Chromium single cell 3 library and gel beads and chromium chip kit

Single-cell sequencing was conducted as described in-text, figure legends, and depicted in our schematic pipeline (see Fig. 2f). Briefly Organoids were dissociated using Accutase, serially filtered to remove debris, and were subjected to high-throughput FACS (Aria II flow cytometer, Becton Dickson). This procedure allowed us to isolate only live cells in a defined concentration (2000 live cells/ µL) that could be standardized between lines for microfluidic-device loading. Cell viability was confirmed using Countess-II (Invitrogen, Thermofisher, CAT#: AMQAX1000). Next, cells were prepared for 10X Genomics Chromium library preparation according to manufacturer instructions (see Chromium^TM Single-Cell 3’ Library and Gel Beads and Chromium^TM CHIP kit, 10x Genomics). Post sample generation, barcoded-emulsions were broken, amplified, and libraries prepared. cDNA was examined on a Fragment Analyzer running PROSize v3.0 3.0.1.6 (Advanced Analytical Technologies). Libraries were subsequently subjected to next generation sequencing via Next-Seq High-Output 150-cycled 26-8-98.

To define cell-specific transcriptomes in CTRL and SCZ organoids, we performed scRNA-seq. First, organoids from 3 CTRL and 3 SCZ lines were dissociated using Accutase, filtered to remove debris and subjected to high-throughput FACS (Aria II flow cytometer, Becton Dickson). This allowed for isolation of only live cells at concentration of 2000 live cells/µL, standardizing microfluidic-device loading between lines. Cell viability was confirmed using Countess-II (Invitrogen, Thermofisher, CAT#: AMQAX1000). Next, live cell suspensions we rapidly loaded into 10x chromium microfluidic devices to produce barcoded single-cell nanodroplet emulsions and cells were prepared for 10X Genomics Chromium library preparation according to manufacturer instructions (ChromiumTM Single-Cell 3’ Library and Gel Beads and ChromiumTM CHIP kit, 10x Genomics). After sample generation, barcoded-emulsions were broken, amplified, and libraries prepared. cDNA was examined on a Fragment Analyzer running PROSize v3.0 3.0.1.6 (Advanced Analytical Technologies). Libraries were subsequently subjected to next generation sequencing via Next-Seq High-Output 150-cycled 26-8-9. Raw reads were processed after sequencing as subsequently described.