Data supplement to Manuscript "A 5-Gene Signature (PROGRESS-STYCK) predicts ICU Admission and Death in Community Acquired Pneumonia"

Supplementary RNAseq data for correlation analysis with HT12v4 Chip data This refers to the publication <strong>A 5-Gene </strong><strong>Signature (PROGRESS-STYCK) predicts ICU Admission and Death in Community Acquired Pneumonia</strong> Holger Kirsten¹*, Sebastian Weis^2,3,4*, Peter Ahnert¹, Martin Witzenrath^5,6, Brendon P. Scicluna^7,8, Knut Krohn⁹, Friedmann Horn¹⁰Michael Rade¹⁰, Catharina Bertram¹⁰, Kristin Reiche¹⁰, Dennis Löffler¹⁰, Conny Blumert¹⁰, Kai Sohn¹¹, Stefan Jenner¹¹,, Kai Sohn¹¹, Geraldine Nouailles⁵, Michael Kiehntopf^12,13, Petra Creutz⁵, Markus Loeffler¹, Norbert Suttorp^5,6,PROGRESS Study Group, Markus Scholz¹⁺, Michael Bauer²⁺ ¹ Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Leipzig University, Leipzig, Germany, ² Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich-Schiller-University Jena, Germany ³Institute for Infectious Disease and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany ⁴Leibniz Institute for Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena ⁵Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany. ⁶ German Center for Lung Research (DZL), Partner Site Charité, Berlin, Germany. ⁷ Centre for Molecular Medicine and Biobanking, University of Malta, Malta ⁸ Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Malta ⁹ Core Unit DNA Technologies, Medical Faculty, Leipzig University, Leipzig, Germany. ¹⁰ Department of Diagnostics, Institute for Cell Therapy and Immunology, Leipzig, Germany ¹¹ Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany ¹²Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany. ¹³Integrated Biobank Jena (IBBJ), Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany. *+ these authors contributed equally to the work. For sequencing-based expression quantification, libraries were prepared using globin-mRNA depleted RNA and sequencing was performed with HiSeq2500 sequencing (Illumina, San Diego, CA, USA), with an average sequencing depth of 100 million clusters per sample and 2x100b paired-end reads. Data analysis included demultiplexing, trimming, filtering, removal of low-quality bases, quantification at gene-level, and quality-assessment. Data of measured genes and individuals can be found in file <strong>s816_1_expression_levels_ngs.txt</strong>. For array-based expression quantification, purified RNA was hybridized to Illumina HT-12v4 Expression-BeadChips (Illumina, San Diego, CA, USA). Low-quality samples were removed, and data was log2-transformed, quantile-normalized, batch-corrected and filtered for minimum expression levels, resulting in 26,601 transcripts representing 16,329 unique genes.Data of measured genes and individuals can be found in <strong>s816_1_expression_levels_array.txt</strong> Data showing corresponding genes between NGS gene IDs and Array probe IDs can be found in <strong>s816_1_assignment_genes_ngs_array.txt</strong><br>本数据集为用于与HT12v4芯片（HT12v4 Chip）数据开展相关性分析的补充RNA测序（RNAseq）数据，关联于发表论文<strong>《5基因特征（PROGRESS-STYCK）可预测社区获得性肺炎患者的ICU收治与死亡风险》</strong>。 作者：Holger Kirsten¹*，Sebastian Weis^2,3,4*，Peter Ahnert¹，Martin Witzenrath^5,6，Brendon P. Scicluna^7,8，Knut Krohn⁹，Friedmann Horn¹⁰，Michael Rade¹⁰，Catharina Bertram¹⁰，Kristin Reiche¹⁰，Dennis Löffler¹⁰，Conny Blumert¹⁰，Kai Sohn¹¹，Stefan Jenner¹¹，Kai Sohn¹¹，Geraldine Nouailles⁵，Michael Kiehntopf^12,13，Petra Creutz⁵，Markus Loeffler¹，Norbert Suttorp^5,6，PROGRESS研究组，Markus Scholz¹⁺，Michael Bauer²⁺ ¹ 德国莱比锡大学医学信息学、统计学与流行病学研究所（IMISE）； ² 德国耶拿弗里德里希·席勒大学耶拿大学医院麻醉与重症医学科； ³ 德国耶拿弗里德里希·席勒大学耶拿大学医院传染病与感染控制研究所； ⁴ 德国耶拿莱布尼茨天然产物研究与感染生物学研究所（汉斯·克诺尔研究所）； ⁵ 柏林夏里特医学院（柏林自由大学与洪堡大学附属机构）感染病与呼吸内科； ⁶ 德国肺研究中心（DZL）夏里特合作站点； ⁷ 马耳他大学分子医学与生物样本库中心； ⁸ 马耳他大学健康科学学院应用生物医学系马耳他母德医院； ⁹ 德国莱比锡大学医学院核心DNA技术实验室； ¹⁰ 德国莱比锡细胞治疗与免疫学研究所诊断科； ¹¹ 德国斯图加特弗劳恩霍夫界面工程与生物技术研究所； ¹² 德国耶拿弗里德里希·席勒大学耶拿大学医院临床化学与检验医学科； ¹³ 德国耶拿弗里德里希·席勒大学耶拿大学医院综合生物样本库（IBBJ）。 *+ 上述作者对本工作贡献均等。 在基于测序的表达定量实验中，采用去除珠蛋白mRNA的RNA构建测序文库，使用HiSeq2500测序平台（Illumina公司，美国加利福尼亚州圣迭戈）进行测序，单样本平均测序深度为1亿个测序簇，采用2×100bp双端测序读长。数据分析流程包含解多重测序、序列修剪、质量过滤、低质量碱基切除、基因水平表达定量以及质量评估。已检测基因及样本的表达数据可在文件<strong>s816_1_expression_levels_ngs.txt</strong>中获取。 在基于芯片的表达定量实验中，将纯化后的RNA与Illumina HT12v4表达微珠芯片（Illumina公司，美国加利福尼亚州圣迭戈）进行杂交。剔除低质量样本后，对数据进行log₂转换、分位数归一化、批次校正，并按最低表达阈值进行过滤，最终得到26601个转录本，对应16329个独特基因。已检测基因及样本的芯片表达数据可在<strong>s816_1_expression_levels_array.txt</strong>中获取；二代测序（NGS）基因ID与芯片探针ID的对应基因信息可在<strong>s816_1_assignment_genes_ngs_array.txt</strong>中获取<br>