MC3T3 osteoblast-like cells cultured at alkaline pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST).

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We cultured differentiating MC3T3-E1 osteoblast-like cells at pH 7.4, 7.8, and 8.4 for 14 days. To identify differential gene expression, microarray data were collected with Affymetrix GeneChips. The data were validated by real-time PCRs for five genes that were found to be greatly regulated in the GeneChip-experiments (DMP1, FABP4, SFRP2 and TNFRSF19) or considered relevant for the terminal function of osteoblasts (DMP1 and ATF4). All the data are available from the Gene Expression Omnibus database (GEO accession: GSE84907). Here, we provide pathway analyses of known protein coding genes that were down-regulated or up-regulated by greater than 2.0-fold. The regulation datasets obtained from comparisons of pH 7.8 and 7.4, as well as pH 8.4 and 7.4 share a high number of differentially expressed genes. When comparing pH 8.4 and 7.8, other genes mainly emerge, suggesting not only a simple amplification of the effects at pH 8.4 that were already induced at pH 7.8 but also the induction of different pathways. For a more detailed analysis, different mammalian functional gene networks were assigned to each dataset. After merging and manual optimization of the network graphs, three combined functional gene networks were obtained that reflected distinct pH-dependent cellular responses. A common feature of the networks was the central role of p38 MAP kinase. The microarray data presented here are related to the research article doi:10.1016/j.bbrep.2017.02.001 (Galow et al., 2017) [1].", "claims": [{"id": "claim-method", "statement": "Primary data analysis was carried out with the Affymetrix Expression Console 1.4.1.46 software including the Robust Multiarray Average module for normalization.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28580407", "locator": "sections[7] \"Statistical analyses of changes in global gene expression\" paragraph 2", "quote": "Primary data analysis was carried out with the Affymetrix Expression Console 1.4.1.46 software including the Robust Multiarray Average module for normalization."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Pathway analyses data are within this article; microarray data are available from the Gene Expression Omnibus database (GEO accession:GSE84907)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28580407", "locator": "sections[1] \"Specifications Table\" paragraph 2", "quote": "Pathway analyses data are within this article; microarray data are available from the Gene Expression Omnibus database (GEO accession:GSE84907)"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline result was that p38 MAP kinase had a central role in the pH-dependent cellular responses; the statistical analysis used Robust Multi-Array Average normalization with significance defined as q<0.01 and fold changes >|2|, and the source microarray data are available through GEO accession GSE84907.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28580407", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A common feature of the networks was the central role of p38 MAP kinase."}, {"asset": "source:pmid:28580407", "locator": "sections[7] \"Statistical analyses of changes in global gene expression\" paragraph 2", "quote": "Primary data analysis was carried out with the Affymetrix Expression Console 1.4.1.46 software including the Robust Multiarray Average module for normalization."}, {"asset": "source:pmid:28580407", "locator": "sections[7] \"Statistical analyses of changes in global gene expression\" paragraph 2", "quote": "A change was considered significant when the false discovery rate-corrected p-value/q-value thresholds met the criterion q<0.01 at fold changes >|2|, i.e. expression increments or declines larger than two."}, {"asset": "source:pmid:28580407", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All the data are available from the Gene Expression Omnibus database (GEO accession: GSE84907)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper’s headline result was that p38 MAP kinase had a central role in the pH-dependent cellular responses; the statistical analysis used Robust Multi-Array Average normalization with significance defined as q<0.01 and fold changes >|2|, and the source microarray data are available through GEO accession GSE84907.", "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:28580407"], "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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To identify differential gene expression, microarray data were collected with Affymetrix GeneChip", "was the central role of p38 MAP kinase. The microarray data presented here are related to the resea"], "order_basis": "paper_text_order:8", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ine pH: Microarray data (Affymetrix GeneChip Mouse 2.0 ST).", "sign, materials and methods Cell culture The mouse-osteoblast precursor cell line MC3T3-E1 [3]"], "order_basis": "paper_text_order:45", "id": "assay:2"}]}