Libraries were sequenced at the Boston University Single Cell Sequencing Core. The pool of snRNA-seq libraries were sequenced on 7 Next-seq P3 flow cells with an intermediate re-pooling scheme to optimize for 50–80% sequencing saturation, > 8000 average UMI per cell. Between sequencing runs, we preliminarily aligned the sequencing reads as outlined below to assess quality per sample and estimate the number of viable nuclei and sample complexity. We identified two samples, C-13291 and C-612, to have low QC metrics due to wetting failures, mean UMI per cell < 1000 and estimated # cells > 50,000. These samples were excluded from subsequent re-pooling and further analyses (Supplementary Data 1–S1: tab STARsolo QC).
