We tested for distortion of cell type abundance by comparing our frontal cortex dataset to tissue (Figure S4D–M and STAR Methods). Neurons were over-represented relative to non-neurons (Drop-seq: 0.76 ± 02 mean±sem; tissue: 0.51 ± 03) and exhibited a twofold greater GABAergic/glutamatergic ratio (ISH: 5.1:1; Drop-seq: 11:1). Both effects could be partially explained by cell-inclusion thresholds, in which small but real transcript libraries had been excluded from downstream analysis (neurons: 5,039±15 mean±sem; non-neurons: 1,696±9; Glu: 5,299±16; GABA: 2,626±21)(Figure S4D–I). Among GABAergic interneurons, Vip+ cells were over-represented and Sst+ and Pvalb+ cells were underrepresented (ISH vs Drop-seq: Vip+, 16% vs 35%; Pvalb+, 31% vs 25%; Sst+, 28% vs 22%), which cannot be explained by higher transcript counts (Pvalb+: 2,996 ± 61; Sst+: 2,758 ± 53; Vip+: 2,236 ± 32), suggesting a preferential depletion (Figure S4K–M). We conclude our data exhibit modest skews in cellular representation driven by transcript abundance and viability.
