Gene expression profiling of mononuclear cells from patients with sepsis secondary to community-acquired pneumonia.

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Microarray-based expression profiling is a powerful approach for the investigation of complex clinical conditions such as sepsis. In this study, we investigated whole-genome expression profiles in mononuclear cells from septic patients admitted in intensive care units with community-acquired pneumonia. Blood samples were collected at the time of sepsis diagnosis and seven days later since we aimed to evaluate the role of biological processes or genes possibly involved in patient recovery. Here we provide a detailed description of the study design, including clinical information, experimental methods and procedures regarding data analysis. Metadata corresponding to microarray results deposited in the database Gene Expression Omnibus (GEO) under the accession number GSE48080 are also described in this report. Our dataset allows the identification of genes possibly associated with host defense to infection as well as gene expression patterns associated with patient outcome.", "claims": [{"id": "claim-method", "statement": "For subsequent statistical analysis we used the ANOVA implementation of Partek.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484123", "locator": "sections[7] \"Gene expression profiling using DNA microarrays\" paragraph 3", "quote": "For subsequent statistical analysis we used the ANOVA implementation of Partek."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw microarray data (background-corrected signal) can be assessed at Gene Expression Omnibus (GEO accession GSE48080).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484123", "locator": "sections[7] \"Gene expression profiling using DNA microarrays\" paragraph 3", "quote": "The raw microarray data (background-corrected signal) can be assessed at Gene Expression Omnibus (GEO accession GSE48080)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the ANOVA implementation of Partek for statistical analysis and made the raw, background-corrected microarray data available through GEO accession GSE48080.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide a detailed description of the study design, including clinical information, experimental methods and procedures regarding data analysis."}, {"asset": "source:pmid:26484123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Metadata corresponding to microarray results deposited in the database Gene Expression Omnibus (GEO) under the accession number GSE48080 are also described in this report."}, {"asset": "source:pmid:26484123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our dataset allows the identification of genes possibly associated with host defense to infection as well as gene expression patterns associated with patient outcome."}, {"asset": "source:pmid:26484123", "locator": "sections[7] \"Gene expression profiling using DNA microarrays\" paragraph 3", "quote": "For subsequent statistical analysis we used the ANOVA implementation of Partek."}, {"asset": "source:pmid:26484123", "locator": "sections[7] \"Gene expression profiling using DNA microarrays\" paragraph 3", "quote": "The raw microarray data (background-corrected signal) can be assessed at Gene Expression Omnibus (GEO accession GSE48080)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the ANOVA implementation of Partek for statistical analysis and made the raw, background-corrected microarray data available through GEO accession GSE48080.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26484123"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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