Dna standards

ATAC-seq processing followed the original protocol (Buenrostro et al., 2013 (link)), which involves enzymatic dissociation of tissue using papain inactivated by ovomucoid (Worthington) followed by aliquoting of 50,000 cells, nuclear isolation using an IGEPAL solution, transposition using Nextera Tn5 transposase (Illumina), barcoding and amplification (8-11 cycles), quality control via gel electrophoresis, quantification via qPCR with DNA Standards (Kapa Biosystems), and massively parallel 50 bp paired end (PE) sequencing on an Illumina HiSeq2000 or HiSeq2500 to acquire ∼25M fragments per sample. For each donor, GZ and CP samples were dissected, library prepped, and sequenced within the same batch to prevent batch effects correlated with the biological condition of interest. Following preparation of a homogeneous suspension of cells isolated from the GZ or CP, 3-4 technical replicates consisting of independent nuclear isolations, Tn5 tagmentation, and library preparation were generated. phNPC samples were processed for ATAC-seq library preparation at 0 wks (3 replicates - independent nuclear isolations, Tn5 tagmentation, and library preparation from the same differentiation), 2 wks (3 replicates), 4 wks (2 replicates), and 8 wks (3 replicates) post differentiation as above.