RNA-Seq analysis and whole genome DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS).

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H-NS is a nucleoid-associated protein with two interrelated functions: organization of the bacterial nucleoid and transcriptional silencing [3]. Both functions require DNA binding and protein oligomerization [4, 5]. H-NS commonly silences the expression of virulence factors acquired by lateral gene transfer [6]. The highly pleiotropic nature of hns mutants in V. cholerae indicates that H-NS impacts a broad range of cellular processes such as virulence, stress response, surface attachment, biofilm development, motility and chemotaxis. We used a V. cholerae strain harboring a deletion of hns and a strain expressing H-NS tagged at the C-terminus with the FLAG epitope to generate datasets representing the hns transcriptome and DNA binding profile under laboratory conditions (LB medium, 37°C). The datasets are publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE62785 and GSE64249.", "claims": [{"id": "claim-method", "statement": "The MACS (Model-Based Analysis for ChIP-Seq) algorithm within SeqMonk was used for peak calling with p-value 1.0E − 05, a sonicated fragment size of 300 bp and input sample as control.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26097806", "locator": "sections[10] \"ChiP-Seq and data analysis\" paragraph 2", "quote": "The MACS (Model-Based Analysis for ChIP-Seq) algorithm within SeqMonk was used for peak calling with p-value 1.0E − 05, a sonicated fragment size of 300 bp and input sample as control."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and processed RNA-Seq datasets have been deposited in the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) and assigned accession number GSE62785. 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The ChIP-Seq raw and processed data files are accessible through the GEO series accession number GSE64249."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used differential RNA-Seq analysis with Cufflinks, treating genes with a fold change of at least ±2.0 and q-value < 0.05 as differentially expressed, and made the raw and processed RNA-Seq data publicly available through GEO under accession number GSE62785.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26097806", "locator": "sections[8] \"Differential RNA-Seq and data analysis\" paragraph 2", "quote": "Genes exhibiting a fold change ≥±2.0 and q-value < 0.05 were considered differentially expressed in the hns mutant."}, {"asset": "source:pmid:26097806", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The datasets are publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSE62785 and GSE64249."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used differential RNA-Seq analysis with Cufflinks, treating genes with a fold change of at least ±2.0 and q-value < 0.05 as differentially expressed, and made the raw and processed RNA-Seq data publicly available through GEO under accession number GSE62785.", "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:26097806"], "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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