Project description:To study the effect of GLI3 knockout on early brain organoid development, we collected single-cell multiome data from 18 day old brain organoids
Project description:We used a pooled, multiplexed CRISPR/Cas9 gene knock-out (KO) experiment with single-cell transcriptomic readout to perturb and validate selected TF regulomes . We designed gRNAs and generated a pooled lentiviral library targeting 12 TFs with specific midbrain or hindbrain expression or high regulatory centrality. IPSCs carrying a doxycycline-inducible Cas9 cassette in the AAVS1 safe harbor locus were transduced, mosaic organoids were generated, and perturbations were induced at neuroepithelium stage from day 7 to 14. Mosaic organoids were analyzed using scRNA-seq and gRNA amplicon sequencing at day 30 and day 70, recovering 31,857 cells, among which a gRNA was detected in 8711 cells.
Project description:To investigate how SHH treatment influences patterning of early brain organoids, we performed multiome sequencing of brain organoids during 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:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.