RNAseq analysis of gene expression profiles in a mouse model of tuberous sclerosis

We have generated a tuberous sclerosis complex (TSC) mouse model through mouse Gfap-Cre mediated conditional knockout of Tsc1 gene. Tsc1 depletion occurs in most astrocytes and a fraction of upper cortical and hippocampal neurons. The mice develop spontaneous seizures after 10 weeks of age. To determine the effect of Tsc1 deficiency on astrocytes, we compared astrocyte gene expressio profiles between mGfap-Cre:Tsc1CKO and littermate control mice at 4 weeks and 15 weeks of age. At 4 weeks, mGfap-Cre:Tsc1CKO mice showed increased transcription of a few astrocyte genes, including Vim, Amigo2, Thbs4, Slc7a11, Gjb6 and ALDH1L1, and there were not changes in protein products of these genes. At 15 Weeks, mGfap-Cre:Tsc1CKO mice with seizures showed increased transcription of reactive astrocyte genes, including Gfap, Vim, CD44, Sparc, Serpina3n and many others. The transcriptional changes were consistent with enhanced protein levels. Total RNA (RIN>=9.8) was extracted from upper half cortex of somatosensory and parietal cortices of mGfap-Cre+:Tsc1CKO and control mice. mRNAs were enriched using poly-A-pull-down. Library was prepared using the Illumina TruSeq RNA prep kit, and sequenced using an Illumina HiSeq 2000 system with a read length of 100 bases. RTA (Illumina) was used for base calling and bcl2fastq (1.8.4) was applied to covert BCL to fastaq format. The reads were mapped to a mouse reference genome mm9 using Tophat (2.0.4). Differential gene experssion analysis was conducted using DESeq2 pipeline, with a FDR of 0.1, and an adjusted p value cutoff 0.05.