Processed DepMap data (.h5mu)

<p><strong>Disclaimer</strong></p> <p>The DepMap data were generated and shared by the Broad Institute of Harvard and MIT and the Sanger Institute.</p> <p>We reprocessed the data and packaged it in a single h5mu file for easier access and to reproduce analyses with Semi-supervised Omics Factor Analysis (SOFA).&nbsp; Please see https://www.biorxiv.org/content/10.1101/2024.10.10.617527v3 for more details on how the data was processed and analysed.</p> <p><strong>Data Usage Policy</strong></p> <p>The Broad Institute publishes its data under the <a href="https://depmap.org/portal/ccle/terms_and_conditions">Terms and Conditions linked here.</a></p> <p>The Sanger Institute publishes its data under the <a href="https://depmap.sanger.ac.uk/documentation/data-usage-policy/">Terms and Conditions linked here.</a></p> <p>The DepMap data&nbsp; are provided under <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 license</a>.</p> <p>Contact <a href="mailto:depmap@broadinstitute.org">depmap@broadinstitute.org</a> or <a href="mailto:depmap@sanger.ac.uk">depmap@sanger.ac.uk</a> for more information</p> <p><strong>Please cite the following when using these data</strong></p> <ul> <li><strong>Drug response</strong>:&nbsp;<a href="https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00274-4?dgcid=raven_jbs_aip_email">Gon&ccedil;alves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835&ndash;849.e8 (2022).</a><strong>&nbsp;</strong>(https://figshare.com/articles/dataset/Pan-cancer_proteomic_map_of_949_human_cell_lines/19345397)</li> <li><strong>Proteomics:</strong> <a href="https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00274-4?dgcid=raven_jbs_aip_email">Gon&ccedil;alves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835&ndash;849.e8 (2022).</a><strong>&nbsp;</strong>(https://figshare.com/articles/dataset/Pan-cancer_proteomic_map_of_949_human_cell_lines/19345397)</li> </ul> <ul> <li><strong>RNA-Seq: <a href="https://aacrjournals.org/cancerres/article/78/3/769/633178/Transcription-Factor-Activities-Enhance-Markers-of">Garcia-Alonso, L. et al. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Res. 78, 769&ndash;780 (2018).</a></strong> (https://cellmodelpassports.sanger.ac.uk/downloads)</li> <li><strong><strong>Methylation</strong>: <a href="https://www.cell.com/fulltext/S0092-8674(16)30746-2">Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740&ndash;754 (2016).</a></strong> (https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Home.html)</li> <li><strong>Mutation: <a href="https://www.cell.com/fulltext/S0092-8674(16)30746-2">Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740&ndash;754 (2016).</a> </strong>(https://cellmodelpassports.sanger.ac.uk/downloads)</li> <li><strong>CRISPR-Cas9: <a href="https://www.nature.com/articles/s41467-021-21898-7">Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021)</a>.</strong> (https://score.depmap.sanger.ac.uk/downloads)</li> <li><strong>Metadata</strong> for all cell lines was obtained from: <ul> <li><a href="https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00274-4?dgcid=raven_jbs_aip_email">Gon&ccedil;alves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835&ndash;849.e8 (2022).</a><strong>&nbsp;</strong></li> <li><strong><a href="https://www.nature.com/articles/s41467-021-21898-7">Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021)</a>.</strong></li> </ul> </li> </ul> <p>&nbsp;</p> <p>&nbsp;</p>