Microarray analysis of microRNA expression in mouse fetus at 13.5 and 14.5 days post-coitum in ear and back skin tissues.

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The purpose of this study was to determine the stage-specific expression of microRNA during external ear development in mice under normal conditions. GeneChip miRNA 3.0 arrays by Affymetrix were used to obtain miRNA expression profiles from mice fetal pinnae and back skin tissues at 13.5 days-post-coitum (dpc) and 14.5 dpc. Biological triplicates for each tissue were analyzed; one litter represents one biological replica, each litter had 16 fetuses on average. The results were analyzed with Affymetrix's Transcriptome Analysis Console software to identify differentially expressed miRNAs. The inquiry showed significant differential expression of 25 miRNAs at 13.5 dpc and 31 at 14.5 dpc, some of these miRNAs were predicted to target genes implicated in external ear development. One example is mmu-miR-10a whose low expression in pinnae is known to impact ear development by modulating Hoxa1 mRNA levels Garzon et al. (2006), Gavalas et al. (1998) [1], [2]. Other findings like the upregulation of mmu-miR-200c and mmu-miR-205 in the pinnae tissues of healthy mice are in agreement with what has been reported in human patients with microtia, in which down regulation of both miRNAs has been found Li et al. (2013) [3]. This study uncovered a spatiotemporal pattern of miRNA expression in the external ear, which results from continuous transcriptional changes during normal development of body structures. All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945.", "claims": [{"id": "claim-method", "statement": "The identification of differentially expressed miRNAs at each stage, was achieved by using linear regression and hierarchical clustering analysis with the Transcriptome Analysis Console software from Affymetrix.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408816", "locator": "sections[6] \"microRNA array analysis\" paragraph 4", "quote": "The identification of differentially expressed miRNAs at each stage, was achieved by using linear regression and hierarchical clustering analysis with the Transcriptome Analysis Console software from Affymetrix."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27408816", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differentially expressed miRNAs were identified by linear regression and hierarchical clustering with the Transcriptome Analysis Console software; 25 miRNAs were significant at 13.5 dpc and 31 at 14.5 dpc, and the source microarray data are available through GEO accession GSE64945.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27408816", "locator": "sections[6] \"microRNA array analysis\" paragraph 4", "quote": "The identification of differentially expressed miRNAs at each stage, was achieved by using linear regression and hierarchical clustering analysis with the Transcriptome Analysis Console software from Affymetrix."}, {"asset": "source:pmid:27408816", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The inquiry showed significant differential expression of 25 miRNAs at 13.5 dpc and 31 at 14.5 dpc, some of these miRNAs were predicted to target genes implicated in external ear development."}, {"asset": "source:pmid:27408816", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differentially expressed miRNAs were identified by linear regression and hierarchical clustering with the Transcriptome Analysis Console software; 25 miRNAs were significant at 13.5 dpc and 31 at 14.5 dpc, and the source microarray data are available through GEO accession GSE64945.", "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:27408816"], "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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"microRNA array analysis", "row_count": 112, "column_count": 4}, "table": {"label": "Table 2", "caption": "Differentially expressed microRNA in ear (pinnae) versus back skin at 14.5 dpc.", "rows": [["microRNA ID", "Ear 14.5 dpc", "Back 14.5 dpc", "Fold change"], ["mmu-miR-205_st", "12.87", "6.8", "67.04"], ["mmu-miR-200b-star_st", "6.78", "0.86", "60.56"], ["mmu-miR-205-star_st", "6.94", "1.08", "58.14"], ["mmu-miR-200a_st", "7.93", "2.07", "57.91"], ["mmu-miR-375_st", "8.27", "2.6", "50.82"], ["mmu-miR-200b_st", "8.2", "3.49", "26.15"], ["mmu-miR-429_st", "9.1", "4.54", "23.51"], ["mmu-miR-200c_st", "11.6", "7.16", "21.63"], ["mmu-miR-141_st", "5.43", "1.14", "19.67"], ["mmu-miR-203_st", "10.84", "6.56", "19.51"], ["mmu-miR-706_st", "5.61", "2.41", "9.15"], ["mmu-miR-27b-star_st", "7.65", "4.63", "8.14"], ["mmu-miR-23b-star_st", "5.39", "2.52", "7.31"], ["mmu-miR-34a_st", "7.75", "5.3", "5.48"], ["mmu-miR-184_st", "5.98", "3.69", "4.89"], ["mmu-miR-199b-star_st", "9.91", "7.65", 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