bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 1 from A Bioluminescent Transposon Reporter-Trap Identifies Tumor-Specific Microenvironment-Induced Promoters in Salmonella for Conditional Bacterial-Based Tumor Therapy
Authors: Flentie Kelly , Kocher Brandon , Gammon Seth T. , Novack Deborah V. , McKinney Jeffrey S. , Piwnica-Worms David
Published: April 2023

PDF file - 52K, Tumor localization of constitutively bioluminescent Salmonella mutants.
Supplementary Materials from From Differences in Means between Cases and Controls to Risk Stratification: A Business Plan for Biomarker Development
Authors: Wentzensen Nicolas , Wacholder Sholom
Published: April 2023

XLS file - 430K, From difference in Means to Risk Stratification: A spreadsheet
Supplementary Figure 7 from Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer
Authors: Bose Ron , Kavuri Shyam M. , Searleman Adam C. , Shen Wei , Shen Dong , Koboldt Daniel C. , Monsey John , Goel Nicholas , Aronson Adam B. , Li Shunqiang , Ma Cynthia X. , Ding Li , Mardis Elaine R. , Ellis Matthew J.
Published: April 2023

PDF file - 106K, Protein structure modeling suggests that HER2 D769 is located near the HER2-HER3 kinase domain dimer interface
Supplementary Figure 6 from Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer
Authors: Bose Ron , Kavuri Shyam M. , Searleman Adam C. , Shen Wei , Shen Dong , Koboldt Daniel C. , Monsey John , Goel Nicholas , Aronson Adam B. , Li Shunqiang , Ma Cynthia X. , Ding Li , Mardis Elaine R. , Ellis Matthew J.
Published: April 2023

PDF file - 14K, MCF7-HER2 V777L cells formed tumors more rapidly than MCF7-HER2 WT cells
Supplementary Figure 4 from Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer
Authors: Bose Ron , Kavuri Shyam M. , Searleman Adam C. , Shen Wei , Shen Dong , Koboldt Daniel C. , Monsey John , Goel Nicholas , Aronson Adam B. , Li Shunqiang , Ma Cynthia X. , Ding Li , Mardis Elaine R. , Ellis Matthew J.
Published: April 2023

PDF file - 469K, HER2 targeted drugs, lapatinib or neratinib, inhibit the spiculated and invasive-appearing morphology of MCF10A-HER2 mutants cells
Supplementary Figure 5 from First-in-Human Trial of a STAT3 Decoy Oligonucleotide in Head and Neck Tumors: Implications for Cancer Therapy
Authors: Sen Malabika , Thomas Sufi M. , Kim Seungwon , Yeh Joanne I. , Ferris Robert L. , Johnson Jonas T. , Duvvuri Umamaheswar , Lee Jessica , Sahu Nivedita , Joyce Sonali , Freilino Maria L. , Shi Haibin , Li Changyou , Ly Danith , Rapireddy Srinivas , Etter Jonathan P. , Li Pui-Kai , Wang Lin , Chiosea Simion , Seethala Raja R. , Gooding William E. , Chen Xiaomin , Kaminski Naftali , Pandit Kusum , Johnson Daniel E. , Grandis Jennifer R.
Published: April 2023

PDF file - 2MB, Modified STAT3 decoys abrogate STAT3 target gene expression in vitro
Supplementary Figure 1 from Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer
Authors: Bose Ron , Kavuri Shyam M. , Searleman Adam C. , Shen Wei , Shen Dong , Koboldt Daniel C. , Monsey John , Goel Nicholas , Aronson Adam B. , Li Shunqiang , Ma Cynthia X. , Ding Li , Mardis Elaine R. , Ellis Matthew J.
Published: April 2023

PDF file - 99K, HER2 mutations activate signaling in NIH3T3 fibroblasts
Supplementary Figure Legends 1-6, Table 1 from Chimeric Transcript Generated by cis-Splicing of Adjacent Genes Regulates Prostate Cancer Cell Proliferation
Authors: Zhang Yanmei , Gong Mei , Yuan Huiling , Park Hong G. , Frierson Henry F. , Li Hui
Published: April 2023

PDF file - 116K, Supplementary figure legends and Table S1: Primer, probe and siRNA target sequences
Supplementary Movie 6 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 5 MB.
Supplementary Movie 4A from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: <1 MB.
Supplementary Movie 11 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 2 MB.
Supplementary Movie 10 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 13 MB.
Download Video 1 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Authors: Iwanicki Marcin P. , Davidowitz Rachel A. , Ng Mei Rosa , Besser Achim , Muranen Taru , Merritt Melissa , Danuser Gaudenz , Ince Tan , Brugge Joan S.
Published: April 2023

File Type: .mov; File Size: 4 MB.
Supplementary Methods, Figures 1-2, Tables 1-4 from A Novel Platform for Detection of CK+ and CK− CTCs
Authors: Pecot Chad V. , Bischoff Farideh Z. , Mayer Julie Ann , Wong Karina L. , Pham Tam , Bottsford-Miller Justin , Stone Rebecca L. , Lin Yvonne G. , Jaladurgam Padmavathi , Roh Ju Won , Goodman Blake W. , Merritt William M. , Pircher Tony J. , Mikolajczyk Stephen D. , Nick Alpa M. , Celestino Joseph , Eng Cathy , Ellis Lee M. , Deavers Michael T. , Sood Anil K.
Published: April 2023

PDF file - 619K
Supplementary Figure 3 from TGF-β Receptor II Loss Promotes Mammary Carcinoma Progression by Th17-Dependent Mechanisms
Authors: Novitskiy Sergey V. , Pickup Michael W. , Gorska Agnieszka E. , Owens Philip , Chytil Anna , Aakre Mary , Wu Huiyun , Shyr Yu , Moses Harold L.
Published: April 2023

PDF file - 111K
Supplementary Figures 1-17 from The Outgrowth of Micrometastases Is Enabled by the Formation of Filopodium-like Protrusions
Authors: Shibue Tsukasa , Brooks Mary W. , Inan M. Fatih , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

PDF file - 1.8MB
Supplementary Figure 7 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia
Authors: Sanda Takaomi , Tyner Jeffrey W. , Gutierrez Alejandro , Ngo Vu N. , Glover Jason , Chang Bill H. , Yost Arla , Ma Wenxue , Fleischman Angela G. , Zhou Wenjun , Yang Yandan , Kleppe Maria , Ahn Yebin , Tatarek Jessica , Kelliher Michelle A. , Neuberg Donna S. , Levine Ross L. , Moriggl Richard , Müller Mathias , Gray Nathanael S. , Jamieson Catriona H.M. , Weng Andrew P. , Staudt Louis M. , Druker Brian J. , Look A. Thomas
Published: April 2023

PDF file - 24K, Effect of JAK kinase inhibitors with varying TYK2-specificity on growth and viability of T-ALL cells.
Supplementary Figure 2 from TYK2–STAT1–BCL2 Pathway Dependence in T-cell Acute Lymphoblastic Leukemia
Authors: Sanda Takaomi , Tyner Jeffrey W. , Gutierrez Alejandro , Ngo Vu N. , Glover Jason , Chang Bill H. , Yost Arla , Ma Wenxue , Fleischman Angela G. , Zhou Wenjun , Yang Yandan , Kleppe Maria , Ahn Yebin , Tatarek Jessica , Kelliher Michelle A. , Neuberg Donna S. , Levine Ross L. , Moriggl Richard , Müller Mathias , Gray Nathanael S. , Jamieson Catriona H.M. , Weng Andrew P. , Staudt Louis M. , Druker Brian J. , Look A. Thomas
Published: April 2023

PDF file - 68K, Cell cycle distribution after TYK2 knockdown in T-ALL cells.
Supplementary Figure Legends 1-10, Methods from Metabolomics Strategy Reveals Subpopulation of Liposarcomas Sensitive to Gemcitabine Treatment
Authors: Braas Daniel , Ahler Ethan , Tam Brenna , Nathanson David , Riedinger Mirielle , Benz Matthias R. , Smith Kathleen B. , Eilber Fritz C. , Witte Owen N. , Tap William D. , Wu Hong , Christofk Heather R.
Published: April 2023

PDF file - 114K
Supplementary Figures 1-3 from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing
Authors: Wagle Nikhil , Berger Michael F. , Davis Matthew J. , Blumenstiel Brendan , DeFelice Matthew , Pochanard Panisa , Ducar Matthew , Van Hummelen Paul , MacConaill Laura E. , Hahn William C. , Meyerson Matthew , Gabriel Stacey B. , Garraway Levi A.
Published: April 2023

PDF file - 325K
Supplementary Table 1 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Authors: Hammerman Peter S. , Sos Martin L. , Ramos Alex H. , Xu Chunxiao , Dutt Amit , Zhou Wenjun , Brace Lear E. , Woods Brittany A. , Lin Wenchu , Zhang Jianming , Deng Xianming , Lim Sang Min , Heynck Stefanie , Peifer Martin , Simard Jeffrey R. , Lawrence Michael S. , Onofrio Robert C. , Salvesen Helga B. , Seidel Danila , Zander Thomas , Heuckmann Johannes M. , Soltermann Alex , Moch Holger , Koker Mirjam , Leenders Frauke , Gabler Franziska , Querings Silvia , Ansén Sascha , Brambilla Elisabeth , Brambilla Christian , Lorimier Philippe , Brustugun Odd Terje , Helland Åslaug , Petersen Iver , Clement Joachim H. , Groen Harry , Timens Wim , Sietsma Hannie , Stoelben Erich , Wolf Jürgen , Beer David G. , Tsao Ming Sound , Hanna Megan , Hatton Charles , Eck Michael J. , Janne Pasi A. , Johnson Bruce E. , Winckler Wendy , Greulich Heidi , Bass Adam J. , Cho Jeonghee , Rauh Daniel , Gray Nathanael S. , Wong Kwok-Kin , Haura Eric B. , Thomas Roman K. , Meyerson Matthew
Published: April 2023

Supplementary Table 1 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Supplementary Table 5 from Molecular Ontogeny of Donor-Derived Follicular Lymphomas Occurring after Hematopoietic Cell Transplantation
Authors: Weigert Oliver , Kopp Nadja , Lane Andrew A. , Yoda Akinori , Dahlberg Suzanne E. , Neuberg Donna , Bahar Anita Y. , Chapuy Bjoern , Kutok Jeffery L. , Longtine Janina A. , Kuo Frank C. , Haley Terry , Salois Maura , Sullivan Timothy J. , Fisher David C. , Fox Edward A. , Rodig Scott J. , Antin Joseph H. , Weinstock David M.
Published: April 2023

PDF file - 52K
Supplementary Figures 1-7 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Authors: Hammerman Peter S. , Sos Martin L. , Ramos Alex H. , Xu Chunxiao , Dutt Amit , Zhou Wenjun , Brace Lear E. , Woods Brittany A. , Lin Wenchu , Zhang Jianming , Deng Xianming , Lim Sang Min , Heynck Stefanie , Peifer Martin , Simard Jeffrey R. , Lawrence Michael S. , Onofrio Robert C. , Salvesen Helga B. , Seidel Danila , Zander Thomas , Heuckmann Johannes M. , Soltermann Alex , Moch Holger , Koker Mirjam , Leenders Frauke , Gabler Franziska , Querings Silvia , Ansén Sascha , Brambilla Elisabeth , Brambilla Christian , Lorimier Philippe , Brustugun Odd Terje , Helland Åslaug , Petersen Iver , Clement Joachim H. , Groen Harry , Timens Wim , Sietsma Hannie , Stoelben Erich , Wolf Jürgen , Beer David G. , Tsao Ming Sound , Hanna Megan , Hatton Charles , Eck Michael J. , Janne Pasi A. , Johnson Bruce E. , Winckler Wendy , Greulich Heidi , Bass Adam J. , Cho Jeonghee , Rauh Daniel , Gray Nathanael S. , Wong Kwok-Kin , Haura Eric B. , Thomas Roman K. , Meyerson Matthew
Published: April 2023

Supplementary Figures 1-7 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Interview with Dr. Meyerson from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Authors: Hammerman Peter S. , Sos Martin L. , Ramos Alex H. , Xu Chunxiao , Dutt Amit , Zhou Wenjun , Brace Lear E. , Woods Brittany A. , Lin Wenchu , Zhang Jianming , Deng Xianming , Lim Sang Min , Heynck Stefanie , Peifer Martin , Simard Jeffrey R. , Lawrence Michael S. , Onofrio Robert C. , Salvesen Helga B. , Seidel Danila , Zander Thomas , Heuckmann Johannes M. , Soltermann Alex , Moch Holger , Koker Mirjam , Leenders Frauke , Gabler Franziska , Querings Silvia , Ansén Sascha , Brambilla Elisabeth , Brambilla Christian , Lorimier Philippe , Brustugun Odd Terje , Helland Åslaug , Petersen Iver , Clement Joachim H. , Groen Harry , Timens Wim , Sietsma Hannie , Stoelben Erich , Wolf Jürgen , Beer David G. , Tsao Ming Sound , Hanna Megan , Hatton Charles , Eck Michael J. , Janne Pasi A. , Johnson Bruce E. , Winckler Wendy , Greulich Heidi , Bass Adam J. , Cho Jeonghee , Rauh Daniel , Gray Nathanael S. , Wong Kwok-Kin , Haura Eric B. , Thomas Roman K. , Meyerson Matthew
Published: April 2023

mp3 file (6.8 MB). In the inaugural edition of the Cancer Discovery podcast, Executive Editor Mark Landis talks with Matthew Meyerson about his paper, which describes the identification of the DDR2 kinase as a therapeutic target in squamous cell lung cancer.
Supplementary Methods, Figures 1-4 from PPM1H Is a p27 Phosphatase Implicated in Trastuzumab Resistance
Authors: Lee-Hoeflich Si Tuen , Pham Thinh Q. , Dowbenko Don , Munroe Xander , Lee James , Li Li , Zhou Wei , Haverty Peter M. , Pujara Kanan , Stinson Jeremy , Chan Sara M. , Eastham-Anderson Jeffrey , Pandita Ajay , Seshagiri Somasekar , Hoeflich Klaus P. , Turashvili Gulisa , Gelmon Karen A. , Aparicio Samuel A. , Davis David P. , Sliwkowski Mark X. , Stern Howard M.
Published: April 2023

Figures PDF file - 501K
Supplementary Figure 4 from Molecular Ontogeny of Donor-Derived Follicular Lymphomas Occurring after Hematopoietic Cell Transplantation
Authors: Weigert Oliver , Kopp Nadja , Lane Andrew A. , Yoda Akinori , Dahlberg Suzanne E. , Neuberg Donna , Bahar Anita Y. , Chapuy Bjoern , Kutok Jeffery L. , Longtine Janina A. , Kuo Frank C. , Haley Terry , Salois Maura , Sullivan Timothy J. , Fisher David C. , Fox Edward A. , Rodig Scott J. , Antin Joseph H. , Weinstock David M.
Published: April 2023

PDF file - 348K
Supplementary Figure Legends 1-10, Table 2 from Targeting C4-Demethylating Genes in the Cholesterol Pathway Sensitizes Cancer Cells to EGF Receptor Inhibitors via Increased EGF Receptor Degradation
Authors: Sukhanova Anna , Gorin Andrey , Serebriiskii Ilya G. , Gabitova Linara , Zheng Hui , Restifo Diana , Egleston Brian L. , Cunningham David , Bagnyukova Tetyana , Liu Hanqing , Nikonova Anna , Adams Gregory P. , Zhou Yan , Yang Dong-Hua , Mehra Ranee , Burtness Barbara , Cai Kathy Q. , Klein-Szanto Andres , Kratz Lisa E. , Kelley Richard I. , Weiner Louis M. , Herman Gail E. , Golemis Erica A. , Astsaturov Igor
Published: April 2023

PDF file - 105K
Supplementary Figure Legend from Outlier Kinase Expression by RNA Sequencing as Targets for Precision Therapy
Authors: Kothari Vishal , Wei Iris , Shankar Sunita , Kalyana-Sundaram Shanker , Wang Lidong , Ma Linda W. , Vats Pankaj , Grasso Catherine S. , Robinson Dan R. , Wu Yi-Mi , Cao Xuhong , Simeone Diane M. , Chinnaiyan Arul M. , Kumar-Sinha Chandan
Published: April 2023

PDF file - 103K
Supplementary Table 1, Figure Legends 1-13 from Kinetics of Inhibitor Cycling Underlie Therapeutic Disparities between EGFR-Driven Lung and Brain Cancers
Authors: Barkovich Krister J. , Hariono Sujatmi , Garske Adam L. , Zhang Jie , Blair Jimmy A. , Fan Qi-Wen , Shokat Kevan M. , Nicolaides Theodore , Weiss William A.
Published: April 2023

PDF file - 155K
Supplementary Figure 1 from Oncogenic and Wild-type Ras Play Divergent Roles in the Regulation of Mitogen-Activated Protein Kinase Signaling
Authors: Young Amy , Lou David , McCormick Frank
Published: April 2023

PDF file - 254K, siRNA-mediated depletion of wild-type and oncogenic Ras in additional cell lines
Supplementary Methods from Discovery of Mdm2-MdmX E3 Ligase Inhibitors Using a Cell-Based Ubiquitination Assay
Authors: Herman Ariel G. , Hayano Miki , Poyurovsky Masha V. , Shimada Kenichi , Skouta Rachid , Prives Carol , Stockwell Brent R.
Published: April 2023

PDF file - 102K
Supplementary Figure 6 from Kinetics of Inhibitor Cycling Underlie Therapeutic Disparities between EGFR-Driven Lung and Brain Cancers
Authors: Barkovich Krister J. , Hariono Sujatmi , Garske Adam L. , Zhang Jie , Blair Jimmy A. , Fan Qi-Wen , Shokat Kevan M. , Nicolaides Theodore , Weiss William A.
Published: April 2023

PDF file - 70K
Supplementary Methods, Figure Legends 1-8 from Loss of the 14-3-3σ Tumor Suppressor Is a Critical Event in ErbB2-Mediated Tumor Progression
Authors: Ling Chen , Su Vi-Minh-Tri , Zuo Dongmei , Muller William J.
Published: April 2023

PDF file - 61K
Supplementary Figure 3 from Kinetics of Inhibitor Cycling Underlie Therapeutic Disparities between EGFR-Driven Lung and Brain Cancers
Authors: Barkovich Krister J. , Hariono Sujatmi , Garske Adam L. , Zhang Jie , Blair Jimmy A. , Fan Qi-Wen , Shokat Kevan M. , Nicolaides Theodore , Weiss William A.
Published: April 2023

PDF file - 54K
Supplementary Figure 13 from Kinetics of Inhibitor Cycling Underlie Therapeutic Disparities between EGFR-Driven Lung and Brain Cancers
Authors: Barkovich Krister J. , Hariono Sujatmi , Garske Adam L. , Zhang Jie , Blair Jimmy A. , Fan Qi-Wen , Shokat Kevan M. , Nicolaides Theodore , Weiss William A.
Published: April 2023

PDF file - 86K
Supplementary Table 9 from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 22K
Supplementary Table 5d from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 49K
Supplementary Table 5c from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 22K
Supplementary Table 3 from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

XLS file - 51K
Supplementary Figures 1-8 from Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Authors: Marcotte Richard , Brown Kevin R. , Suarez Fernando , Sayad Azin , Karamboulas Konstantina , Krzyzanowski Paul M. , Sircoulomb Fabrice , Medrano Mauricio , Fedyshyn Yaroslav , Koh Judice L.Y. , van Dyk Dewald , Fedyshyn Bohdana , Luhova Marianna , Brito Glauber C. , Vizeacoumar Franco J. , Vizeacoumar Frederick S. , Datti Alessandro , Kasimer Dahlia , Buzina Alla , Mero Patricia , Misquitta Christine , Normand Josee , Haider Maliha , Ketela Troy , Wrana Jeffrey L. , Rottapel Robert , Neel Benjamin G. , Moffat Jason
Published: April 2023

PDF file - 310K
Supplementary Figures Legends 1-11 from DDX5 Regulates DNA Replication and Is Required for Cell Proliferation in a Subset of Breast Cancer Cells
Authors: Mazurek Anthony , Luo Weijun , Krasnitz Alexander , Hicks James , Powers R. Scott , Stillman Bruce
Published: April 2023

PDF file - 68K
Supplementary Figures 1-11 from DDX5 Regulates DNA Replication and Is Required for Cell Proliferation in a Subset of Breast Cancer Cells
Authors: Mazurek Anthony , Luo Weijun , Krasnitz Alexander , Hicks James , Powers R. Scott , Stillman Bruce
Published: April 2023

PDF file - 1.2MB, Supplemental Figures 1 through 11 contain additional results from the plasmid stability screen, analysis of the effect of DDX5 knockdown on cell cycle progression and BrdU incorporation by HCT116 cells, exogenous DDX5 expression studies, impact of DDX5 knockdown on expression of genes containing promoter E2F binding sites, effect of knockdown of E2F-family members on abundance of replication proteins, effect of combined DDX5 knockdown and trastuzumab treatment on MDA-MB-453 proliferation, chromosome 17 copy number plots for breast cancer cell lines presented in the manuscript either having or lacking amplification of the DDX5 locus, and co-immunoprecipitation analysis of DDX5 and E2F1 in SK-BR-3, MDA-MB-453, and MCF10A cells.
Supplementary Tables 1-2, Figure Legends 1-9 from Forced Mitotic Entry of S-Phase Cells as a Therapeutic Strategy Induced by Inhibition of WEE1
Authors: Aarts Marieke , Sharpe Rachel , Garcia-Murillas Isaac , Gevensleben Heidrun , Hurd Melissa S. , Shumway Stuart D. , Toniatti Carlo , Ashworth Alan , Turner Nicholas C.
Published: April 2023

PDF file - 79K
Supplementary Figure 7 from Hypoxia-Dependent Modification of Collagen Networks Promotes Sarcoma Metastasis
Authors: Eisinger-Mathason T.S. Karin , Zhang Minsi , Qiu Qiong , Skuli Nicolas , Nakazawa Michael S. , Karakasheva Tatiana , Mucaj Vera , Shay Jessica E.S. , Stangenberg Lars , Sadri Navid , Puré Ellen , Yoon Sam S. , Kirsch David G. , Simon M. Celeste
Published: April 2023

Supplementary Figure 7 - PDF file 786K, Minoxidil treatment does not affect primary tumor volume or overall animal weight
Supplementary Tables from Addressing Genetic Tumor Heterogeneity through Computationally Predictive Combination Therapy
Authors: Zhao Boyang , Pritchard Justin R. , Lauffenburger Douglas A. , Hemann Michael T.
Published: April 2023

XLSX file 390K, Table S1 - Drugs Used;Table S2 - all possible combinations of three-component population
Supplementary Figure 2 from NSD3–NUT Fusion Oncoprotein in NUT Midline Carcinoma: Implications for a Novel Oncogenic Mechanism
Authors: French Christopher A. , Rahman Shaila , Walsh Erica M. , Kühnle Simone , Grayson Adlai R. , Lemieux Madeleine E. , Grunfeld Noam , Rubin Brian P. , Antonescu Cristina R. , Zhang Songlin , Venkatramani Rajkumar , Dal Cin Paola , Howley Peter M.
Published: April 2023

PDF file - 171KB, Supplementary Fig. S2. NUT is translocated to the NSD3 locus in 1221 cell line as demonstrated by FISH on metaphase spread.
Supplementary Figure 1 from NSD3–NUT Fusion Oncoprotein in NUT Midline Carcinoma: Implications for a Novel Oncogenic Mechanism
Authors: French Christopher A. , Rahman Shaila , Walsh Erica M. , Kühnle Simone , Grayson Adlai R. , Lemieux Madeleine E. , Grunfeld Noam , Rubin Brian P. , Antonescu Cristina R. , Zhang Songlin , Venkatramani Rajkumar , Dal Cin Paola , Howley Peter M.
Published: April 2023

PDF file - 140KB, Supplementary Fig. S1. Karyotype of the 1221 NSD3-NUT-positive cell line.
Supplementary Table S1 from A Functional Cancer Genomics Screen Identifies a Druggable Synthetic Lethal Interaction between MSH3 and PRKDC
Authors: Dietlein Felix , Thelen Lisa , Jokic Mladen , Jachimowicz Ron D. , Ivan Laura , Knittel Gero , Leeser Uschi , van Oers Johanna , Edelmann Winfried , Heukamp Lukas C. , Reinhardt H. Christian
Published: April 2023

PDF file 37K, List of all cell lines included in this study. Cell line name, GI50 of KU60648 from initial cell line screen, sensitivity classification as well as mutation annotation source are recorded
Supplementary Figure 3 from Identifying the Ubiquitin Ligase Complex That Regulates the NF1 Tumor Suppressor and Ras
Authors: Hollstein Pablo E. , Cichowski Karen
Published: April 2023

Supplementary Figure 3 - PDF file 65K, CUL3 knockdown stabilizes neurofibromin in GBM cells
Supplementary Tables 1 - 9 from EGFR Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing
Authors: Francis Joshua M. , Zhang Cheng-Zhong , Maire Cecile L. , Jung Joonil , Manzo Veronica E. , Adalsteinsson Viktor A. , Homer Heather , Haidar Sam , Blumenstiel Brendan , Pedamallu Chandra Sekhar , Ligon Azra H. , Love J. Christopher , Meyerson Matthew , Ligon Keith L.
Published: April 2023

XLSX file - 424KB, 9 tables containing segmented copy number, SCNAs, chromosomal rearrangements and whole-exomes sequencing data for BT325 and BT340. Table S1: EGFR alterations in TCGA samples with matching RNA and DNA sequencing. Table S2: Genes identified in the chromosome 6-9 amplicon in BT340. Table S3: BT325 segmented copy number data. Table S4: BT340 segmented copy number data. Table S5: BT340 copy number aberrations. Table S6: BT340 chromosomal rearrangements. Table S7: BT325 copy number aberrations and chromosomal rearrangements (each color denotes segments that are joined in one derivative chromosome). Table S8: Somatic SNVs and short insertion/deletions detected in BT325 from whole-exome sequencing data. Table S9: Somatic SNVs and short insertion/deletions detected in BT340 from whole-exome sequencing data.
Supplementary Figure 2 from Elucidating Distinct Roles for NF1 in Melanomagenesis
Authors: Maertens Ophélia , Johnson Bryan , Hollstein Pablo , Frederick Dennie T. , Cooper Zachary A. , Messiaen Ludwine , Bronson Roderick T. , McMahon Martin , Granter Scott , Flaherty Keith , Wargo Jennifer A. , Marais Richard , Cichowski Karen
Published: April 2023

PDF file - 175K, Dose response curves for PLX4720 in BRAFV600E mutant melanoma cell lines (WM3526 (A) and A375 (B)) in the absence or presence of a short hairpin RNA (shRNA) specific for NF1. Cells were treated with PLX4720 at the indicated concentrations, counted and plotted relative to untreated controls.
Supplementary Figures from Acquired Resistance and Clonal Evolution in Melanoma during BRAF Inhibitor Therapy
Authors: Shi Hubing , Hugo Willy , Kong Xiangju , Hong Aayoung , Koya Richard C. , Moriceau Gatien , Chodon Thinle , Guo Rongqing , Johnson Douglas B. , Dahlman Kimberly B. , Kelley Mark C. , Kefford Richard F. , Chmielowski Bartosz , Glaspy John A. , Sosman Jeffrey A. , van Baren Nicolas , Long Georgina V. , Ribas Antoni , Lo Roger S.
Published: April 2023

PDF file 6308K, This includes all supplementary figures except S2 and contains additional clinical data, sequence and copy number analysis as well as immunohistochemical and functional studies
Supplementary Figure 7 from Stromal EGF and IGF-I Together Modulate Plasticity of Disseminated Triple-Negative Breast Tumors
Authors: Castaño Zafira , Marsh Timothy , Tadipatri Ramya , Kuznetsov Hanna S. , Al-Shahrour Fatima , Paktinat Mahnaz , Greene-Colozzi April , Nilsson Björn , Richardson Andrea L. , McAllister Sandra S.
Published: April 2023

PDF file - 279K, EGFR/IGFR Inhibitors do not Affect the Phenotype of Responding Tumor Cells in Animals Bearing Control Matrigel.
Supplementary Methods from Discovery of Biomarkers Predictive of GSI Response in Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma
Authors: Stoeck Alexander , Lejnine Serguei , Truong Andrew , Pan Li , Wang Hongfang , Zang Chongzhi , Yuan Jing , Ware Chris , MacLean John , Garrett-Engele Philip W. , Kluk Michael , Laskey Jason , Haines Brian B. , Moskaluk Christopher , Zawel Leigh , Fawell Stephen , Gilliland Gary , Zhang Theresa , Kremer Brandon E. , Knoechel Birgit , Bernstein Bradley E. , Pear Warren S. , Liu X. Shirley , Aster Jon C. , Sathyanarayanan Sriram
Published: April 2023

File includes genomic analysis, cell cycle and cell proliferation analysis.
Supplementary Table S3 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: April 2023

Summary of clinically informative (TARGET) genes.
Supplementary Methods from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 72K
Supplementary Table S2 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: April 2023

Data describing results of deep targeted sequencing.
Supplementary Figure 9 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 263K, Kras regulates GSK-3α mRNA levels. HKRAS cells were transiently transfected with non-targeting control or KRAS siRNA. RNA was isolated, reverse transcribed to cDNA and real time RT-PCR performed for Kras and GSK-3α. Gus B was used as endogenous control.
Supplementary Methods, Figures S1 - S20 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: April 2023

Supplementary Methods, Figures S1 - S20. Figure S1. Branched evolution leads to tissue-sampling bias in primary tumor samples. Figure S2. Results of ABSOLUTE on samples from patient 418. Figure S3. 2D Bayesian clustering analysis of point-mutation CCF distributions in case 418. Figure S4. Bayesian clustering of private point-mutation CCF distributions in all sequenced tissue samples from case 418. Figure S5. Genetic alterations supporting phylogeny construction in case 418. Figure S6. Phylogenetic tree for case 418 Figure S7. Evolutionary relationships between primary tumor-samples and brain metastasis samples Figure S8. Detection of homozygous deletion in CDKN2A in the brain metastasis of case 24. Figure S9. Amplification of FGFR1 and MYC detected in the brain metastasis of case 331. Figure S10. Additional alterations under investigation for association with various targeted therapies. Figure S11. Power for paired-detection of somatic mutations. Figure S12. Amplification of CCNE1 detected in the brain metastasis of case 314. Figure S13. Amplification of EGFR detected in the brain metastasis of case 314. Figure S14. Amplification of MYC detected in the brain metastasis of case 308. Figure S15. Amplification of MYC detected in the brain metastasis of case 138. Figure S16. Amplifications of CDK6 and MET detected in the brain metastasis of case 138. Figure S17. Amplifications of CCNE1 and AKT2 detected in the brain metastasis of case 138. Figure S18. Amplification of EGFR detected in a regional lymph node from case 296. Figure S19. Power for somatic mutation detection in 86 matched primary-tumor and brain-metastasis samples. Figure S20. Calling of amplifications in primary-tumor samples and paired brain metastases.
Supplementary Figure 7 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 85K, NF-κB2 depletion leads to increase in PARP cleavage. Indicated cell lines were transiently transfected with specified siRNAs, and 72 hours later whole cell extracts immunoblotted for cleaved PARP.
Supplementary Figure 6 from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: April 2023

PDF file - 118K, GSK-3 inhibition leads to a decrease in TAK1 protein Panc-1 and MiaPaCa-2 cells were treated with GSK-3 inhibitor, AR-A014418 or vehicle control, DMSO in the presence or absence of MG132 for 24 hours. Whole cell extracts were immunoblotted for indicated antibodies.
Supplementary Table 1 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 46K, Supplementary Table 1: List of genes on chromosome 4q recurrently lost in tetraploid clones
Supplementary Movie B from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

MOV file 1063K, Cell undergoing a segregation error followed by cell cycle arrest in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplementary Text from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Authors: Lui Vivian W.Y. , Hedberg Matthew L. , Li Hua , Vangara Bhavana S. , Pendleton Kelsey , Zeng Yan , Lu Yiling , Zhang Qiuhong , Du Yu , Gilbert Breean R. , Freilino Maria , Sauerwein Sam , Peyser Noah D. , Xiao Dong , Diergaarde Brenda , Wang Lin , Chiosea Simion , Seethala Raja , Johnson Jonas T. , Kim Seungwon , Duvvuri Umamaheswar , Ferris Robert L. , Romkes Marjorie , Nukui Tomoko , Kwok-Shing Ng Patrick , Garraway Levi A. , Hammerman Peter S. , Mills Gordon B. , Grandis Jennifer R.
Published: April 2023

Supplementary Text - PDF file 99K, Contains figure legends for supplemental figures 1-4, and text describing supplemental methodology
Supplementary Figure 6 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 167K, Supplementary Figure 6: A) LOH profiles across whole genome of diploid and tetraploid clones. B) SNP6.0 gain and loss profiles of HCT-116_MLH clones
Supplementary Figure 5 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 106K, Supplementary Figure 5: DNA ploidy analysis of diploid and tetraploid clones at different passages
Supplementary Information from Inhibition of KRAS-Driven Tumorigenicity by Interruption of an Autocrine Cytokine Circuit
Authors: Zhu Zehua , Aref Amir R. , Cohoon Travis J. , Barbie Thanh U. , Imamura Yu , Yang Shenghong , Moody Susan E. , Shen Rhine R. , Schinzel Anna C. , Thai Tran C. , Reibel Jacob B. , Tamayo Pablo , Godfrey Jason T. , Qian Zhi Rong , Page Asher N. , Maciag Karolina , Chan Edmond M. , Silkworth Whitney , Labowsky Mary T. , Rozhansky Lior , Mesirov Jill P. , Gillanders William E. , Ogino Shuji , Hacohen Nir , Gaudet Suzanne , Eck Michael J. , Engelman Jeffrey A. , Corcoran Ryan B. , Wong Kwok-Kin , Hahn William C. , Barbie David A.
Published: April 2023

PDF file 146K, This file contains the legends to Supplementary Figures 1-7 and Supplementary methods
Supplementary Figure 4 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 701K,Supplementary Figure 4: A-F) Still images from Supplementary Movies A-F. G) Individual clone cell-fate graph for live-cell imaging analysis and full table of numbers of cells analysed
Supplementary Figure 3 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 41K, Supplementary Figure 3: A-B) Segregation error type analysis in diploid and tetraploid clones. C) Colony-to-colony variation in chromosome number for HCT-116_MLH clones
Supplementary Figure 2 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 80K, Supplementary Figure 2: A-C) Growth curves of diploid and tetraploid clones at different passages. D) HCT-116_MLH clones DNA profiles and E) cell-to-cell variation in chromosome number using clonal FISH in HCT-116 _MLH clones
Supplementary Figure 1 from Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution
Authors: Dewhurst Sally M. , McGranahan Nicholas , Burrell Rebecca A. , Rowan Andrew J. , Grönroos Eva , Endesfelder David , Joshi Tejal , Mouradov Dmitri , Gibbs Peter , Ward Robyn L. , Hawkins Nicholas J. , Szallasi Zoltan , Sieber Oliver M. , Swanton Charles
Published: April 2023

PDF file 393K,Supplementary Figure 1: A) Relationship of wGII and ploidy across cancer types. B) p53 and p21 up-regulation in response to DNA damage in diploid and tetraploid clones
Supplementary Table 3 from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Authors: Wagle Nikhil , Van Allen Eliezer M. , Treacy Daniel J. , Frederick Dennie T. , Cooper Zachary A. , Taylor-Weiner Amaro , Rosenberg Mara , Goetz Eva M. , Sullivan Ryan J. , Farlow Deborah N. , Friedrich Dennis C. , Anderka Kristin , Perrin Danielle , Johannessen Cory M. , McKenna Aaron , Cibulskis Kristian , Kryukov Gregory , Hodis Eran , Lawrence Donald P. , Fisher Sheila , Getz Gad , Gabriel Stacey B. , Carter Scott L. , Flaherty Keith T. , Wargo Jennifer A. , Garraway Levi A.
Published: April 2023

XLSX file 3709K, Alterations with Significantly Enriched CCF from Pretreatment to Resistant
Supplementary Table S1 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints
Authors: Llosa Nicolas J. , Cruise Michael , Tam Ada , Wicks Elizabeth C. , Hechenbleikner Elizabeth M. , Taube Janis M. , Blosser Richard L. , Fan Hongni , Wang Hao , Luber Brandon S. , Zhang Ming , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Sears Cynthia L. , Anders Robert A. , Pardoll Drew M. , Housseau Franck
Published: April 2023

Supplementary Table S1. Patient Demographics.
Supplementary Figure S3 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints
Authors: Llosa Nicolas J. , Cruise Michael , Tam Ada , Wicks Elizabeth C. , Hechenbleikner Elizabeth M. , Taube Janis M. , Blosser Richard L. , Fan Hongni , Wang Hao , Luber Brandon S. , Zhang Ming , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Sears Cynthia L. , Anders Robert A. , Pardoll Drew M. , Housseau Franck
Published: April 2023

Supplementary Figure S3. Characterization of immune infiltration in MSS CRC outlier.
Supplementary Figures from MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Authors: Wagle Nikhil , Van Allen Eliezer M. , Treacy Daniel J. , Frederick Dennie T. , Cooper Zachary A. , Taylor-Weiner Amaro , Rosenberg Mara , Goetz Eva M. , Sullivan Ryan J. , Farlow Deborah N. , Friedrich Dennis C. , Anderka Kristin , Perrin Danielle , Johannessen Cory M. , McKenna Aaron , Cibulskis Kristian , Kryukov Gregory , Hodis Eran , Lawrence Donald P. , Fisher Sheila , Getz Gad , Gabriel Stacey B. , Carter Scott L. , Flaherty Keith T. , Wargo Jennifer A. , Garraway Levi A.
Published: April 2023

PDF file 550K, Contains supplementary figures 1-3
Supplementary Movie 2 from Access to Follicular Dendritic Cells Is a Pivotal Step in Murine Chronic Lymphocytic Leukemia B-cell Activation and Proliferation
Authors: Heinig Kristina , Gätjen Marcel , Grau Michael , Stache Vanessa , Anagnostopoulos Ioannis , Gerlach Kerstin , Niesner Raluca A. , Cseresnyes Zoltan , Hauser Anja E. , Lenz Peter , Hehlgans Thomas , Brink Robert , Westermann Jörg , Dörken Bernd , Lipp Martin , Lenz Georg , Rehm Armin , Höpken Uta E.
Published: April 2023

Supplemental Movie S2. Follicular motility of B cells. The Movie complements Figure 4J.
Supplementary Figures S1 - S9 from HIF2α-Dependent Lipid Storage Promotes Endoplasmic Reticulum Homeostasis in Clear-Cell Renal Cell Carcinoma
Authors: Qiu Bo , Ackerman Daniel , Sanchez Danielle J. , Li Bo , Ochocki Joshua D. , Grazioli Alison , Bobrovnikova-Marjon Ekaterina , Diehl J. Alan , Keith Brian , Simon M. Celeste
Published: April 2023

Supplementary Figures S1 - S9: Supplementary Figure S1. Regulation of PLIN2 and other LD coat protein genes in ccRCC tissue. Supplementary Figure S2. PPARγ function is not required for PLIN2 expression in ccRCC. Supplementary Figure S3. HIF-2alpha dependent PLIN2 expression promotes cell viability in nutrient deprived regions of 3D tumor spheroids. Supplementary Figure S4. PLIN2 is required for lipid storage, cell viability, and maintenance of ER homeostasis in A498 cells. Supplementary Figure S5. Validation of IRE-1alpha inhibitor, PERK inhibitor, and ATF6 siRNA in A498 cells. Supplementary Figure S6. Suppression of UPR signaling in A498 cells following PLIN2 depletion. Supplementary Figure S7. Energetic effects of PLIN2 depletion in ccRCC cell lines and evidence for suppression of beta-oxidation in ccRCC tumor tissue. Supplementary Figure S8. UPR or fatty acid synthesis modulation in PLIN2 depleted cells. Supplementary Figure S9. Lipid storage protects against brefeldin A induced ER stress.
Supplementary Figure Legends from HIF2α-Dependent Lipid Storage Promotes Endoplasmic Reticulum Homeostasis in Clear-Cell Renal Cell Carcinoma
Authors: Qiu Bo , Ackerman Daniel , Sanchez Danielle J. , Li Bo , Ochocki Joshua D. , Grazioli Alison , Bobrovnikova-Marjon Ekaterina , Diehl J. Alan , Keith Brian , Simon M. Celeste
Published: April 2023

Supplementary Figure Legends: Legends for all supplementary figures.