Global gene expression profiling analysis reveals reduction of stemness after B-RAF inhibition in colorectal cancer cell lines.

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(2015) \"B-RAF inhibitors induce epithelial differentiation in BRAF-mutant colorectal cancer cells\" we described how inhibition of mutant BRAF in colorectal cancer cell lines induces cell re-differentiation that is correlated with the loss of tumor growth in vitro and in vivo. We used Illumina HumanHT-12 v4 Expression BeadChip to characterize the gain of differentiation of PLX4720-treated 3D cultures of HT29 and Colo-205 cells. Here, we describe the experimental design and statistical analysis that were performed on the data set leading to the above hypothesis. The data are publicly available at the Gene Expression Omnibus (GEO) database under the accession number GSE50791.", "claims": [{"id": "claim-method", "statement": "As we did not have replicate samples for the Colo-205, we performed for both cell lines a moderated F-test using the R ‘limma’ package [8] on the treatment versus control samples to identify genes that responded differently over time.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484206", "locator": "sections[6] \"RNA isolation and microarray analysis\" paragraph 6", "quote": "As we did not have replicate samples for the Colo-205, we performed for both cell lines a moderated F-test using the R ‘limma’ package [8] on the treatment versus control samples to identify genes that responded differently over time."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data are publicly available at the Gene Expression Omnibus (GEO) database under the accession number GSE50791.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484206", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are publicly available at the Gene Expression Omnibus (GEO) database under the accession number GSE50791."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used a moderated F-test with false-discovery-rate correction to identify time-dependent treatment responses, and the underlying data are publicly available through GEO accession GSE50791.", "kind": "quantitative", "target": {"value": 0.71, "unit": "correlation coefficient", "tolerance": null, "source": "There was a significant Pearson correlation of r = 0.71 for all differentially genes between PLX4720 and control in both cell lines (adjusted p-value < 0.001), supporting our initial hypothesis."}, "evidence": [{"asset": "source:pmid:26484206", "locator": "sections[6] \"RNA isolation and microarray analysis\" paragraph 6", "quote": "As we did not have replicate samples for the Colo-205, we performed for both cell lines a moderated F-test using the R ‘limma’ package [8] on the treatment versus control samples to identify genes that responded differently over time. p-Values from the F-statistic were corrected for false discovery rate estimation according to Benjamini and Hochberg."}, {"asset": "source:pmid:26484206", "locator": "sections[6] \"RNA isolation and microarray analysis\" paragraph 6", "quote": "There was a significant Pearson correlation of r = 0.71 for all differentially genes between PLX4720 and control in both cell lines (adjusted p-value < 0.001), supporting our initial hypothesis."}, {"asset": "source:pmid:26484206", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are publicly available at the Gene Expression Omnibus (GEO) database under the accession number GSE50791."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used a moderated F-test with false-discovery-rate correction to identify time-dependent treatment responses, and the underlying data are publicly available through GEO accession GSE50791.", "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:26484206"], "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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