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 Weis2,3,4*, Peter Ahnert1, Martin Witzenrath5,6, 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 Kiehntopf12,13, Petra Creutz5, Markus Loeffler1, Norbert Suttorp5,6,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