biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsHolger Kirstentranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-11796Clinical decision-making in patients with community-acquired pneumonia at risk of organ dysfunction and death is currently aided by clinical scores. Here, we compare transcriptomes of patients to identify a signature to better identifie patients-at-risk for ICU admission and death. For this, we analyse time-course transcriptomic data from samples of a prospective observational cohort study that included hospitalized CAP across 63 centers in Germany (‘PROGRESS’; clinicaltrials.gov NCT02782013). This case-control study consisted of discovery (n=240) and validation cohorts (n=215) where transcriptomic data were analyzed for association with a composite endpoint (cEP) of qualified ICU admission and 28-day mortality.biostudies-arrayexpressNucleic Acid Extraction - Whole venous blood was collected into PAXgene blood RNA tubes (Qiagen, Hilden, Germany) and stored at -80 °C until processing. A PAXgene miRNA kit (Qiagen) was used for RNA isolation. In brief, frozen whole blood was thawed and equilibrated at room temperature for 2 h. The samples were centrifuged at 4,000g, the supernatant was decanted, and the pellets were resuspended in 4 ml of water. Further purification was carried out according to the manufacturer's instructions using a QIAcube. After two steps of DNase digestion (TURBO DNA-free Kit, Ambion) and sample concentration (RNA Clean & Concentrator-5 Kit, Zymo Research), the extracted RNA was quantified using a Qubit RNA Kit and a DeNovix instrument (Biozym). or Nanodrop 2000c (Thermo Scientific). The quality of RNA was assessed with a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, California, USA) with the RNA 6000 Nano Kit.Hybridization - Samples were hybridized to Illumina HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA)according to the manufacturer’s suggestions.Sample Collection - The samples were collected within the Study of Progression of Community Acquired Pneumonia in the Hospital (PROGRESS), a prospective multicenter observational cohort study that has been recruiting CAP patients requiring hospitalization in Germany and Austria (ClinicalTrials.gov: NCT02782013)Labeling - Purified RNA was dissolved at a concentration of 50–300 ng/μl prior to probe synthesis. Samples were labeled following the suggestions for Illumina HT-12 v4 Expression BeadChips by the manufacturer,Illumina, San Diego, CA, US.Scaning - Hybridization was measured using an Illumina HiScan according to the manufacturer’s suggestions. Raw data for all 47,231 gene-expression probes were extracted by Illumina GenomeStudio without additional background correction.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsPROGRESS Study GroupMarkus ScholzKnut KrohnMarkus LoefflerPetra CreutzHolger KirstenMartin WitzenrathMichael BauerSebastian WeissNorbert SuttorpGeraldine NouaillesMichael KiehntopfDennis LöfflerPeter AhnertConny BlumertData Transformation - The data were further processed for normalization within R (version 3.4.3). Expression values were log2-transformed and quantile-normalized to allow parametric analysis. Batch effects of BeadChip expression were corrected using an empirical Bayes method implemented in the R-packages sva 3.26.0. During preprocessing, gene-expression probes detected by Illumina GenomeStudio as being expressed in less than 5% of the samples were excluded, as were probes still found to be significantly associated with processing batches after Bonferroni correction. These filters resulted in 26,601 valid gene-expression probes.falseComparison of CAP-patients with a severe disease course vs. CAP-patients with non-severe disease courseClinical decision-making in patients with community-acquired pneumonia at risk of organ dysfunction and death is currently aided by clinical scores. Here, we compare transcriptomes of patients to identify a signature to better identifie patients-at-risk for ICU admission and death. For this, we analyse time-course transcriptomic data from samples of a prospective observational cohort study that included hospitalized CAP across 63 centers in Germany (‘PROGRESS’; clinicaltrials.gov NCT02782013). This case-control study consisted of discovery (n=240) and validation cohorts (n=215) where transcriptomic data were analyzed for association with a composite endpoint (cEP) of qualified ICU admission and 28-day mortality.2026-01-31T00:00:00Z2026-01-31T02:02:04.692Z2022-06-07T15:00:32.712ZE-MTAB-11796EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815