Limiting the level of piglet losses before weaning is a growing demand from producers and society to improve the welfare and health of sows and piglets. In particular, perinatal mortality, which can be defined as the complete development allowing survival at birth, is mostly due to reduced piglet maturity that occurs at the end of gestation. Fetal growth and maturation depend on a fine balance between the nutrient requirements for optimal fetal growth and the maternal nutrient requirements. This balance occurs at the feto-maternal interface, defined as the interaction between the mother (uterus/endometrium) and the fetus (placenta). Thus, the CO-LOCATION project (ANR20-CE20-0020-01) studies the feto-maternal system in relation to fetal maturation and piglet survival at birth. To this end, we documented the transcriptome of endometrial and placental tissues in late gestation from pure and reciprocal crossbred fetuses using two breeds with extreme fetal maturity: Large White and Meishan, showing substantial and low neonatal mortality, respectively. 224 endometrial and 224 placental samples were selected from the PORCINET tissue collection (ANR-09-GENM-005) together with sow breed, day of gestation, sex, fetal genotypes and maturity. RNA was processed for RNA-seq analysis using NovaSeq6000. with an average of 107 and 105 million reads per endometrial and placental sample, respectively. Sequences were processed using the Nextflow nf-core/rnaseq pipeline for transcript and gene quantification. The average mapping rate was 91 % and 86 % for endometrial and placental samples, respectively. Then, the TAGADA pipeline was used to reconstruct RNA-seq de novo, predict lncRNA and quantify them. The data generated from this analysis provides a complete transcriptional profile of the feto-maternal interface during late gestation. These data sets are the starting point for further analyses, including differential expression analysis, enrichment analysis and investigation of the feto-maternal dialog.