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## Registered report: Systematic identification of genomic markers of drug sensitivity in cancer cells <br> **Abstract:** The [Reproducibility Project: Cancer Biology][1] seeks to address growing concerns about the reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of [citations and Altmetric scores][2] ([Errington et al., 2014][3]). This Registered Report describes the proposed replication plan of key experiments from “Systematic identification of genomic markers of drug sensitivity in cancer cells” by Garnett and colleagues, published in *Nature* in 2012 ([Garnett et al., 2012][4]). The experiments to be replicated are those reported in Figures 4C, 4E, 4F, and Supplemental Figures 16 and 20. Garnett and colleagues performed a high throughput screen assessing the effect of 130 drugs on 639 cancer-derived cell lines in order to identify novel interactions for possible therapeutic approaches. They then tested this approach by exploring in more detail a novel interaction they identified in which Ewing’s sarcoma cell lines showed an increased sensitivity to PARP inhibitors (Figure 4C). Mesenchymal progenitor cells (MPCs) transformed with the signature *EWS-FLI1* translocation, the hallmark of Ewing’s sarcoma family tumors, exhibited increased sensitivity to the PARP inhibitor olaparib as compared to MPCs transformed with a different translocation (Figure 4E). Knockdown mediated by siRNA of *EWS-FLI1* abrogated this sensitivity to olaparib (Figure 4F). The Reproducibility Project: Cancer Biology is a collaboration between the [Center for Open Science][5] and [Science Exchange][6], and the results of the replications will be published by *eLife*. ---------- ### Contents This component contains additional materials relating to the Registered Report for Study 37: Garnett et al., 2012, *Nature*. The Registered Report can be found [here][7]. ---------- **Registered Report Initial Draft**: - This document represents the first draft of the selected experimental protocols. It contains the information that the Core team, with help from scientist volunteers, was able to glean from the original publication and its supplemental materials before the original authors were contacted for their input. - [Study 37 Registered Report Initial Draft][8] **Power Calculations**: - These documents contain details about how power calculations were performed, and include spreadsheets documenting statistical tests as well as any R scripts, PRISM files, or additional materials used. - [Study 37 Power Calculations.xlsx][9] - [Study 37 Figure 4C MannWhitney ordinal.R][10] - [Study 37 Figure 4E data.csv][11] - [Study 37 Figure 4E Spline interpolation.R][12] - [Study 37 Figure 4F data.csv][13] - [Study 37 Figure 4F IC50.R][14] - [Study 37 Supplemental Figure 20 estimation.pptx][15] - [Study 37 Supplemental Figure 20 2-way ANOVA.R][16] **Additional Information** - [Mouse mesenchymal progenitor cell culture conditions][17] - This describes how to culture mouse mesenchymal progenitor cells, generously shared by the Stamenkovic lab in August 2015. [1]: [2]: [3]: [4]: [5]: [6]: [7]: [8]: [9]: [10]: [11]: [12]: [13]: [14]: [15]: [16]: [17]:
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