Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism.

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Cancer cell secretomes are significantly different to that of normal cells reflecting the changes that normal cells have undergone during their transition to malignancy. More importantly, cancer secretomes are known to be active mediators of both local and distant host cells and play an important role in the progression and dissemination of cancer. Here we have quantitatively profiled both the composition of breast cancer secretomes associated with osteotropism, and their modulation under normoxic and hypoxic conditions. We detect and quantify 162 secretome proteins across all conditions which show differential hypoxic induction and association with osteotropism. Mass Spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000397 and the complete proteomic, bioinformatic and biological analyses are reported in Cox et al. (2015) [1].", "claims": [{"id": "claim-method", "statement": "Results were analysed using scripts written in-house in Python and R (deposited in the ProteomeXchange repository alongside data), and tested for statistical significance using the quantile function in the R statistical framework.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26649326", "locator": "sections[10] \"Data processing protocol\" paragraph 2", "quote": "Results were analysed using scripts written in-house in Python and R (deposited in the ProteomeXchange repository alongside data), and tested for statistical significance using the quantile function in the R statistical framework."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Mass Spectrometry proteomics data for the article “The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase” doi:10.1038/nature14492 [1] have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [2] with the dataset identifier PXD000397", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26649326", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "The Mass Spectrometry proteomics data for the article “The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase” doi:10.1038/nature14492 [1] have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [2] with the dataset identifier PXD000397"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper reports detection and quantification of 162 secretome proteins, with statistical significance tested using the quantile function in the R statistical framework; the source mass-spectrometry data are available through ProteomeXchange via the PRIDE partner repository under identifier PXD000397.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26649326", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We detect and quantify 162 secretome proteins across all conditions which show differential hypoxic induction and association with osteotropism."}, {"asset": "source:pmid:26649326", "locator": "sections[10] \"Data processing protocol\" paragraph 2", "quote": "Results were analysed using scripts written in-house in Python and R (deposited in the ProteomeXchange repository alongside data), and tested for statistical significance using the quantile function in the R statistical framework."}, {"asset": "source:pmid:26649326", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "The Mass Spectrometry proteomics data for the article “The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase” doi:10.1038/nature14492 [1] have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [2] with the dataset identifier PXD000397"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper reports detection and quantification of 162 secretome proteins, with statistical significance tested using the quantile function in the R statistical framework; the source mass-spectrometry data are available through ProteomeXchange via the PRIDE partner repository under identifier PXD000397.", "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:26649326"], "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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