ATACseq data for phs004321
Cells were lifted and counted to isolate 50k cells per sample to be used as input for the Omni-ATAC protocol for library preparation. To summarize, 50k nuclei from fresh NPCs were counted via hemocytometer and tagmented using TDE1 enzyme (Illumina 20034198) and tagmentation buffer composed of 20mM Tris-HCl pH 7.6, 10mM MgCl2, and 20% Dimethyl Formamide. All libraries were PCR amplified (NEB M0544S) for 5 cycles, and then each library was further amplified for a sample-specific additional number of cycles (average 2 additional cycles across all samples) determined by a qPCR side reaction to avoid overamplification. Nextera-compatible unique dual-indexing primers barcoded each sample during amplification (Illumina 20027213). We purified libraries to remove primer dimers and eliminate fragments over 1000bp (Roche 07983298001). We validated ATAC-seq library quality before sequencing for a subset of samples by observing appropriate nucleosomal banding patterns via capillary gel electrophoresis on an Agilent 4150 TapeStation system (Agilent 5067-5584). We then pooled ~70 ATAC-seq libraries with unique barcodes in each of four pools, and sent pooled libraries for multiplexed sequencing. ATAC-seq libraries were sequenced at the NYGC to an average read depth of 49M (SD = 13.6M) paired-end reads (2x100bp) per sample on the Illumina Novaseq platform.