Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.
Project description:Real- time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a technique that allows for the quantification of mRNA transcripts present within a tissue of interest. To ensure that quantified amounts of mRNA determined by RT qPCR is due to biological differences rather than a product of variation in testing protocol, results need to be normalized. Normalization has historically relied on the use of reference genes, or genes whose transcript expression does not differ in the tissue of interest independent of the experimental condition. In the field of equine reproductive studies, ACTB and GAPDH have been the most widely used reference genes for normalization of RT-qPCR results. However, recent studies have demonstrated that these genes may have drastically varied expression levels in different tissues and in different physiological states. Our study was aimed at examining different putative reference genes (historic reference genes as well as genes identified by RNA-seq to be stable across different sample types) in equine corpus luteum samples at day 11 and day 13 in pregnant and non-pregnant animals. Stability of genetic expression was evaluated via three stability software analyses (GeNorm, NormFinder and BestKeeper). We hypothesized that the most commonly used historic reference genes (ACTB, GAPDH and B2M) would be the most stably expressed genes in equine corpus luteum samples. COX4I1 and SRP14 were both found to be within the top three most stable genes of all samples for all methods. When assessing the least stably expressed genes, the historic reference genes were frequently identified across the three softwares. Exploration of putative reference genes should be considered when investigating dynamic endocrine organs such as those used in reproductive studies. RT-qPCR studies evaluated with historic genes should be interpreted cautiously.
Project description:This study investigates the transcriptional consequences of an inducible deletion of RetSat in epithelial cells of the intestine. Kiefer MF et. al, American Journal of Physiology-Endocrinology and Metabolism, 2024