High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

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This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500. All sequencing data are deposited in the GEO database under accession number GSE87097.", "claims": [{"id": "claim-data-access", "statement": "All sequencing data are deposited in GEO, accession number GSE87097.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27766205", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "All sequencing data are deposited in GEO, accession number GSE87097."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RRBS can be sequenced on the NextSeq500 with comparable quality to the HiSeq2500; methylation calls from the two instruments were highly concordant (R = 0.996), and the source sequencing data are deposited in GEO under accession number GSE87097.", "kind": "quantitative", "target": {"value": 0.996, "unit": "correlation coefficient", "tolerance": null, "source": "We next quantified 5mC over CGIs and found that the methylation calls obtained from the HiSeq2500 data were highly correlated to those of the NextSeq500 data (R = 0.996, Fig. 2B)."}, "evidence": [{"asset": "source:pmid:27766205", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500."}, {"asset": "source:pmid:27766205", "locator": "sections[8] \"Results\" paragraph 4", "quote": "We next quantified 5mC over CGIs and found that the methylation calls obtained from the HiSeq2500 data were highly correlated to those of the NextSeq500 data (R = 0.996, Fig. 2B)."}, {"asset": "source:pmid:27766205", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All sequencing data are deposited in the GEO database under accession number GSE87097."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RRBS can be sequenced on the NextSeq500 with comparable quality to the HiSeq2500; methylation calls from the two instruments were highly concordant (R = 0.996), and the source sequencing data are deposited in GEO under accession number GSE87097.", "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:27766205"], "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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