The species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells

• Published in: Scientific data 2014-06, Vol.1 (1), p.140009-140009, Article 140009
• Main Authors: Poussin, Carine, Mathis, Carole, Alexopoulos, Leonidas G, Messinis, Dimitris E, Dulize, Rémi H J, Belcastro, Vincenzo, Melas, Ioannis N, Sakellaropoulos, Theodore, Rhrissorrakrai, Kahn, Bilal, Erhan, Meyer, Pablo, Talikka, Marja, Boué, Stéphanie, Norel, Raquel, Rice, John J, Stolovitzky, Gustavo, Ivanov, Nikolai V, Peitsch, Manuel C, Hoeng, Julia
• Format: Article
• Language: English
• Subjects: 631/114/2114; 631/181/735; 631/80; 706/648/697; Animals; Bronchi - cytology; Bronchi - metabolism; Cytokines - metabolism; Data Descriptor; Epithelial Cells - metabolism; Humanities and Social Sciences; Humans; Models, Animal; multidisciplinary; Proteomics; Rats; Science; Systems Biology - methods; Transcriptome; Translational Medical Research
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/sdata.2014.9

The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to ‘translate’ the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies. Design Type(s) in vitro design • compound treatment design • cell type comparison design Measurement Type(s) transcription profiling assay • protein expression profiling Technology Type(s) DNA microarray • sandwich ELISA Factor Type(s) Compound • dose • organism Sample Characteristic(s) Homo sapiens • Rattus norvegicus • bronchus • Bronchial epithelial cell line Machine-accessible metadata file describing the reported data (ISA-Tab format)