Transcriptomic analysis of ZHX3-depleted HepG2 cells

The aim of this RNA-Seq analysis was to identify target genes of the transcription repressor ZHX3 in HepG2 cells. To do so, four stable lines were generated in HepG2 using three different ZHX3-targeting CRISPR constructs and an empty vector construct. Bulk RNA-Seq analysis was performed on these four lines. Sequencing was done by NovogeneAIT Genomics using the Illumina® NovaSeq6000-PE150 platform and 63-82 million base pairs were sequenced per sample. A total of 47 and 156 genes were found to be consistently upregulated and downregulated (fold change = 2 and FDR < 0.05), respectively, in all three KO lines as compared to the empty control line. Functional enrichment analysis of the 156 upregulated genes using g:profiler revealed the enrichment of two biological processess, urate transport and urate metabolic process. qPCR analysis validated the upregulation of uric acid transporter gene SLC17A1. Overall design: Four different HepG2 stable lines were generated by transfecting with four different CRISPR constructs: (1) empty vector control (termed as Empty), (2) sgZHX3-2 (Z2) , (3) sgZHX3-5 (Z5) and, (4) sgZHX3-9 (Z9). Each stable line was seeded in three wells of a 24-well plate (triplicates).