Single-cell RNA-seq of ASPM mutant ferret embryonic forebrain

As described in our paper "Aspm knockout ferret reveals an evolutionary mechanism governing cerebral cortical size" (Johnson et al., Nature 2018), we used the standard Drop-seq method and analysis of Macosko et al. (2015) to capture, sequence, and analyze mRNA from single cells from Aspm wild-type, heterozygous, and knock-out littermate ferrets at embryonic day 35. Bulk reference samples were processed using standard Illumina mRNA-seq library prep and sequencing protocols, and the samples were described previously (Johnson, Wang et al., Nature Neurosci 2015) Embryonic forebrain tissue was harvested and cryopreserved, then processed into single-cell suspension for Drop-seq after genotyping. An equal number of KO and WT/Het littermates from two litters were sequenced in three runs, with genotypes and litters balanced across runs to minimize batch effects.