Single-cell RNA-seq dataset of innate lymphoid cells

The helper-like ILC contains various functional subsets, such as ILC1, ILC2, ILC3 and LTi cells, mediating the immune responses against viruses, parasites, and extracellular bacteria, respectively. Among them, LTi cells are also crucial for the formation of peripheral lymphoid tissues, such as lymph nodes. Our research, along with others’, indicates a high proportion of LTi cells in the fetal ILC pool, which significantly decreases after birth. Conversely, the proportion of non-LTi ILCs increases postnatally, corresponding to the need for LTi cells to mediate lymphoid tissue formation during fetal stages and other ILC subsets to combat diverse pathogen infections postnatally. However, the regulatory mechanism for this transition remains unclear. In this study, we observed a preference for fetal ILC progenitors to differentiate into LTi cells, while postnatal bone marrow ILC progenitors preferentially differentiate into non-LTi ILCs. Particularly, this differentiation shift occurs within the first week after birth in mice. Further analysis revealed that adult ILC progenitors exhibit stronger activation of the Notch signaling pathway compared to fetal counterparts, accompanied by elevated <i>Gata3</i> expression and decreased <i>Rorc</i> expression, leading to a transition from fetal LTi cell-dominant states to adult non-LTi ILC-dominant states. This study suggests that the body can regulate ILC development by modulating the activation level of the Notch signaling pathway, thereby acquiring different ILC subsets to accommodate the varying demands within the body at different developmental stages.<br><br><br>Data usage```import scanpy as sc<br># read the data using scanpyadata= sc.read_h5ad('./220516-ABM.velo.h5ad')<br># draw umap for visualization. `ann0608` is the cell type label.sc.pl.umap(adata,color='ann0608')<br># get gene expression matrixadata.X<br>```

辅助样固有淋巴细胞（helper-like ILC）包含多个功能亚群，包括ILC1、ILC2、ILC3以及淋巴组织诱导细胞（LTi cells），它们分别介导针对病毒、寄生虫与胞外细菌的免疫应答。其中，淋巴组织诱导细胞（LTi cells）对于外周淋巴组织（如淋巴结）的形成具有关键作用。本研究与其他团队的研究均证实，胎儿固有淋巴细胞库中淋巴组织诱导细胞的占比较高，但该占比在出生后会显著降低。与之相反，非LTi固有淋巴细胞的占比在出生后呈上升趋势，这与胎儿阶段依赖淋巴组织诱导细胞介导淋巴组织形成、出生后则依靠其他固有淋巴细胞亚群抵御多种病原体感染的生理需求相匹配。然而，这一转变的调控机制目前仍未阐明。本研究观察到，胎儿固有淋巴细胞祖细胞更倾向于分化为淋巴组织诱导细胞，而出生后骨髓中的固有淋巴细胞祖细胞则优先分化为非LTi固有淋巴细胞。尤为值得注意的是，这一分化转变在小鼠出生后的第一周内即可发生。进一步分析显示，与胎儿阶段的固有淋巴细胞祖细胞相比，成年个体的该类祖细胞的Notch信号通路激活程度更强，同时伴随<i>Gata3</i>表达上调与<i>Rorc</i>表达下调，进而促成从胎儿阶段以淋巴组织诱导细胞为主的状态向成年阶段以非LTi固有淋巴细胞为主的状态转变。本研究表明，机体可通过调控Notch信号通路的激活水平来调节固有淋巴细胞的发育进程，从而产生不同的固有淋巴细胞亚群，以适应机体在不同发育阶段的多样化生理需求。

数据使用说明
import scanpy as sc
# 使用scanpy读取数据
adata= sc.read_h5ad('./220516-ABM.velo.h5ad')
# 绘制UMAP图以可视化，`ann0608`为细胞类型标签
sc.pl.umap(adata,color='ann0608')
# 获取基因表达矩阵
adata.X