Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
Project description:This project used snRNA-seq and Molecular Cartography (single cell spatial transcriptomics) to investigate the relation between morphology and molecular identity in human brain organoids.
Project description:All samples are 50 day old cerebral organoids differentiated from human iPSCs using human the Lancaster protocol (Lancaster et al Nature Protoc, 2014). 4 samples are wild-type (WT) organoids derived from the iPSC line IPSO; 4 samples are Fragile X Syndrome (FX) organoids derived from the iPSC line FX52 in the presence of 15mM HEPES vehicle (Urbach et al, Cell Stem Cell, 2010). 4 samples are Ascorbic Acid treated FX52 cells differentiated into cerebral organoids (FX +AsA). FX +AsA samples were prepared by exposing FX52 iPSCs to 500uM Ascorbic Acid (+15mM HEPES vehicle) for 6 passages (36 days) as iPSCs and then differentiated into cerebral organoids in the presence of Ascorbic Acid throughout the differentiation protocol. By day 50 of the cererbral organoid protocol all organoids were collected for analysis.
Project description:To investigate the heterogeneity during the neuroepithelial stage of organoid development, we performed a multiome experiment on day 15-18 old brain organoids
Project description:Brain organoids (BO) enabled the investigation of human corticogenesis in-vitro with an increasing range of protocols achieving its remarkable recapitulation. However, we lack a resource gathering fetal cortex-specific gene co-expression patterns and their behavior in BO. We complement the current knowledge with a benchmarking of BO versus human corticogenesis, integrating: transcriptomes from in-house differentiated cortical BO (CBO), in-house processed human fetal brain samples, analysis of transcriptomes from different BO systems and of pre-natal cortical samples from the BrainSpan Atlas.