sNucDrop-seq for Profiling Cortical Nuclei

sNucDrop-seq of cortical nuclei was performed as previously described^{36 (link)}. Briefly, nuclei suspensions were run through an Aquapel-coated PDMS microfluidic device (uFluidix) with barcoded beads (ChemGenes) to co-encapsulate individual nuclei with a single bead. barcoded beads were resuspended in lysis buffer (200 mM Tris-HCl pH 8.0, 20 mM EDTA, 6% Ficoll PM-400 (GE Healthcare/Fisher Scientific), 0.2% Sarkosyl (Sigma-Aldrich), and 50 mM DTT (Fermentas) at a concentration of 120 beads/uL. Droplet breakage with Perfluoro-1-octanol (Sigma-Aldrich), reverse transcription using Maxima H Minus Reverse Transcriptase (ThermoFisher) and exonuclease I treatment were subsequently performed. cDNA was amplified by PCR (KAPA HiFi hotstart Readymix, KAPA biosystems) using a pre-determined, optimized number of cycles and purified twice with 0.6X SPRISelect beads (Beckman Coulter). cDNA was then tagmented using the Nextera XT DNA sample preparation kit (Illumina, cat# FC-131-1096) and further amplified using 12 enrichment PCR cycles. Libraries were sequenced on an Illumina NextSeq 500 using the 75-cycle High Output v2 Kit (Illumina), each loaded at a concentration of 2.0 pM. In total, 8 individual mouse cortex samples (4 controls, 4 CUS) were analyzed by sNucDrop-seq with 2 independent batches (2 controls, 2 CUS samples per batch), which were sequenced twice.