GSM8002543: scRNA-seq, Neural organoid, Line 409b2, Day 90 Chr-Veh, Replicate 1; Homo sapiens; RNA-Seq
Single cells were dissociated using StemPro Accutase Cell Dissociation Reagent (Life Technologies), filtered through 30uM and 20uM filters (Miltenyi Biotec) and cleaned of debris using a Percoll (Sigma, P1644) gradient. Single cells were resuspended in ice-cold Phosphate-Buffered Saline (PBS) supplemented with 0.04 % Bovine Serum Albumin and prepared for single-cell separation. Experiments were performed in a paired case-control design with 2 or 4 conditions at day 70 and day 90 respectively run in parallel. Single cells were run through the Chromium controller to form gel emulsion beads containing barcoded single cells and prepared into single-cell libraries using the Chromium Single Cell 3' Reagent Kits v2 according to the manufacturer's recommendations without any modifications (10x Genomics). To reach an optimal target cell number, 10,000 cells per sample were loaded onto a channel of the 10x chip. All libraries were assessed using a High Sensitivity DNA Analysis Kit for the 2100 Bioanalyzer (Agilent) and KAPA Library Quantification kit for Illumina (KAPA Biosystems). Sequencing of the 10x Genomics single-cell RNA-seq libraries was performed on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) at the sequencing core facility of the Max Planck Institute for Molecular Genetics (Berlin, Germany).