Figure 4
DIEM filtering keeps an increased number and proportion of nuclear droplets in snRNA-seq. (a) The bar plots show the number and type of droplets that pass 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 pass filtering, while the height of the red bar indicates the number of background droplets. DIEM filtering tends to result in a higher number and proportion of nuclear droplets. Background and nuclear droplets are defined using the percent spliced reads. (b) The percent of reads spliced is shown in a boxplot for droplets that pass the indicated 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-filtered droplets. DIEM shows a decrease in percent spliced reads for all comparisons (black bar and asterisks) except for AT4 with EmptyDrops (red bar and asterisks). 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 clusters after filtering with the indicated method in the combined adipose tissue snRNA-seq data set. Clusters were identified with Seurat20 and 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%.
