DataSheet_1_Differential in vivo labeling with barcoded antibodies allows for simultaneous transcriptomic profiling of airway, lung tissue and intravascular immune cells.docx

Single-cell RNA sequencing (scRNA-seq) is the state-of-the-art approach to study transcriptomic signatures in individual cells in respiratory health and disease. However, classical scRNA-seq approaches provide no spatial information and are performed using either bronchoalveolar lavage fluid (BAL) or lung single cell suspensions to assess transcript levels in airway and tissue immune cells, respectively. Herein we describe a simple method to simultaneously characterize transcriptomic features of airway, lung parenchymal and intravascular immune cells based on differential in vivo labeling with barcoded antibodies. In addition to gaining basic spatial information, this approach allows for direct comparison of cells within different anatomical compartments. Furthermore, this method provides a time- and cost-effective alternative to classical scRNA-seq where lung and BAL samples are processed individually, reducing animal and reagent use. We demonstrate the feasibility of this approach in a preclinical mouse model of bacterial lung infection comparing airway, parenchymal and vasculature neutrophils early after infection.

单细胞RNA测序（scRNA-seq）是研究呼吸系统健康与疾病中单个细胞转录组特征的尖端技术。然而，传统的scRNA-seq方法无法提供空间信息，且分别采用支气管肺泡灌洗液（BAL）或肺单细胞悬液来评估气道和组织免疫细胞的转录水平。本文介绍了一种基于差异体内标记条形码抗体的简单方法，以同时表征气道、肺实质和血管免疫细胞的转录组特征。除了获得基本的空间信息外，该方法还允许直接比较不同解剖部位的细胞。此外，该方法提供了一种时间与成本效益更高的替代方案，对于传统的scRNA-seq而言，在处理肺和BAL样本时，可以单独进行，从而减少动物和试剂的使用。我们在一项临床前小鼠细菌性肺感染模型中展示了该方法的可行性，通过比较感染早期气道、实质和血管中的中性粒细胞。