Fig. 2: Hash ladder expands our ability to detect global reduction in transcript levels caused by flavopiridol.
From: Nuclear oligo hashing improves differential analysis of single-cell RNA-seq
a Overview of the experiment. HEK293T cells were treated with flavopiridol for different periods of time and labeled with a ladder of hash oligos and additional hash oligo for multiplexing prior to sci-RNA-seq preparation. b Boxplot showing total RNA UMI counts for cells treated with flavopiridol at different time points (n = 1370 cells). c UMAP projections of flavopiridol treated HEK293T cells colored by treatment time and normalized by conventional (left) and hash ladder (right) size factors. d Barplot showing number of differentially expressed genes in response to flavopiridol using the conventional and hash ladder normalization approaches. e Conventional and hash ladder normalized expression levels of CD151 and LAMC1 at different flavopiridol treatment times. Bars represent the percentage of cells with normalized expression value greater than 1, and the error bars show the 95% confidence interval obtained using a bootstrap method (n = 100 bootstrap samples). f Violin plot showing the ratio of effect size estimates of common differentially expressed genes computed with hash ladder vs. conventional normalization. The centerline of the boxplots in b and f indicates the median, the box displays the first and third quartile, and the whiskers show the 1.5 IQR. Outlier values are displayed as points.
