Transcriptional profiling of UlaR-regulated genes in Streptococcus pneumoniae.

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The role of the transcriptional regulator UlaR in Streptococcus pneumoniae has recently been described [1]. Here, we report detailed genome-wide transcriptional profiling of UlaR-regulated genes in S. pneumoniae D39 and its ∆ulaR derivative, either in the presence of 10 mM ascorbic acid in M17 medium using microarray analysis. 10 mM concentration of ascorbic acid was supplemented to the M17 medium because our lacZ-fusion studies indicated that UlaR acts as a transcriptional activator of its targets in the presence of ascorbic acid and the expression of the ula operon was maximal at a 10 mM ascorbic acid concentration [1]. All transcriptional profiling data of UlaR-regulated genes was deposited to Gene Expression Omnibus (GEO) database under accession number GSE61649.", "claims": [{"id": "claim-method", "statement": "CyberT implementation of a variant of t-test (http://bioinformatics.biol.rug.nl/cybert/index.shtml) was performed and false discovery rates (FDRs) were calculated as described [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484177", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "CyberT implementation of a variant of t-test (http://bioinformatics.biol.rug.nl/cybert/index.shtml) was performed and false discovery rates (FDRs) were calculated as described [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray data have been submitted to GEO under the accession number GSE61649.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484177", "locator": "sections[8] \"Microarray data analysis\" paragraph 2", "quote": "Microarray data have been submitted to GEO under the accession number GSE61649."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:26484177"], "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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