Published July 13, 2025
| Version v2
Dataset
Open
Source Data and Scripts - Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols
Authors/Creators
- 1. Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- 2. Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- 3. Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- 4. Institute of Molecular Pathology (IMP), Vienna, Austria
- 5. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- 6. Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
- 7. Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- 8. Ludwig Boltzmann Institute for Network Medicine at the University of Vienna, Vienna, Austria
- 9. Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
- 10. Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
Description
Source data and scripts associated with the manuscript "Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols" (Naas et al. 2024, bioRxiv, DOI: 10.1101/2024.11.15.623576). Corresponding scripts to reproduce all figures and tables presented in the manuscript are also available on https://github.com/jn-goe/brain_organoids_four_protocols.
The therein introduced NEST-Score is available as R package on https://github.com/jn-goe/NESTScore.
The interactive Shiny App data explorer is available on https://vienna-brain-organoid-explorer.vbc.ac.at.
Other
We integrated our in vitro data with two in vivo reference datasets
- Braun, et al. 'Comprehensive cell atlas of the first-trimester developing human brain.' Science (2023) (see also corresponding GitHub repository), and
- Bhaduri, et al. 'An atlas of cortical arealization identifies dynamic molecular signatures.' Nature (2021)
to obtain respective UMAP coordinates and metadata.
Files
brain_organoids_v0.0.2.zip
Additional details
Related works
- Is supplement to
- https://github.com/jn-goe/brain_organoids_four_protocols (URL)
- Requires
- https://github.com/jn-goe/NESTScore (URL)
Software
- Programming language
- R