GSM9451643: Control sample 2, WT;Dlx1-EGFP+ FACsorted Medial Ganglionic Eminence cells (GABAergic) dissociated at E12.5; Mus musculus; RNA-Seq
After dissociation, the sample consisted of two independent pools of cell suspensions per genotype (BACHD and WT). Each pool was fluorescence-activated cell sorted (FACS) using a MoFlo XDP high-speed cell sorter (Beckman Coulter) equipped with a 120-µm nozzle and operated at a sheath pressure of 16.6 PSI, yielding >80% cell viability. Each independent pool of single-cell suspensions (up to 10,000 cells per sample) was then separately processed for scRNA-seq library preparation. Chromium Next GEM Single Cell 3′ v3.1 kit (10x Genomics, Pleasanton, CA), following the manufacturer's protocol.  Within the Chromium microfluidic chip, single cells were encapsulated in oil droplets (Gel Beads-in-Emulsion, or GEMs) together with barcoded gel beads and lysis reagents. Upon partitioning, cells were lysed within GEMs and released RNA was immediately hybridized to barcoded oligonucleotides on the gel beads. Reverse transcription (RT) was performed within GEMs to convert captured polyadenylated RNA into barcoded cDNA. Each cDNA molecule contains a unique cell barcode and unique molecular identifier (UMI), enabling identification of the cell of origin and molecule counting after sequencing. After RT, emulsions were broken, and pooled, barcoded cDNA was recovered, amplified by PCR, and used for library preparation according to the 10x Genomics protocol.