Multi-omic profiling of MYCN-amplified neuroblastoma cell-lines.

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Its most aggressive subtype, characterized by the amplification of the MYCN oncogene, has a dismal prognosis and no effective treatment is available. Understanding the alterations induced by the tumor on the various layers of gene expression is therefore important for a complete characterization of this neuroblastoma subtype and for the discovery of new therapeutic opportunities. Here we describe the profiling of 13 MYCN-amplified neuroblastoma cell lines at the genome (copy number), transcriptome, translatome and miRome levels (GEO series GSE56654, GSE56552 and GSE56655). We provide detailed experimental and data analysis procedures by means of which we derived the results described in [1].", "claims": [{"id": "claim-method", "statement": "Differential representation of genes between the transcriptome and the transaltome was computed with RankProd [7], SAM (cran.r-project.org/web/packages/samr) and the T-test [8].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697401", "locator": "sections[11] \"Transcriptome and translatome data analysis\" paragraph 2", "quote": "Differential representation of genes between the transcriptome and the transaltome was computed with RankProd [7], SAM (cran.r-project.org/web/packages/samr) and the T-test [8]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Transcriptome and translatome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56552\nGenome (copy number) profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56654\nmiRome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56655", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697401", "locator": "sections[2] \"Direct link to deposited data\" paragraphs 1-4", "quote": "Transcriptome and translatome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56552\nGenome (copy number) profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56654\nmiRome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56655"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports multi-omic profiling of 13 MYCN-amplified neuroblastoma cell lines at the genome, transcriptome, translatome, and miRome levels, using statistical analyses that included differential-expression testing with RankProd, SAM, and the T-test; the raw and analyzed data are deposited in GEO under GSE56654, GSE56552, and GSE56655.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697401", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we describe the profiling of 13 MYCN-amplified neuroblastoma cell lines at the genome (copy number), transcriptome, translatome and miRome levels (GEO series GSE56654, GSE56552 and GSE56655)."}, {"asset": "source:pmid:26697401", "locator": "sections[11] \"Transcriptome and translatome data analysis\" paragraph 2", "quote": "Differential representation of genes between the transcriptome and the transaltome was computed with RankProd [7], SAM (cran.r-project.org/web/packages/samr) and the T-test [8]."}, {"asset": "source:pmid:26697401", "locator": "sections[2] \"Direct link to deposited data\" paragraphs 1-4", "quote": "Transcriptome and translatome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56552\nGenome (copy number) profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56654\nmiRome profiling: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56655"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports multi-omic profiling of 13 MYCN-amplified neuroblastoma cell lines at the genome, transcriptome, translatome, and miRome levels, using statistical analyses that included differential-expression testing with RankProd, SAM, and the T-test; the raw and analyzed data are deposited in GEO under GSE56654, GSE56552, and GSE56655.", "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:26697401"], "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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