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Next Generation Sequencing Facilitates Quantitative Analysis of FLox and SMYD2 KO Aortic Smooth Muscle Cell Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of FLox and SMYD2 KO Aortic Smooth Muscle Cell Transcriptomes

PROVIDER: PRJNA675094 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of FLox and SMYD2 KO Aortic Smooth Muscle Cell Transcriptomes

Project description:Purpose: Methyltransferase SMYD2 has been implicated in cancer cell growth and cardiomyocytes development. However, its role in vascular smooth muscle cell(VSMC) is still unknown. This study aims to investigate differentially expressed genes in Flox and SMYD2 knockout VSMC. Methods:RNA profiles of Aortic Smooth Muscle Cell isolated from Flox and SMYD2 knockout (SMYD2−/−) mice were generated by deep sequencing, in triplicate, using BGISEQ-500 platform. Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations. Results: In our project, we sequenced 6 samples on BGISEQ-500 Platform in total and generated about 4.69 Gb per sample. The average genome mapping rate is 96.62% and the average gene mapping rate is 80.92%. 18,112 genes were identified in which 16,992 of them are known genes and 1,351 of them are novel genes. 13,680 novel transcipts were identified in which 11,251 of them are previously unknown splicing event for known genes, 1,351 of them are novel coding transcripts without any known features, and the remaining 1,078 are long noncoding RNA. Conclusions: Our study represents the first detailed analysis of SMYD2 KO VSMC transcriptomes, with biologic replicates, generated by RNA-seq technology.

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RNA-seq of human HT-29 WT and SMYD2-KO xenograft implanted into the flanks of Rag1−/− mice

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