High-throughput whole-genome sequencing of E14 mouse embryonic stem cells.

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More than 2 × 10 E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7 × 10 E6 single nucleotide variant [6]. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variants are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because it could be a target of DNA methylation. Data were deposited in GEO datasets under reference GSM1283021 and here: http://epigenetics.hugef-research.org/data.php.", "claims": [{"id": "claim-data-access", "statement": "These data can be found at: http://epigenetics.hugef-research.org/data.php.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484140", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 5", "quote": "These data can be found at: http://epigenetics.hugef-research.org/data.php."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study built and externally validated a database of approximately 2.7 × 10^6 SNVs and used a new E14 reference assembly to increase the number of mapped reads by about 5%.", "kind": "quantitative", "target": {"value": 5.0, "unit": "per cent", "tolerance": null, "source": "We observed an increase in the number of mapped reads of about 5%."}, "evidence": [{"asset": "source:pmid:26484140", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "More than 2 × 10 E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7 × 10 E6 single nucleotide variant [6]."}, {"asset": "source:pmid:26484140", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The database was validated using other two sequencing datasets from other laboratory and high overlap was observed."}, {"asset": "source:pmid:26484140", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We observed an increase in the number of mapped reads of about 5%."}, {"asset": "source:pmid:26484140", "locator": "sections[3] \"Experimental design, materials and methods\" paragraph 4", "quote": "Variants calling was performed using the mpileup tool from SAMtools [8]."}, {"asset": "source:pmid:26484140", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data were deposited in GEO datasets under reference GSM1283021 and here: http://epigenetics.hugef-research.org/data.php."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study built and externally validated a database of approximately 2.7 × 10^6 SNVs and used a new E14 reference assembly to increase the number of mapped reads by about 5%.", "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:26484140"], "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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