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Abstract

The placenta is the temporary organ responsible for nutrient, water, gas, and waste exchange between the mother and the fetus. Precise and timely expression and repression of placental genes is essential to ensure a healthy pregnancy, and aberrant expression can result in mild to severe complications for both fetus and/or mother. Gene regulation occurs via numerous mechanisms, one being regulation of gene expression by small non-coding RNAs (sncRNAs). Several biological factors such as sex and trimester of the pregnancy, and technical factors like sample processing and sequencing variables can lead to variation in the gene expression observed, and accounting for their effects is imperative when interpreting results of expression studies. While sncRNAs have been investigated in health and disease of other organs, the placenta has remained overlooked in the characterization of this biological species. In this dissertation, I first compared different methods of sample processing, quality control, and species annotation to optimise and provide a streamlined pipeline for investigation of sncRNAs specifically for placental tissue. I found that the most widely-used protocols and methods may not perform the best for placental tissue, and how a tissue-specific and biological data type-specific approach is necessary. Using the optimised placental protocol and pipeline, I then characterized the sncRNA transcriptome of bulk placental villi across three different cohorts, and analysed how sources of inherent and external variation impact expression data. I observed that technical variables contribute the highest towards expression consistently in the separate cohorts, and that the effect of inherent biological variables is study-dependant. I then extended the analysis towards profiling sncRNAs in four major placental cell types, which revealed expression patterns by cell type, cell-specific expression by sex, and association of sncRNA expression with DNA methylation.