RNA-seq data of wild-type and Abcb11-deficient mice

RNA-seq analysis were applied to elucidate the transcriptional differences of wild-type and Abcb11-deficient mice. Comparison of female Abcb11-/- (Abcb11F) and female C57BL/6J mouse (WTF) livers identified 3,652 RNA species that were differentially expressed (1,809 genes upregulated and 1,843 genes downregulated; Padj < 0.05). Comparison of liver gene expression in Abcb11F versus non-tumor tissue of female Abcb11-/- mice (NTF) revealed 47 differentially expressed genes. Cross-comparison of the lists of differentially expressed genes in Abcb11F versus WTF and in Abcb11F versus NTF revealed 36 genes common to the two data sets. The RNA was extracted from the livers of 3 mice (12-month-old) per group. The RNA was extracted from the livers of 3 mice (12-month-old) per group. RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq platform, and 125 bp/150 bp paired-end reads were generated. All reads that passed quality metrics were mapped using HISAT2 software. Differential expression analysis was performed using the DESeq2 R package (1.16.1). The P values were adjusted using the Benjamini and Hochberg method. An adjusted P-value (Padj) of 0.05 was set as the threshold for differentially expression.