Transcriptome of E9.5 WT and Smyd1-KO mouse hearts

Purpose: The goal of this study is to identify the differential cardiac transcriptome profiling between WT and Smyd1 null (Smyd1-KO) hearts at E9.5 using RNA-seq. Methods: mRNA profiles of E9.5 WT and Smyd1-KO mouse hearts were generated by deep sequencing, n=3 for each genotype, using Illumina HiSeq2500. The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. Differential gene expression was determined by DEseq2. Results: 1756 genes were differentially expressed between WT and Smyd1-KO hearts [adjusted P value <0.05, |log2(Fold Change)| > 0.5], with 1130 upregulated and 626 downregulated in E9.5 Smyd1-KO hearts. Overall design: WT and Smyd1-KO hearts at E9.5, n=3 for each genotype, were dissected in cold PBS and immediately stored in RNAlater (Thermo, AM7020) solution, and were kept in -20C until use. RNA from individual embryonic hearts was extracted using the RNAqueous-Micro total RNA isolation kit (Thermo, AM1931). The concentration and quality of purified RNA were assessed by Tape Station (Agilent). RNA samples with RNA integrity numbers (RIN) ranged from 8.0 to 10.0 were used for library prep and sequencing.