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Propofol Differentially Modulates Neurodevelopmental Processes in Region-Specific Human Brain Organoids

GSE287509 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/01/16 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × hCS vs 3 × hCS-pro vs 3 × hSS vs 3 × hSS-proGroups 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
Anesthetic-induced neurodevelopmental changes with region-specific responses to propofol in forebrain organoidsStem cell reports · 2026
Summary (written by the submitters)
Background: Propofol, a commonly used anesthetic, has controversial effects on fetal neurodevelopment. This study explores the hypothesis that propofol exerts region- and time-specific effects on distinct brain regions, with implications for clinical safety during pregnancy. Methods: Human dorsal forebrain (hCS) and ventral forebrain (hSS) organoids were exposed to 20 μM propofol for 6 hours on day 11 (D11).
Read the full summary ↓
Morphological changes, including diameter and surface area, were analyzed at D11, D18, and D25. Immunofluorescence and PCR analyses were conducted at early (D18/25), middle (D40), and late stages (D80) post-intervention. Electrophysiological analyses were performed from D40 to D70, and bulk RNA-seq analyses were conducted on organoids at D18 to assess transcriptional changes. Results: Propofol exhibited region-specific effects on hCS and hSS organoids. In hCS organoids, excitatory neuron markers were consistently reduced at all stages, while in hSS organoids, inhibitory neuron markers were transiently affected at early stages but recovered over time. Electrophysiological analysis revealed increased action potential incidence in hCS organoids, indicating enhanced neuronal excitability despite decreased excitatory neuron markers. Transcriptomic analysis demonstrated metabolic reprogramming, including improved oxygen supply and a shift toward efficient aerobic pathways, alongside modulation of developmental signaling pathways. Conclusions: Propofol exerts region- and time-specific effects on neural development, involving both neuronal maturation and metabolic adaptation. These findings emphasize the need for careful evaluation of anesthetic safety in pregnant women and its potential long-term neurodevelopmental consequences.
Published in
Anesthetic-induced neurodevelopmental changes with region-specific responses to propofol in forebrain organoids
She HQ, Fang CL, Li QJ et al. · Stem cell reports 2026 · PMID 41861818 · doi:10.1016/j.stemcr.2026.102859
This dataset
Open GSE287509 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 GSE287509_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 PRJNA1213116 and SRA study SRP558550. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41861818) ↗
Study design
3 × hCS vs 3 × hCS-pro vs 3 × hSS vs 3 × hSS-pro

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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