Complete stranded RNA profiling during early mouse gonad development

The sexual dimorphism in mouse gonads becomes evident at around E12.5 followed by initiation of germ cell development. Previous research has been focusing on protein-coding genes. Accumulating evidence has been showing the active involvement of various ncRNAs in development. However, we are still far from having a complete picture of the RNA regulatory networks in early gonadal development. In this study, we performed sequoia complete stranded RNA-Seq using pooled total RNAs from mouse male and female gonads at E11.5, E12.5, E13.5, and E14.5, respectively. By adding poly(A) tails and unique molecular identifiers (UMI) to all stranded RNAs, we were able to quantify short- and long-stranded RNAs with or without poly(A) tails in one preparation for each time point. This is the first profiling of complete stranded RNAs during early mouse gonad development, specifically emcompassing critical stages such as sex determination and initiation of germ cell development. with this advanced sequencing technique, we aim to gain a comprehensive understanding of RNA landscape and regulatory networks involved in these critical developmental processes. Embryos were collected from pregnant C57BL/6J wild-type mice at E11.5, E12.5, E13.5 and E14.5. The XX and XY gonads were dissected and pooled together in equal numbers for total RNA extraction with Trizol reagent, followed by SEQuoia Complete Stranded RNA-Seq. Each time point contained at least 6 embryos. Long RNA and small RNA expression profiles were compared across the four-time points.