Extended Data Fig. 5: Selection of lncRNA candidates for CRISPR-Cas12a knockout screening.
a, Heatmaps showing the expression of the lncRNA candidates across various cancer samples (left), and the median expression of the indicated lncRNAs in normal tissues excluding testis and in testis tissues (right). TCGA cancer types include BLCA, BRCA, CHOL, DLBC, ESCA, GBM, HNSC, KIRC, KIRP, LAML, LGG, LIHC, LUAD, LUSC, MESO, OV, PAAD, PRAD, SARC, SKCM, STAD, THCA, UCEC, UCS, COADREAD (left to right). b, Pipeline for crRNA library design and construction. c, lncRNA gene knockout strategy and location of primers used for genome PCR. Representative images of genomic DNA PCR amplification of the four indicated lncRNA genes. MW: DNA marker. n = 3 independent biological experiments. d, Quantitative analysis of RP1-212P9.3, RP11-223I10.1, RP1-1055B8.4 and RP11-429B14.1 knockout efficiency based on genome PCR results. The genomic DNA amplified by PCR was first normalized to ACTB and then to HeLa cells treated with control AAVS without addition of Dox. Error bars, means ± SD, n = 3 biologically independent experiments, two-tailed Student’s t test, n.s., not significant. e, RT-qPCR analysis of the lncRNA expression level of RP1-212P9.3, RP11-223I10.1, RP1-1055B8.4 and RP11-429B14.1 in the knockout and complemented HeLa cells. Error bars, means ± SD, n = 3 biologically independent experiments, two-sided Student’s t test, n.s., not significant.
