Methylmercury (MeHg) is a persistent environmental and dietary contaminant that causes serious adverse developmental and physiologic effects at multiple cellular levels. In order to understand more fully the consequences of MeHg exposure at the molecular level, we profiled gene and miRNA transcripts from the model organism Caenorhabditis elegans. Animals were exposed to MeHg (10 μM) from embryo...

Fat deposition is an important economic trait in farm animals as well as obesity related diseases in humans, and the liver is a central organ involved in regulating lipid synthesis and metabolism in mammals. In this study, the pig liver transcriptome of two groups (H and L) showing differences in backfat thickness were profiled using RNA-Seq and miRNA-Seq to further explore the molecular mechan...

Phospholipids, such as 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC), are the major components of cell membranes. Their exposure to reactive oxygen species creates oxidized phospholipids, which predispose to the development of chronic inflammatory diseases and metabolic disorders through endothelial activation and dysfunction. Although the effects of oxidized PAPC (oxPAPC) on en...

Long non‑coding RNAs (lncRNAs) are ncRNA transcripts >200 nucleotides that important genetic regulators. LncRNAs can directly regulate mRNA through a lncRNA‑mRNA regulatory mode and also competitive binding to micro (mi)RNA, which is generally known as the endogenous RNA (ceRNA) network. The present study evaluated functional roles networks of lncRNAs in chronic glomerulonephritis (CGN). pro...

Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different tra...

Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, be...

In order to identify specific plant anti-viral genes related to the miRNA regulatory pathway, RNA-Seq and sRNA-Seq were performed using Arabidopsis WT and dcl1-9 mutant line. A total of 5,204 DEGs were identified in TCV-infected WT plants. In contrast, only 595 DEGs were obtained in the infected dcl1-9 mutant plants. GO enrichment analysis of the shared DEGs and dcl1-9 unique DEGs showed that a...

Background. This letter is a response to a Divergent Views article entitled “The poor 8 performance of TMM on microRNA-Seq” (Garmire and Subramaniam 2013), which was a 9 response to our Divergent Views article entitled “miRNA-seq normalization comparisons need 10 improvement” (Zhou et al. 2013). Using reproducible code examples, we showed that they 11 incorrectly used our normalization method a...