RNA-seq Analysis of HuH-7 Cells

HuH-7 cells were transfected with control, FOXA1, or CEBPA siRNAs (10 nM) for 48 h. Total RNA was extracted from the cells using the RNeasy Plus Mini kit. Agilent Bioanalyzer device (Agilent Technologies) was used to assess the quality of extracted RNA. Subsequently, RNA-seq libraries were prepared with total RNA (100 ng) using an NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s protocol. The libraries were sequenced with 100 bp paired-end reads on the DNBSEQ-G400RS (MGI Tech, Shenzhen, China). The analysis of sequencing data was performed by a standard RNA-seq analytical pipeline. Briefly, STAR(v2.7.3a)^{45 (link)} was used to align the sequencing data to the human genome (hg38). Quantification of gene expression was performed using RSEM (v1.3.3)^{46 (link)}. The DESeq2 package (v1.26.0)^{47 (link)} was used to normalize the read count data and test for differential gene expression.