Extended Data Fig. 7: scRNAseq and functional analysis of 4-months-old SYNGAP1 haploinsufficient organoids.

A. GO-Terms from single cell RNA sequencing preformed in 2-month-old Patient^p.Q503X and Patient^Corrected organoids. Graphical representation of upregulated terms for Patient^p.Q503X Corticofugal Projection Neurons (CFuPN). Main biological process, cellular component, and molecular function GO-Terms are related to neuronal differentiation and synapse formation. Wilcoxon rank sum test was used for DEGs between control and mutant organoids for each cluster. B. GO-Terms from single cell RNA sequencing preformed in 4-month-old Patient^p.Q503X and Patient^Corrected organoids. Graphical representation of upregulated GO-Terms in Patient^p.Q503X Callosal Projection Neurons (CPN). Main biological process and cellular component GO-Terms are related to neuronal differentiation and synapse formation. Wilcoxon rank sum test was used for DEGs between control and mutant organoids for each cluster. C. Combined t-distributed stochastic neighbor embedding (t-SNE) from single cell RNA sequencing analysis of pooled Patientp.^Q503X and Patient^Corrected organoids at 4 months. D. Individual t-SNE plot for pooled Patient^corrected organoids at 4 months (n=7540 cells). E. Individual t-SNE plot for pooled Patient^p.Q503X organoids at 4 months (n=3123 cells). F. ΔF/F(t) from GCaMP6f2 recordings of Patient^Corrected and Patient^p.Q503X organoids. G. Calcium spike frequency analysis on 2-month-old Patient^p.Q503X organoids before and during bath application of glutamate (Glu). Unpaired two-tailed t-test performed on 16 cells from Patient^p.Q503X organoids, from 3 independent experiments. P value = 0.0005. Data shown as mean ± SD. H. ΔF/F(t) from GCaMP6f2 recordings of 03231^Control and 03231^p.Q503X organoids. I. Calcium spike frequency analysis on 2-month-old Patient^p.Q503X organoids before and during bath application of tetrodotoxin (TTX). Unpaired two-tailed t-test performed on 9 cells from Patient^p.Q503X organoids, from 3 independent experiments. P value =0.0001. Data shown as mean ± SD.