Project description:Purpose: rHCI hydrogel injection improves cardiac function within 2 days of treatment in a mouse model of myocardial infarction. The goal of this study was to determine the differences in gene expression with rHCI hydrogel injection post-myocardial infarction. Methods: Total RNA was isolated from left ventricle tissue of samples and mRNA stranded libraries were prepared and sequenced in Illumina NovaSeq 6000 with a depth of 50 million reads per sample. Differential expression analysis of aligned reads was done to compared gene expression between PBS vs. rHCI, PBS vs. sham, and rHCI vs. sham comparisons. Results: Differentially expressed genes between sham and PBS as well as rHCI and PBS showed known gene signatures of myocardial infarction. Seven differentially expressed genes were detected with rHCI hydrogel injection compared to PBS. Conclusions: The target gene ERDR1 that is downregulated with rHCI injection led to discovery of changes in cardiomyocyte apoptosis and reduction of oxidative stress adducts with rHCI injection post-myocardial infarction.
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
