Gene expression profiling of the Peyer's patch mononuclear phagocyte system.

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The PP mononuclear phagocyte system, which encompasses both dendritic cells (DCs) and macrophages, is essential for the initiation of the mucosal immune response. We recently developed a method to isolate each mononuclear phagocyte subset of PP (Bonnardel et al., 2015). We performed a transcriptional analysis of three of these subsets: the CD11b(+) conventional DC, the lysozyme-expressing monocyte-derived DC termed LysoDC and the CD11c(hi) lysozyme-expressing macrophages. Here, we provide details of the gating strategy we used to isolate each phagocyte subset and show the quality controls and analysis associated with our gene array data deposited into Gene Expression Omnibus (GEO) under GSE65514.", "claims": [{"id": "claim-method", "statement": "Hierarchical clustering (HC) by Pearson correlation distance and Ward's aggregation (Fig. 2D) and principal component analysis (PCA, Fig. 2E) were performed after selection of probes with a differential expression in any combination of array > 1.5 (2035 probes).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484215", "locator": "sections[7] \"Quality control and data analysis\" paragraph 2", "quote": "Hierarchical clustering (HC) by Pearson correlation distance and Ward's aggregation (Fig. 2D) and principal component analysis (PCA, Fig. 2E) were performed after selection of probes with a differential expression in any combination of array > 1.5 (2035 probes)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65514.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484215", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65514."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The transcriptional proximity between the subsets determined by hierarchical clustering and principal component analysis revealed a close genetic relationship between LysoDC and LysoMac, apart from CD11b+ cDC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484215", "locator": "sections[7] \"Quality control and data analysis\" paragraph 2", "quote": "Hierarchical clustering (HC) by Pearson correlation distance and Ward's aggregation (Fig. 2D) and principal component analysis (PCA, Fig. 2E) were performed after selection of probes with a differential expression in any combination of array > 1.5 (2035 probes)."}, {"asset": "source:pmid:26484215", "locator": "sections[8] \"Discussion\" paragraph 2", "quote": "The transcriptional proximity between them determined by HC and PCA reveals a close genetic relationship between LysoDC and LysoMac apart from CD11b+ cDC."}, {"asset": "source:pmid:26484215", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we provide details of the gating strategy we used to isolate each phagocyte subset and show the quality controls and analysis associated with our gene array data deposited into Gene Expression Omnibus (GEO) under GSE65514."}, {"asset": "source:pmid:26484215", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65514."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The transcriptional proximity between the subsets determined by hierarchical clustering and principal component analysis revealed a close genetic relationship between LysoDC and LysoMac, apart from CD11b+ cDC.", "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:26484215"], "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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