of tumor-associated seizures. Bouwen BLJ, Bolleboom A, Tang Y, Yu Z, van der Stap A, van Rij JA, van Dis V, Dirven CMF, De Zeeuw CI, van Tellingen O, Liu JK, Vincent AJPE, Gao Z. Nat Commun 16: 2025 10846	0