Mapping the mouse developmental and aging atlas by single cell mRNA-seq

Single-cell mRNA sequencing (mRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built a comprehensive mouse cell atlas to catalog all cell types by collecting scRNA-seq data in the fetal and adult stages. However, systematically study for organism-level dynamic changes of cellular states across mouse life span are still lacking. Here, We made an updated version of mouse cell atlas (MCA) by adding scRNA-seq data covering 14 major mouse organs during different mouse development period. We revealed aging related regulatory networks and pathways that have not been well characterized previously. We found that the expressions of immune-related genes, such as antigen-presenting genes and immunoglobulin genes, appeared in non-immune cell types in aging process. We also focused on the expression of lung epithelial immunoglobulin genes and revealed their related transcriptional regulation mechanisms. The updated MCA resource provides a valuable resource for studying mammalian development, maturation and aging. Microwell datasets for ten mouse tissues (brain, heart, intestine, kidney, liver, lung, pancreas, stomach, testis and uterus) covering 8 stages including E14.5, neonatal, 10d, 3w, 6-8w, 12m, 18m and 24m, four mouse tissues (bladder, spleen and prostate) covering aging stages including 6-8w, 12m, 18m, 24m, one tissue (thymus) covering aging stages including 6-8w, 12m, 18m and some mouse tissues used in GSE134355 and GSE108097.单细胞mRNA测序（mRNA-seq）技术正在重塑当前的细胞类型分类体系。 既往研究中，我们通过收集胎鼠与成年小鼠的单细胞RNA测序（single-cell RNA-seq, scRNA-seq）数据，构建了一套全面注释全部细胞类型的完整小鼠细胞图谱。 然而，目前仍缺乏针对小鼠整个生命周期内细胞状态的机体层面动态变化的系统性研究。 本研究中，我们新增了覆盖小鼠不同发育阶段的14种主要器官的scRNA-seq数据，构建了更新版的小鼠细胞图谱（Mouse Cell Atlas, MCA）。 我们揭示了此前尚未被充分解析的衰老相关调控网络与信号通路。 研究发现，在衰老进程中，抗原呈递基因、免疫球蛋白基因等免疫相关基因的表达会出现在非免疫细胞类型中。 我们还聚焦于肺上皮细胞的免疫球蛋白基因表达，并解析了其相关的转录调控机制。 这套更新后的MCA数据集为哺乳动物发育、成熟与衰老的相关研究提供了宝贵的资源。 本数据集包含10种小鼠组织（脑、心脏、肠、肾、肝、肺、胰腺、胃、睾丸与子宫）的微井测序数据，覆盖8个发育阶段：E14.5、新生期、10日龄、3周龄、6-8周龄、12月龄、18月龄与24月龄；另有4种小鼠组织（膀胱、脾脏与前列腺）的测序数据，覆盖6-8周龄、12月龄、18月龄、24月龄的衰老阶段；1种组织（胸腺）的测序数据覆盖6-8周龄、12月龄、18月龄的衰老阶段；此外还包含GSE134355与GSE108097数据集所使用的部分小鼠组织数据。