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Fig. 6 | Genome Medicine

Fig. 6

From: Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population

Fig. 6

Results of deletions generation in HEK293T cells and effects on gene expression. a Location of 43 bp deletion at chr9:130330770-130330813 and annotation of the region. The deletion is located in an intronic region on the FAM129B gene, approximately 285 bp away from the nearest exon. The deletion is indicated by the blue bar while the red bar below shows the deletion induced by the CRISPR-Cas9 system. The purple bar indicates the region annotated as having a poised promoter chromatin state according to the ENCODE/Broad database. b Result of eQTL analysis. The eQTL association p value plot for deletion is shown. The red arrow indicates the location of the deletion at chr9:130330770-130330813 (red diamond). The deletion is seen to be a top eQTL hit within the region. c Boxplot of gene expression in the eQTL analysis. The boxplot shows the result of gene expression level change in the eQTL association analysis for the deletion at chr9:130330770-130330813. d Comparison of gene expression levels between HEK293T clones with and without the chr9:130330770-130770813 deletion. The y-axis shows the average relative quantification (RQ) values of the qPCR triplicate experiment. Significant differences were seen for gene expression levels between clones with and without the deletion (Wilcoxon rank-sum test p value = 0.027). e Location of 52 bp deletion at chr12:122230008-122230060 and annotation of the region. The deletion is located in an intronic region of the RHOF gene, approximately 10 kb away from the nearest exon of the TMEM120B gene which gene expression level is affected. The deletion is indicated in blue while the CRISPR-Cas9-induced deletion is shown in red. f Result of eQTL analysis. The eQTL association p value plot for the deletion is shown. The red arrow indicates the location of the deletion at chr12:122230008-122230060 (red diamond). The deletion is seen to be one of the top association hits in the region. g Boxplot of gene expression of the eQTL analysis. The boxplot shows the result of gene expression level change in the eQTL analysis for the deletion at chr12:122230008-122230060. h Comparison of gene expression levels between HEK293T clones with and without the chr12:122230008-122230060 deletion. The y-axis shows the average relative quantification (RQ) values of the qPCR triplicate experiment. Significant differences were seen for gene expression levels between clones with and without the deletion (Wilcoxon rank-sum test p value = 0.003)

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