The whole is lesser than the sum of its parts? Dissecting layer-enriched samples of rodent placenta is worth the effort

Gene expression in the placenta, assessed by bulk RNA-seq, is a common method to explore placental function. Many rodent studies homogenize the entire placenta, and yet doing so may obscure differences within specific functional regions such as the labyrinth, junctional zone and decidua. Conversely, analysis of the whole placenta could generate apparent differences due to changes in composition (e.g., relative amounts of labyrinth vs junctional zone) rather than differential gene expression. We assess the value of dissecting and separately analysing the labyrinth and junctional zone/decidua by comparing RNA-seq results from the labyrinth, junctional zone/decidua combined, and whole placenta from an experiment examining effects of maternal food restriction and fetal sex in C57BL6/J mice at gestational day 17.5. The number of genes identified as differentially expressed in response to maternal food restriction was substantially higher in the labyrinth (910 genes), than in the junctional zone/decidua (50 genes), which in turn was slightly higher than in the whole placenta (3 genes). Only one gene was differentially expressed in all 3 tissue types, and 20 genes were differentially expressed in both the labyrinth and junctional zone/decidua. The larger number of differentially expressed genes in the labyrinth was due to both larger effect sizes and estimates of effect sizes having smaller standard errors. While dissection to obtain layer-enriched samples is slightly more time-consuming than collection of whole placenta and requires some practice, our results show that layer-enrichment is clearly worth the effort. •Studies of rodent placenta generally examine whole placenta.•We compared RNA-seq analyses of whole placenta with layer-enriched samples.•Analysis of labyrinth revealed more effects of food restriction than whole placenta.•Junctional zone/decidua combined also revealed more effects than whole placenta.•Analyses of labyrinth showed both larger effect sizes and smaller standard errors.