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

A 5-Gene Signature (PROGRESS-STYCK) predicts ICU Admission and Death in Community Acquired Pneumonia

Holger Kirsten¹*, Sebastian Weis^2,3,4*, Peter Ahnert¹, Martin Witzenrath^5,6, Brendon P. Scicluna ^7,8, Knut Krohn⁹, Friedmann Horn¹⁰Michael Rade ¹⁰, 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

³ Institute for Infectious Disease and Infection Control, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany

⁴ Leibniz Institute for Leibniz Institute for Natural Product Research and Infection Biology

Hans Knöll Institute, Jena

⁵ Charité - 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

¹² Department of Clinical Chemistry and Laboratory Medicine, Jena University Hospital, Friedrich-Schiller-University Jena, Jena, Germany.

¹³ Integrated 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 s816_1_expression_levels_ngs.txt.  

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  s816_1_expression_levels_array.txt

Data showing corresponding genes between NGS gene IDs and Array probe IDs can be found in s816_1_assignment_genes_ngs_array.txt