snRNA-seq for Donor 3, baseline multiome gene expression
Mutliome ATAC + Gene Expression libraries were prepared using Chromium Next GEM Single-cell Multiome ATAC + Gene Expression Reagent Bundle (10X Genomics, cat \# 1000283) following the manufacturers recommended protocol (10X Genomics, CG000338, Rev F).  Briefly, a total of 8,000 nuclei were targeted for loading into a transposition reaction, which incubated at 37 C for 60 minutes.  The output was then loaded into a single channel of a Chromium Next GEM Chip J (10X Genomics, cat \# 1000234) and partitioned into droplets with gel beads using a Chromium controller (10X Genomics, cat \# 1000204).  After emulsion droplets were formed and collected, reverse transcription and transposed DNA fragment barcoding reactions were incubated at 37C for 45 minutes.  Both products were purified, amplified and size fractionated to create the ATAC and transcriptome fractions from each sample.  ATAC libraries had indexed sequencing adapters added.  Transcriptome libraries were fragmented and ligated to indexed sequencing adapters.  ATAC libraries were sequenced on an Illumina NovaSeq6000 with paired end reads as follows: Read 1 = 50 cycles, i7 Index = 8 cycles, i5 = 24 cycles, Read 2 = 49 cycles.  Transcriptome libraries were sequenced on an Illumina NovaSeq6000 with paired end reads as follows:  Read 1 = 28 cycles, i7 Index = 10 cycles, i5 = 10 cycles, Read 2 = 89 cycles.  Cell Ranger ARC (v2.0) mkfastq was used to generate all demultiplexed FASTQ files from the raw sequencing data.  Cell Ranger ARC count was used to align transcriptome reads to the human GRCh38 genome reference provided by 10X Genomics and generate all downstream count matrices.