Transcriptome data and gene ontology analysis in human macrophages ingesting modified lipoproteins in the presence or absence of complement protein C1q.

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RNA-sequencing was used to identify the pathways modulated by complement protein C1q during HMDM ingestion of the atherogenic lipoproteins oxidized low density lipoprotein (oxLDL) and acetylated low density lipoprotein (acLDL). All raw data were submitted to the MIAME-compliant database Gene Expression Omnibus (accession number GEO: GSE80442; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80442). Data presented here include Venn diagram overviews of up- and down-regulated genes for each condition tested, gene ontology analyses of biological processes, molecular functions and cellular components and KEGG pathway analysis. Further investigation of the pathways modulated by C1q in HMDM during ingestion of atherogenic lipoproteins and their functional relevance are described in \"Macrophage molecular signaling and inflammatory responses during ingestion of atherogenic lipoproteins are modulated by complement protein C1q\" (M.M. Ho, A. Manughian-Peter, W.R. Spivia, A. Taylor, D.A. Fraser, 2016) [1].", "claims": [{"id": "claim-method", "statement": "Statistically significant differences in gene expression (p<0.05) were determined using UCI׳s CyberT in-house software [4].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27699187", "locator": "sections[8] \"Data analysis\" paragraph 2", "quote": "Statistically significant differences in gene expression (p<0.05) were determined using UCI׳s CyberT in-house software [4]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Analyzed data is within this article and raw data is available at the NCBI database at GEO series accession number GEO:GSE80442,http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80442", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27699187", "locator": "sections[1] \"p\" paragraph 1", "quote": "Analyzed data is within this article and raw data is available at the NCBI database at GEO series accession number GEO:GSE80442,http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80442"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used RNA-sequencing to identify pathways modulated by C1q during human macrophage ingestion of oxLDL and acLDL, and deposited the raw data in GEO under accession GSE80442.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Statistically significant differences in gene expression (p<0.05) were determined using UCI׳s CyberT in-house software [4]."}, "evidence": [{"asset": "source:pmid:27699187", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "RNA-sequencing was used to identify the pathways modulated by complement protein C1q during HMDM ingestion of the atherogenic lipoproteins oxidized low density lipoprotein (oxLDL) and acetylated low density lipoprotein (acLDL)."}, {"asset": "source:pmid:27699187", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All raw data were submitted to the MIAME-compliant database Gene Expression Omnibus (accession number GEO: GSE80442; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80442)."}, {"asset": "source:pmid:27699187", "locator": "sections[8] \"Data analysis\" paragraph 2", "quote": "Statistically significant differences in gene expression (p<0.05) were determined using UCI׳s CyberT in-house software [4]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used RNA-sequencing to identify pathways modulated by C1q during human macrophage ingestion of oxLDL and acLDL, and deposited the raw data in GEO under accession GSE80442.", "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:27699187"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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