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. Overall design: 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.