Single cell RNA-sequencing of lungs of Ifngr1-/-Rag-2-/- mice

We discovered Ifngr1-/-Rag-2-/- mice spontaneously develop severe pulmonary fibrosis (PF), and divided the progression process of PF in this strain into 3 phases; the pre-disease phase (until 12 weeks old; intact), the onset phase (from 12 to 18 weeks old; characterized by inflammations), and the chronic phase (after 18 weeks old; characterized by collagen deposition and obvious clinical symptoms). For the purpose of understanding the transcriptome dynamics of each phase, we performed single-cell RNA-Seq analysis on the whole lung cells from Rag-2-/- mice and Ifngr1-/-Rag-2-/- mice of different ages, including the pre-disease (7 weeks old), the onset (12 and 16 weeks old), and chronic phases (19 and 24weeks old). The whole lungs of Ifngr1-/-Rag-2-/- mice (7, 12, 16, 19, and 24 weeks old), and Rag-2-/- mice (18 weeks old; control) were isolated and dissociated, and then single-cell libraries of the whole lung cells were generated using the Chromium Single Cell 3' v2 Reagents kit (10x Genomics).本研究发现，Ifngr1-/-Rag-2-/-小鼠可自发形成重度肺纤维化（pulmonary fibrosis, PF）；我们将该品系小鼠的肺纤维化进展过程划分为三个阶段：疾病前驱期（12周龄前，肺部结构完整）、发病期（12至18周龄，以炎症反应为特征）以及慢性期（18周龄后，以胶原沉积与明显临床症状为特征）。为解析各阶段的转录组动态变化，我们对不同周龄的Rag-2-/-小鼠及Ifngr1-/-Rag-2-/-小鼠的全肺细胞开展了单细胞RNA测序（single-cell RNA-Seq）分析，样本涵盖疾病前驱期（7周龄）、发病期（12、16周龄）与慢性期（19、24周龄）的个体。我们分离并解离了7、12、16、19、24周龄的Ifngr1-/-Rag-2-/-小鼠，以及18周龄的Rag-2-/-小鼠（对照组）的全肺组织，随后采用10x Genomics的Chromium单细胞3' v2试剂试剂盒构建全肺细胞的单细胞测序文库。