Extended Data Fig. 8: CARPID Result of lncRNA DANCR.
From: CRISPR-assisted detection of RNA–protein interactions in living cells
a, Scatter plots show comparison of gene expression level in HEK293T cells (WT) or cells transfected with pre-gRNA sets (control). The axes in each figure represent the log2 transformed gene expression. The expression levels of XIST/MALAT1/DANCR are highlighted (n = 3 independent experiments, two-sided Pearson correlation test). b, The location of gRNA sets (Upper: DANCR-L1/2; Lower: MALAT1-L1/L2) and qPCR primers (Upper: DANCR: P1/P2; Lower: MALAT1: P1/P2) for DANCR used in CARPID. F, forward strand primer; R, reverse strand primer. The numbers within parentheses indicate the location of the gRNA sets in the corresponding RNA transcript, starting from 1 nt. c, The volcano plots show the enrichment of DANCR-associated proteins in HEK293T cells. Significantly enriched proteins are labelled as orange dots (n = 3 independent experiments for control and each gRNA group, respectively). d, DANCR-protein interaction network. White nodes indicate proteins identified with one set of gRNAs. Pink nodes represent proteins identified with two sets of gRNAs. Edges are drawn between two proteins with annotated interaction (STRING interaction score ≥ 0.40). The width of the edge is adjusted in proportion to the STRING interaction score.
