A Signac object, containing both RNA and ATAC-seq data, was created for each pool from the multiome assay using the HDF5 file from the Cell Ranger output. Cells with below 800 or above 20,000 genes, below 800 or above 500,000 detected RNA molecules, above 20% mitochondrial RNA, or above 8% ribosomal RNA were removed from further analysis. An additional round of filtering was performed using the ATAC-seq data. The following cells were removed from further analysis (Supplementary Data 20):Cells with less than 100 or over 100,000 features;Less than 100 or over 1,000,000 counts;TSS enrichment less than 2;Nucleosome signal greater than 4;Percentage of reads in peaks less than 15%;Total number of fragments in peaks less than 800 or over 100,000;Ratio reads in genomic blacklist regions greater than 0.05.
