GEO series

Engineered 3D Immuno-Glial-Neurovascular Human miBrain Model

GSE308670 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2025/09/24 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 27 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: 27 samples: 27 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: Engineered 3D immuno-glial-neurovascular human miBrain modelProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

Patient- specific, human-based cellular models integrating a biomimetic blood–brain barrier, immune, and myelinated neuron components are critically needed to enable accelerated, translationally relevant discovery of neurological disease mechanisms and interventions.

Read the full summary ↓

To construct a human cell-based model that includes these features and all six major brain cell types needed to mimic disease and dissect pathological mechanisms, we have constructed, characterized, and utilized a multicellular integrated brain (miBrain) immuno-glial-neurovascular model by engineering a brain-inspired 3D hydrogel and identifying conditions to coculture these six brain cell types, all differentiated from patient induced pluripotent stem cells. miBrains recapitulate in vivo–like hallmarks inclusive of neuronal activity, functional connectivity, barrier function, myelin-producing oligodendrocyte engagement with neurons, multicellular interactions, and transcriptomic profiles. We implemented the model to study Alzheimer’s Disease pathologies associated with APOE4 genetic risk. APOE4 miBrains differentially exhibit amyloid aggregation, tau phosphorylation, and astrocytic glial fibrillary acidic protein. Unlike the coemergent fate specification of glia and neurons in other organoid approaches, miBrains integrate independently differentiated cell types, a feature we harnessed to identify that APOE4 in astrocytes promotes neuronal tau pathogenesis and dysregulation through crosstalk with microglia.

Published in

Engineered 3D immuno-glial-neurovascular human miBrain model

Stanton AE, Bubnys A, Agbas E et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 41105712 · doi:10.1073/pnas.2511596122

This dataset

Open GSE308670 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 GSE308670_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 PRJNA1332429 and SRA study SRP624169. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41105712) ↗

Study design

27 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 27 sample titles: 27 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

GSM9251027 miBrain microglia A
GSM9251028 miBrain microglia B
GSM9251029 miBrain microglia C
GSM9251030 monoculture microglia A
GSM9251031 monoculture microglia B
GSM9251032 monoculture microglia C
GSM9251033 monoculture BMEC A
GSM9251034 monoculture BMEC B
GSM9251035 monoculture BMEC C
GSM9251036 miBrain astrocyte A
GSM9251037 miBrain astrocyte B
GSM9251038 miBrain astrocyte C
GSM9251039 monoculture astrocyte A
GSM9251040 monoculture astrocyte B
GSM9251041 monoculture astrocyte C
GSM9251042 miBrain oligo A
GSM9251043 miBrain oligo B
GSM9251044 miBrain oligo C
GSM9251045 monoculture oligo A
GSM9251046 monoculture oligo B
GSM9251047 monoculture oligo C
GSM9251048 monoculture neurons A
GSM9251049 monoculture neurons B
GSM9251050 monoculture neurons C
GSM9251051 miBrain neurons A
GSM9251052 miBrain neurons B
GSM9251053 miBrain neurons C

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