Severe COVID-19 is marked by a dysregulated myeloid cell compartment. Schulte-Schrepping et al., 2020

Supplemental tables of the publication "Severe COVID-19 is marked by a dysregulated myeloid cell compartment." Schulte-Schrepping et al., 2020.

Table S1 - Cohort details (related to all Figures)
Table S2 - Detailed information on antibody panels used for mass cytometry analysis (related to Figure 1,3,6)
Table S3 - List of antibodies used for multi-color flow cytometry (related to Figure 1,3,6).
Table S4 - Cluster-specific marker gene lists from the scRNA-seq analyses (related to Figure 2,4,5,7 + S2-4,S6)

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro, Elena De Domenico, Daniel Wendisch, Martin Grasshoff, Theodore S. Kapellos, Michael Beckstette, Tal Pecht, Adem Saglam, Oliver Dietrich, Henrik E. Mei, Axel R. Schulz, Claudia Conrad, Désirée Kunkel, Ehsan Vafadarnejad, Cheng-Jian Xu, Arik Horne, Miriam Herbert, Anna Drews, Charlotte Thibeault, Moritz Pfeiffer, Stefan Hippenstiel, Andreas Hocke, Holger Müller-Redetzky, Katrin-Moira Heim, Felix Machleidt, Alexander Uhrig, Laure Bosquillon de Jarcy, Linda Jürgens, Miriam Stegemann, Christoph R. Glösenkamp, Hans-Dieter Volk, Christine Goffinet, Markus Landthaler, Emanuel Wyler, Philipp Georg, Maria Schneider, Chantip Dang-Heine, Nick Neuwinger, Kai Kappert, Rudolf Tauber, Victor Corman, Jan Raabe, Kim Melanie Kaiser, Michael To Vinh, Gereon Rieke, Christian Meisel, Thomas Ulas, Matthias Becker, Robert Geffers, Martin Witzenrath, Christian Drosten, Norbert Suttorp, Christof von Kalle, Florian Kurth, Kristian Händler, Joachim L. Schultze, Anna C Aschenbrenner, Yang Li, Jacob Nattermann, Birgit Sawitzki, Antoine-Emmanuel Saliba, Leif Erik Sander, Deutsche COVID-19 OMICS Initiative (DeCOI)

Coronavirus Disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progresses to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19, associated with increased neutrophil counts and dysregulated immune responses, remains unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 (242 samples from 109 individuals) over time. HLA-DR high CD11c high inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DR low monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

论文《重症COVID-19以髓系细胞室失调为特征（Severe COVID-19 is marked by a dysregulated myeloid cell compartment）》的补充表格，作者为Schulte-Schrepping等人，2020年发表。

表S1：研究队列详情（对应所有附图）
表S2：用于质谱流式细胞术（mass cytometry）分析的抗体组合详细信息（对应图1、3、6）
表S3：用于多色流式细胞术（multi-color flow cytometry）的抗体列表（对应图1、3、6）
表S4：单细胞RNA测序（scRNA-seq）分析得到的聚类特异性标记基因列表（对应图2、4、5、7及补充图S2-4、S6）

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

Jonas Schulte-Schrepping, Nico Reusch, Daniela Paclik, Kevin Baßler, Stephan Schlickeiser, Bowen Zhang, Benjamin Krämer, Tobias Krammer, Sophia Brumhard, Lorenzo Bonaguro, Elena De Domenico, Daniel Wendisch, Martin Grasshoff, Theodore S. Kapellos, Michael Beckstette, Tal Pecht, Adem Saglam, Oliver Dietrich, Henrik E. Mei, Axel R. Schulz, Claudia Conrad, Désirée Kunkel, Ehsan Vafadarnejad, Cheng-Jian Xu, Arik Horne, Miriam Herbert, Anna Drews, Charlotte Thibeault, Moritz Pfeiffer, Stefan Hippenstiel, Andreas Hocke, Holger Müller-Redetzky, Katrin-Moira Heim, Felix Machleidt, Alexander Uhrig, Laure Bosquillon de Jarcy, Linda Jürgens, Miriam Stegemann, Christoph R. Glösenkamp, Hans-Dieter Volk, Christine Goffinet, Markus Landthaler, Emanuel Wyler, Philipp Georg, Maria Schneider, Chantip Dang-Heine, Nick Neuwinger, Kai Kappert, Rudolf Tauber, Victor Corman, Jan Raabe, Kim Melanie Kaiser, Michael To Vinh, Gereon Rieke, Christian Meisel, Thomas Ulas, Matthias Becker, Robert Geffers, Martin Witzenrath, Christian Drosten, Norbert Suttorp, Christof von Kalle, Florian Kurth, Kristian Händler, Joachim L. Schultze, Anna C Aschenbrenner, Yang Li, Jacob Nattermann, Birgit Sawitzki, Antoine-Emmanuel Saliba, Leif Erik Sander, Deutsche COVID-19 OMICS Initiative (DeCOI)

新型冠状病毒病2019（COVID-19）是一种轻至中度的呼吸道感染性疾病，但部分患者会进展为重症并引发呼吸衰竭。轻症患者的保护性免疫机制，以及与中性粒细胞（neutrophil）计数升高、免疫应答失调相关的重症COVID-19发病机制，目前仍不明确。本研究采用双中心、两队列设计，对全血及外周血单个核细胞（peripheral blood mononuclear cells, PBMC）进行单细胞RNA测序（single-cell RNA-sequencing）与单细胞蛋白质组学分析，以明确轻症与重症COVID-19患者的免疫细胞组成及活化状态随时间的变化（共纳入109名受试者的242份样本）。轻症COVID-19患者体内可见携带干扰素刺激基因特征的HLA-DR高表达、CD11c高表达的炎性单核细胞增多。重症COVID-19则以中性粒细胞前体细胞（即应急髓系生成的标志）、功能异常的成熟中性粒细胞以及HLA-DR低表达单核细胞的出现为特征。本研究深入阐明了机体针对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）感染的系统性免疫应答，并揭示了与重症COVID-19相关的髓系细胞室的显著改变。