Paired ATAC and gene expression libraries were generated following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338_RevB (10X Genomics, Inc). In brief, the isolated nuclei from a pool of samples were first incubated in a transposition mix. The single nuclei master mixture containing tagmented single nuclei suspension was loaded into two wells of a Next GEM Chip J, along with the single cell multiome gel beads and partition oil. The chip was then loaded into the Chromium X Controller for GEM generation and barcoding. Barcoded transposed DNA and cDNA were amplified after the GEMs were released. At each step, the quality of the cDNA, ATAC library, and cDNA library was examined by Bioanalyzer 2000. The final single-indexed ATAC libraries and the dual-indexed gene expression libraries were sequenced on an Illumina Novaseq 6000, with index reads of 10 bp + 24 bp, and 100 bp paired-end reads.
