title: Brain PairedTag Batch 1 Library SDC2 dna
design: Nuclei were permeabilized and incubated with antibodies at 4C overnight, washed, and resuspended. Barcoded pA-Tn5 was addedto perform multiplex targeted tagmentation. Nuclei were extracted by centrifugation or lectin beads and re-suspended, and RT performed using a standard thermocycler program with a sample-specific multiplex barcode. The RT barcode and Tn5 barcode contain differing endonuclease cutting sites. Nuclei were pooled, and two rounds of 96-well combinatorial barcoding performed. Nuclei are pelleted and resuspended for counting, and split into individual wells of 5,000-15,000 nuclei for library preparation. Nuclei are lysed, TdT tailing is performed and the resulting tailed lysate amplified via linear amplification. The amplified lysate was split into two tubes; each tube treating with a different endonuclease to eliminate either the cDNA or DNA portion of the library (by cleaving the barcodes). The lysate is cleaned with SPRI beads and Tn5-N5 is added to add a second adapter to libraries.