Analysis of age-associated transcriptome changes in uterus and decidua

We use RNA-sequencing to measure global transcription in uteri of young and aged (~1yr old) C57BL/6 females at day 3.5 (E3.5) of pregnancy, and of the decidual part of E11.5 placentas developed in young and aged (~1yr old) females. We report dys-regulation of gene expression in the E3.5 uteri and E11.5 deciduae of aged mice. We compare the transcriptome of young and aged E11.5 deciduae with that of young deciduae from E9.5-E12.5 of pregnancy, and report that aged E11.5 deciduae are developmentally retarded in comparison to young deciduae. Overall design: For E3.5 uterus RNA-seq data, we generated biological replicates from 3 young (8-20 week old) and 3 aged (47-49 week old) mice. Data for each biological replicate was generated by constructing RNA-seq libraries from 2 equivalent portions of each uterus, data from both libraries was treated as technical replicates and pooled at the analysis stage, after confirming there was no significant difference between the replicates from a single uterus. For E11.5 data, we generated biological replicates of 6 deciduae from 3 litters (2 from each litter) from young mothers (9-10 weeks, n=6) and 10 deciduae from 5 litters of aged mothers (43-47 weeks, 2 deciduae from each litter). Aged E11.5 samples were split into 2 groups: those accompanying embryos that appeared normal (An, n=5) and those with morphologically abnormal embryos (Aa, n=5). One An and one Aa decidua was taken from each litter. For decidua timecourse data, 3 biological replicates each were generated from 3 separate litters from young 9-10 week old mothers at E9.5, E10.5, E11.5, and E12.5 of pregnancy.