All data is easily accessible in our Vienna brain organoid data explorer. You can look for your favorite gene or search for entire biological processes based on GO Terms. Check it out: vienna-brain-organoid-explorer.vbc.ac.at

We also provide RNA-seq data for cell lines in all protocols across organoid development. We quantify sources of variability (1. organoid developmental stage, 2. protocol, 3. cell line) and provide early signatures consistent with protocol-driven organoid derivation.

By comparison with fetal reference data, we can show that protocol-driven cells largely match cell types found in vivo while cell line-driven cells contribute to in vitro specific cell types.

Using scRNA-seq and a new measure for comparing scRNA-seq datasets from various sources, the NEST-score, we find protocol-driven cells (generated from many cell lines) as well as outlier, cell line-driven cells (generated from a single cell line only) for each protocol.

We characterized four regional brain organoid protocols across several cell lines using scRNA-seq on mature organoids and RNA-seq over time to generate a large fraction of human brain cells in vitro.

Find the article here: www.biorxiv.org/content/10.1...

We characterized four regional brain organoid protocols across several cell lines using scRNA-seq on mature organoids and RNA-seq over time to generate a large fraction of human brain cells in vitro.