Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae.

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G1 synchronized yeast cells can be released into S-phase in the presence of hydroxyurea (HU) (1), which slows down DNA replication and retains replication forks in proximity of DNA replication origins. In this condition, the Chromatin Immuno-Precipitation on chip (ChIP on chip) (2-4) of replisome components allows the precise localization of all active DNA replication forks. This analysis can be coupled with the ssDNA-BromodeoxyUridine (ssDNA-BrdU) Immuno-Precipitation on chip (ssDNA-BrdU IP on chip) technique (5-7), which detects the location of newly synthesized DNA. Comparison of binding and BrdU incorporation profiles allows to locate a factor of interest at DNA replication forks genome wide. We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks.", "claims": [{"id": "claim-method", "statement": "Conditions for clusters detection in whole range (at least 600 bps), except for segments within the range shorter than 600 bps, were: log2 signal (IP/SUP binding ratio) positive and change in p-value (evaluated using Wilcoxon signed rank test) < 0.2 [2].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981397", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 2", "quote": "Conditions for clusters detection in whole range (at least 600 bps), except for segments within the range shorter than 600 bps, were: log2 signal (IP/SUP binding ratio) positive and change in p-value (evaluated using Wilcoxon signed rank test) < 0.2 [2]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981397", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s statistical analysis used TAS with the Wilcoxon signed-rank test and a Montecarlo-like null model for testing binding–BrdU cluster overlaps; the source data are available through GEO accession GSE68214, and the headline result is that the datasets show how Rrm3 and Pif1 associate with active and inactive DNA replication forks.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981397", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper’s statistical analysis used TAS with the Wilcoxon signed-rank test and a Montecarlo-like null model for testing binding–BrdU cluster overlaps; the source data are available through GEO accession GSE68214, and the headline result is that the datasets show how Rrm3 and Pif1 associate with active and inactive DNA replication forks.", "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:26981397"], "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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