Employing PALM-Seq technology to capture signals associated with embryonic development in the spent media

It is necessary to select high-quality embryos with normal chromosomes before embryo implantation. Here, we used PALM-Seq for comprehensive characterization of the cell free RNA in the spent media that was used to culture human in vitro fertilization embryos. We captured 8,000 to 10,000 genes at cleavage and blastocyst stages, and we also captured miRNA markers in the spent media. Most cell free mRNA and cell free lncRNA fragments in media showed higher rates of C and T bases at 3' ends. During the cleavage stage, we captured signals indicating whether the embryos would develop into a blastocyst or not, while during the blastocyst stage, the genes stably detected in the spent media were enriched in pathways related to cellular development and metabolic processes. The temporal tracing of embryonic stages using our data corresponds to the single-cell RNA-seq data obtained at respective developmental stages of the embryos, demonstrating that using PALM-Seq technology can capture the signals associated with pre-implantation embryo development in media, thereby laying the foundation for further identification of novel markers related to embryonic development.