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>```

固有淋巴细胞（Innate Lymphoid Cell, ILC）中的类辅助亚型涵盖多种功能亚群，例如ILC1、ILC2、ILC3与淋巴组织诱导细胞（Lymphoid Tissue Inducer cell, LTi cell），各亚群分别介导针对病毒、寄生虫及胞外细菌的免疫应答。其中，LTi细胞对于外周淋巴组织（如淋巴结）的形成亦发挥关键作用。本研究与其他相关团队的研究均证实，胎儿ILC库中LTi细胞占比极高，该比例在出生后会显著降低。与之相对，产后非LTi型ILC的占比随发育逐步升高，这一变化与胎儿阶段LTi细胞介导淋巴组织形成、产后其他ILC亚群抵御各类病原体感染的生理需求高度契合。

然而，这一发育转变的调控机制目前仍未明确。在本研究中，我们观察到胎儿ILC祖细胞更倾向于分化为LTi细胞，而产后骨髓ILC祖细胞则优先分化为非LTi型ILC。尤为值得注意的是，这一分化转向在小鼠出生后的第一周内即可完成。

进一步分析显示，相较于胎儿时期的ILC祖细胞，成年个体的ILC祖细胞中Notch信号通路（Notch signaling pathway）激活程度更强，同时伴随*Gata3*基因表达上调、*Rorc*基因表达下调，最终推动免疫细胞谱系从胎儿时期以LTi细胞为主的状态，转变为成年时期以非LTi型ILC为主的状态。

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ILC的发育进程，进而产生不同的ILC亚群，以适配机体在不同发育阶段的多样化生理需求。

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

搜集汇总

背景与挑战

背景概述

该数据集包含先天淋巴样细胞(ILC)的单细胞RNA测序数据，研究了ILC亚群(如ILC1、ILC2、ILC3和LTi细胞)在发育过程中的分化转变机制，特别关注Notch信号通路在胎儿LTi细胞主导状态向出生后非LTi ILC主导状态转变中的作用。数据集提供了基因表达矩阵和细胞类型标签，适用于单细胞RNA分析和RNA速度分析研究。