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Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory

GSE301725 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2025/08/20 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 13 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
13 samples: 3 × Brain Microphysiological Systems, Week 8, 24_VC vs 3 × Brain Microphysiological Systems, Week 8, LD_W8 vs 3 × Brain Microphysiological Systems, Week 12, LD_W12 vs 2 × Brain Microphysiological Systems, Week 13, run29 W13 2Groups 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
Human neural organoid microphysiological systems show the building blocks necessary for basic learning and memoryCommunications biology · 2025
Summary (written by the submitters)
Brain Microphysiological Systems including neural organoids derived from human induced pluripotent stem cells offer a unique lens to study the intricate workings of the human brain. This paper investigates the foundational elements of learning and memory in neural organoids, by quantifying immediate early gene expression in response to chemical modulation, input-specific short- and long-term synaptic plasticity, neuronal network dynamics, connectivity, and criticality to demonstrate the utility of these organoids in basic science research.
Read the full summary ↓
Neural organoids showed synapse formation, glutamatergic and GABAergic receptor expression, immediate early gene expression basally and evoked, functional connectivity, criticality, and synaptic plasticity in response to theta-burst stimulation. In addition, pharmacological interventions on GABAergic and glutamatergic receptors, and input-specific theta-burst stimulation further shed light on the capacity of neural organoids to mirror synaptic modulation, short- and long-term potentiation and depression, demonstrating their potential as tools for studying neurophysiological and neurological processes and informing therapeutic strategies for diseases.
Published in
Human neural organoid microphysiological systems show the building blocks necessary for basic learning and memory
Alam El Din DM, Moenkemoeller L, Loeffler A et al. · Communications biology 2025 · PMID 40819006 · doi:10.1038/s42003-025-08632-5
This dataset
Open GSE301725 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 GSE301725_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 PRJNA1287486 and SRA study SRP598570. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40819006) ↗
Study design
3 × Brain Microphysiological Systems, Week 8, 24_VC vs 3 × Brain Microphysiological Systems, Week 8, LD_W8 vs 3 × Brain Microphysiological Systems, Week 12, LD_W12 vs 2 × Brain Microphysiological Systems, Week 13, run29 W13 2

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 11 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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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.