Fig. 3: Isoviz R package automates experimental design to confirm EEJ-specific RNA knockdown.
From: Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox
a Overview of Isoviz inputs and functions. Required inputs (red boxes) vary by function; default input files are available on GitHub but can be replaced by user-defined data. Pre-processing steps (yellow) reformat input for downstream functions. Main visualization and output functions (purple) operate per user-specified gene. b Isoviz output for COP1 and SPAG9, showing isoform structures and two selected EEJs per gene plotted as introns. EEJs are labeled with read counts and corresponding isoforms. Users can select all or a subset of EEJs for plotting. c Isoviz output table showing gRNAs targeting EEJs in (b) and their TIGER scores. d RT-qPCR quantification of COP1 and SPAG9 RNA knockdown using EEJ-targeting gRNAs from (c) at 24 hours of doxycycline. Knockdown is relative to cells transfected with an empty gRNA cassette (n = 4 gRNAs per EEJ). Each boxplot represents three RT-qPCR measurements from two biological replicates. Box plots were made using ggplot and show the median (center line), the 25th and 75th percentiles (box bounds), and the range of values within 1.5× the interquartile range (whiskers). Outliers beyond this range are shown as individual points. Source data are provided as a Source Data file.
