Unraveling the rat blood genome-wide transcriptome after oral administration of lavender oil by a two-color dye-swap DNA microarray approach.

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With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. In this brief, we investigate the effect of LO ingestion in the blood of rat. Rats were administered LO at usual therapeutic dose (5 mg/kg) in humans, and following collection of the venous blood from the heart and extraction of total RNA, the differentially expressed genes were screened using a 4 × 44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA) in conjunction with a two-color dye-swap approach. A total of 834 differentially expressed genes in the blood were identified: 362 up-regulated and 472 down-regulated. These genes were functionally categorized using bioinformatics tools. The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO): GSE67499. The data will be a valuable resource in examining the effects of natural products, and which could also serve as a human model for further functional analysis and investigation.", "claims": [{"id": "claim-method", "statement": "The functional analysis identified the biological functions that were most significant to the dataset (p-value < 0.05) according to a right-tailed Fisher's exact test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27330992", "locator": "sections[7] \"Functional categorization of differentially expressed genes in the whole blood after LO ingestion and ingenuity pathway analysis of the whole blood transcriptome\" paragraph 3", "quote": "The functional analysis identified the biological functions that were most significant to the dataset (p-value < 0.05) according to a right-tailed Fisher's exact test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The outputs (raw data) of the microarray analysis that were used in this study are open and freely available under the number series GSE 67499 (whole genome) at the NCBI Gene Expression Omnibus (GEO) public functional genomics data repository.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27330992", "locator": "sections[9] \"Differentially expressed genes in the whole blood of rat after LO treatment\" paragraph 2", "quote": "The outputs (raw data) of the microarray analysis that were used in this study are open and freely available under the number series GSE 67499 (whole genome) at the NCBI Gene Expression Omnibus (GEO) public functional genomics data repository."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using two-color dye-swap whole-genome microarray analysis, the study identified 834 differentially expressed blood genes, and the source data were deposited in GEO under accession GSE67499.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27330992", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 834 differentially expressed genes in the blood were identified: 362 up-regulated and 472 down-regulated."}, {"asset": "source:pmid:27330992", "locator": "sections[6] \"Whole blood whole-genome DNA microarray analysis\" paragraph 3", "quote": "Statistical significance of the log ratio values obtained for individual microarray probes was calculated using the “most conservative error model” default function of the Feature Extraction software, by which both a propagated and a universal error model are evaluated, and the higher (more conservative estimate of error) p-value of two error models was reported [6; Agilent Technologies]."}, {"asset": "source:pmid:27330992", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO): GSE67499."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using two-color dye-swap whole-genome microarray analysis, the study identified 834 differentially expressed blood genes, and the source data were deposited in GEO under accession GSE67499.", "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:27330992"], "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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