MiSTR_atlas

Code associated with the bioRxiv manuscript

Frozen manuscript version (bioRxiv):
https://www.biorxiv.org/content/10.1101/2025.05.23.655442v2

Snapshot of the code associated with the manuscript:
https://github.com/gauravsinghrathore/MiSTR_atlas/tree/biorxiv_version

Active development version: code associated with submitted manuscript for reviewers

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Title

Mapping early patterning events in human neural development using an in vitro microfluidic stem cell model

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Abstract

Stem cell models can provide insights into human brain development at embryonic stages which are normally inaccessible. We applied a previously developed Microfluidic Stem Cell Regionalisation (MiSTR) model to recapitulate rostro-caudal patterning of the human neural tube through a WNT activation (WNTa) gradient. Single cell transcriptomics of rostro-caudal and dorso-ventral gradient-patterned MiSTR, showed that rostro-caudal subtypes of the forebrain and hindbrain were regionally specified and fate-determined already during the late epiblast stage, several days before onset of neuralisation. Rostral cells were characterised by expression of HESX1 and SHISA2 during pre-neuralisation and PAX6 during early neuralisation, whereas caudal cells expressed FST and HOXA1 during pre-neuralisation and SOX1 as the dominant neuralising factor. In contrast to the early rostro-caudal specification, response to ventralisation in telencephalic progenitors was developmentally delayed and occurred around day 9. We further uncovered temporal events in human midbrain-hindbrain boundary formation and ventral forebrain patterning, contributing new knowledge on early human neural region-specification.

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Repository structure

This repository is organized into two primary directories:

figures
Contains scripts and notebooks used to generate the figures presented in the manuscript.

preprocessing
Contains scripts and notebooks used for sequencing data preprocessing.

Detailed instructions for executing the notebooks and installing required tools are provided within the respective folders.

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Interactive and downloadable data resource

An interactive version of the MiSTR dataset is available through the UCSC Cell Browser:

https://cells.ucsc.edu/?ds=neural-tube-organoids

bigWig files for Bulk ATAC seq experiments https://www.dropbox.com/scl/fo/jw0d5ogk6iu4ssdpdxrr7/AOWOQqfohj2hisEJudUv3UY?rlkey=quci6c7tp994xdwo03rulll59&st=yppg93nm&dl=0