Data for chromosome contacts and matched transcription profiles at three cell cycle phases in the fission yeast.

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Temperature sensitive Schizosaccharomyces pombe cell division cycle (cdc) mutants, which are induced by a shift in temperature to 36 °C, were chosen for the analysis of genome structure in the G1 phase, G2 phase and mitotic anaphase of the cell cycle. Chromatin and total RNA were isolated from the same cell culture following synchronization. Two biological replicates were analyzed for each condition. The global, three-dimensional organization of the chromosomes was captured at high resolution using Genome Conformation Capture (GCC). GCC libraries and RNA samples were sequenced using an Illumina Hi-Seq 2000 platform (Beijing Genomics Institute (China)). DNA sequences were processed using the Topography suite v1.19 [2] to obtain chromosome contact frequency matrices. RNA sequences were processed using the Cufflinks pipeline [3] to measure gene transcript levels and how these varied between the conditions. All sequence data, processed GCC and transcriptome files are available under the Gene Expression Omnibus (GEO) accession number GSE52287 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52287).", "claims": [{"id": "claim-method", "statement": "We employed two methods for the identification of significant interactions: 1) a statistical method that calculates a false detection rate (FDR) cut-off as in [2]; and 2) the external ligation controls during the GCC library preparation allowed us to measure the rates of intermolecular ligation events.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484169", "locator": "sections[12] \"FDR cut-off calculations\" paragraph 2", "quote": "We employed two methods for the identification of significant interactions: 1) a statistical method that calculates a false detection rate (FDR) cut-off as in [2]; and 2) the external ligation controls during the GCC library preparation allowed us to measure the rates of intermolecular ligation events."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All sequence data, processed GCC and transcriptome files are available under the Gene Expression Omnibus (GEO) accession number GSE52287 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52287).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484169", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All sequence data, processed GCC and transcriptome files are available under the Gene Expression Omnibus (GEO) accession number GSE52287 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52287)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:26484169"], "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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