Single-cell transcriptome analysis of mouse fetal livers from different developmental stages

We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development. Our data demonstrated the existence of two types of stem/progenitor cells with distinct molecular patterns during liver development. Both types of cells exhibit heterogeneity of transcriptional program within each cell population, suggesting they be in distinct status of self-renewal, cell proliferation and different sub-stages of differentiation and maturation. In general, our data depicting the dynamic trajectories with transcriptional profiles at single-cell resolution during mouse liver development provides insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of liver stem/progenitor cells. The transcriptomes of 507 single cells from E11.5, E12.5, E13.5, E14.5, E16.5, E18.5 and P2.5 mouse livers were analyzed in this study. ERCC Spike-ins were included in each sample as control. For E11.5 stage, we analyzed 70 single cells from one embryonic mouse (pooled sibling livers); for E12.5 stage, we analyzed 2 biological replicates (2 embryonic mouse), with 83 single cells from replicate 1 and 17 single cells from replicate 2; for E13.5 stage, we analyzed 71 single cells from one embryonic mouse; for E14.5 stage, we analyzed 2 biological replicates, with 75 single cells from replicate 1 and 24 single cells from replicate 2; for E16.5 stage, we analyzed 2 biological replicates, with 56 single cells from replicate 1 and 22 single cells from replicate 2; for E18.5 stage, we analyzed 2 biological replicates, with 39 single cells from replicate 1 and 19 single cells from replicate 2; for P2.5 stage, we analyzed 2 biological replicates, with 21 single cells from replicate 1 and 10 single cells from replicate 2. All single cell samples were processed on the microfluidic system.我们采用无标记单细胞RNA测序（marker-free single-cell RNA-Seq），对小鼠肝脏发育过程中胚胎第11.5天（E11.5）至出生后第2.5天（P2.5）共7个阶段的507个细胞开展了全面的转录组特征分析。本研究数据证实，在肝脏发育进程中存在两类具备独特分子特征的干细胞/祖细胞（stem/progenitor cells）。两类细胞在各自的细胞群体中均表现出转录程序的异质性，提示它们处于不同的自我更新、细胞增殖状态，以及分化与成熟的不同亚阶段。总体而言，本研究通过单细胞分辨率的转录组数据描绘了小鼠肝脏发育的动态轨迹，为肝脏干细胞/祖细胞的命运决定、自我更新的转录调控以及分化与成熟过程提供了全新见解。本研究共分析了来自E11.5、E12.5、E13.5、E14.5、E16.5、E18.5及P2.5阶段小鼠肝脏的507个单细胞的转录组。所有样本均加入了外部RNA控制序列掺入物（ERCC Spike-ins）作为对照。针对E11.5阶段，我们分析了来自1只胚胎小鼠（合并同窝肝脏）的70个单细胞；针对E12.5阶段，我们设置了2个生物学重复（biological replicates），共使用2只胚胎小鼠，重复1与重复2分别包含83个和17个单细胞；针对E13.5阶段，我们分析了来自1只胚胎小鼠的71个单细胞；针对E14.5阶段，我们设置了2个生物学重复，重复1与重复2分别包含75个和24个单细胞；针对E16.5阶段，我们设置了2个生物学重复，重复1与重复2分别包含56个和22个单细胞；针对E18.5阶段，我们设置了2个生物学重复，重复1与重复2分别包含39个和19个单细胞；针对P2.5阶段，我们设置了2个生物学重复，重复1与重复2分别包含21个和10个单细胞。所有单细胞样本均通过微流控系统（microfluidic system）完成处理。