Mouse Global gene expression profiles of mouse embryonic day 3.75 inner cell mass cells

The goal of this study is elucidating the mechanisms of the primitive endoderm (PrE, founder of the yolk sac) segregates from the epiblast (EPI, founder of the foetus). Within the uterus and ex vivo, precursors of the EPI and PrE emerge in an unsorted manner in inner cell mass (ICM). Coincident with identity acquisition, the cells physically sort, resulting in PrE establishing a single layer of cells covering the cavity-facing surface of the ICM with the EPI enclosed between the PrE and polar trophectoderm. The mechanism that determines this spatial segregation between EPI and PrE is still poorly understood. To achieve this goal, we have compared mouse embryonic day (E) 3.75 ICM cells' transcriptome profiling to other existing mouse E3.5 and E4.5 ICM cells' RNA-seq data. We have identified the timing of EPI and PrE lineages specification and maturation and each stage- and lineage-specific genes expression profiles. Single cells of mouse PDGFRa::H2B-GFP/+ E3.75 ICMs mRNA profiles were generated using Smart-seq2.本研究旨在阐明原始内胚层（primitive endoderm, PrE，卵黄囊的前体）与上胚层（epiblast, EPI，胎儿的前体）的分离机制。在体内子宫环境及体外培养条件下，内细胞团（inner cell mass, ICM）内的上胚层与原始内胚层前体细胞最初呈无序分布状态。随着细胞身份的确立，这些细胞会发生物理分选，最终原始内胚层形成单层细胞，覆盖于内细胞团面向囊腔的表面，而上胚层则被包裹于原始内胚层与极性滋养层细胞之间。目前学界对决定上胚层与原始内胚层这种空间分离的分子机制仍知之甚少。为达成上述研究目标，我们将小鼠胚胎第3.75天（E3.75）的内细胞团细胞转录组谱数据，与已公开的小鼠E3.5及E4.5时期内细胞团的RNA测序（RNA-seq）数据进行了对比分析。本研究明确了上胚层与原始内胚层谱系特化及成熟的时间节点，并解析了各阶段及各谱系特异性基因的表达谱。本研究通过Smart-seq2技术，获取了小鼠PDGFRa::H2B-GFP/+品系E3.75时期内细胞团的单细胞mRNA表达谱。