Embryo as well as visceral yolk sac gene expression differences elicited by maternal diabetes in pregnancies of the NOD mouse

Maternal diabetes during early pregnancy can cause birth defects, notably of the developing heart and nervous system. To recognize the gene expression differences that may be the basis for such birth defects, we performed RNA-Seq on mouse embryos of the Non-Obese Diabetic (NOD) strain. Mice of that strain spontaneously develop type I diabetes. We dissected concepti from diabetic as well as normoglycemic pregnancies at 8.5 days of gestation. Embryos were prepared by further dissection, somite pairs were counted, and RNA was extracted using the Trizol method. Furthermore, the visceral yolk sac was also collected, and RNA was extracted with Trizol. RNA sequencing was performed using the 3’QuantSeq method (Lexogen, Inc.) with the use of Unique Molecular Identifiers. Alignment to the mouse reference genome was performed using STAR, UMI’s were accounted for using the collapse_UMI_Bam utility, and gene counts were extracted using HTSEQ.