Fig. 4

Identification of lncRNAs and protein coding genes involved in transdifferentiation. A Correlation between replicates of the differentiation delaying effect (DDE, ratio of reads from delayed versus transdifferentiated fraction) observed per pgRNA of ratCEBPa (left panel) and intergenic negative controls (right panel) after 6 days (T6) of transdifferentiation. Each dot represents a different pgRNA. Spearman correlation values are stated above. The DDE values of CEBPa pgRNAs are very large and show a positive correlation between replicates, whereas intergenic pgRNAs do not show reproducible DDE values between replicates. B Scatterplot of log10 transformed counts in delayed versus differentiated fractions at T3 and T6 after induction of transdifferentiation. Each dot represents a different pgRNA. pgRNAs targeting positive controls are depicted in blue, intergenic pgRNAs in red, screened candidates in black, and pgRNAs of selected candidates showing high average DDE score in green (merged counts of both replicates). C Decision tree followed to identify candidate genes, from the CRISPR-Cas9 screening, involved in the transdifferentiation process. From the original list of 1,040 pc-genes and lncRNAs, we ended up with a set of seven candidates to undergo further validation