Figure 5
DIEM filtering removes fewer numbers of nuclei in snRNA-seq. (a) The bar plots show the number and type of droplets that are removed by the indicated filtering method in the differentiating preadipocytes (DiffPA), mouse brain, and six human frozen adipose tissue (AT) snRNA-seq samples. The height of the blue bar indicates the number of nuclear droplets that are removed while the height of the red bar indicates the number of background droplets. Background and nuclear droplets are defined using the percent spliced reads. DIEM filtering tends to result in a higher number and proportion of nuclear droplets. Removal of large numbers of nuclear droplets and low numbers of background droplets indicates poor performance. (b) The percent of reads spliced is shown in a boxplot for droplets removed by the filtering method in the DiffPA, mouse brain, and six AT snRNA-seq samples. The horizontal red line indicates the sample-specific midpoint, where droplets above and below are background and nuclear, respectively. A Mann-Whitney U test was performed between DIEM and EmptyDrops12, and DIEM and quantile removed droplets. DIEM shows an increase in percent of reads spliced for all comparisons. P-values were corrected for multiple testing using Bonferroni and are shown in the upper portion of the plot (*p < 0.05; **p < 0.005; ***p < 0.0005). (c) UMAP33 visualization of clustering of removed droplets with the indicated method in the combined adipose tissue snRNA-seq data set. Clusters were classified as adipocyte (Adp), doublet (Dblt), myeloid (Myl), T cell, mast, and stromal (Stm) cell types according to their up-regulated genes. A cluster was classified as debris (Dbr) if it had a mean percent of spliced reads above 50%.
