FBP1 loss disrupts liver metabolism and results in distinct transcriptome

This study set out to globally compare the liver transcriptomes from 24-week old wild type (WT) and FBP1-deficient mice. Total RNA was isolated from 10 snap frozen liver tissue samples using RNeasy Mini Kit (Qiagen). 250~300 bp insert eukaryotic mRNA derived cDNA non-directional libraryRNA libraries were prepared using standard Illumina protocols. The sequencing were performed on Illumina Platform PE150, with 20M raw reads/sample. Overall design: mRNA profiles of 24-week old wild type (WT) and FBP1-deficient mouse livers were generated by RNA sequencing, 5 biological replicates in each group, using Illumina Platform PE150. Data was analyzed at the Molecular Profiling Facility at the University of Pennsylvania. Briefly, Fastq files were checked for quality using FastQC and qualimap. Alignment was performed using the STAR aligner under default settings with the mm10 reference genome. Raw counts of gene transcripts were obtained from the resulting bam files using feature Counts. The raw count matrix was subsequently imported into R-studio (R version 3.3.3) and used as input for DESeq2 following the vignette of the package for normalization and differential gene expression analysis. Salmon/Sailfish was used in parallel to normalize and quantitate gene expression in transcripts per million (TPM) through quasi-alignment. Differentially expressed genes from the DESeq2 analysis were used as input for GSEA MSigDB geneset enrichment analysis68 (http://software.broadinstitute.org/gsea/msigdb).