We obtained ~ 4.8×105 (median, Avg=6.9×105) mapped reads per cell, each containing ~1.0×105 (median, Avg=1.4×105) unique reads that typically detected on average ~10,000 genes (range ~7,500 to ~12,000 genes median), with >95% of the single cells detecting >6,000 genes (Figure S1B–C). In each single cell ERCC spike-in RNA (Life Technologies) were used as internal controls, for which the absolute number of molecules that are added to sample can be calculated; this gave a linear relationship of input-output measures with a slope of 0.92 and adjusted R2=0.96 (Figure S1D). Following quality control screen, we obtained high depth transcriptome of ~584 cells from the 6 PCPs (Figure S1D). This unique dataset thus contains high-resolution transcriptomes of phenotype-defined cortical GABAergic PCPs.
