bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods from Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents
Authors: Birkbak Nicolai J. , Wang Zhigang C. , Kim Ji-Young , Eklund Aron C. , Li Qiyuan , Tian Ruiyang , Bowman-Colin Christian , Li Yang , Greene-Colozzi April , Iglehart J. Dirk , Tung Nadine , Ryan Paula D. , Garber Judy E. , Silver Daniel P. , Szallasi Zoltan , Richardson Andrea L.
Published: April 2023

PDF file - 298K
Supplementary Methods, Figure Legends 1-12 from Cancer-Stimulated Mesenchymal Stem Cells Create a Carcinoma Stem Cell Niche via Prostaglandin E2 Signaling
Authors: Li Hua-Jung , Reinhardt Ferenc , Herschman Harvey R. , Weinberg Robert A.
Published: April 2023

PDF file - 217K
Supplementary Figure 9 from Coordinate Direct Input of Both KRAS and IGF1 Receptor to Activation of PI3 kinase in KRAS-Mutant Lung Cancer
Authors: Molina-Arcas Miriam , Hancock David C. , Sheridan Clare , Kumar Madhu S. , Downward Julian
Published: April 2023

Supplementary Figure 9 - PDF file 500K, KRAS is required for both MEK/ERK and PI3K/AKT signaling in KRAS mutant NSCLC cells
Supplementary Figure Legends 1-12 from Reactivation of ERK Signaling Causes Resistance to EGFR Kinase Inhibitors
Authors: Ercan Dalia , Xu Chunxiao , Yanagita Masahiko , Monast Calixte S. , Pratilas Christine A. , Montero Joan , Butaney Mohit , Shimamura Takeshi , Sholl Lynette , Ivanova Elena V. , Tadi Madhavi , Rogers Andrew , Repellin Claire , Capelletti Marzia , Maertens Ophélia , Goetz Eva M. , Letai Anthony , Garraway Levi A. , Lazzara Matthew J. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

PDF file - 83K
Supplementary Figure 3 from Coordinate Direct Input of Both KRAS and IGF1 Receptor to Activation of PI3 kinase in KRAS-Mutant Lung Cancer
Authors: Molina-Arcas Miriam , Hancock David C. , Sheridan Clare , Kumar Madhu S. , Downward Julian
Published: April 2023

Supplementary Figure 3 - PDF file 485K, Effects of IGF1R inhibitors on signal transduction pathways in NSCLC cell lines
Supplementary Tables 1-2, 4, 7, 9, 10-11 from BRAFL597 Mutations in Melanoma Are Associated with Sensitivity to MEK Inhibitors
Authors: Dahlman Kimberly Brown , Xia Junfeng , Hutchinson Katherine , Ng Charles , Hucks Donald , Jia Peilin , Atefi Mohammad , Su Zengliu , Branch Suzanne , Lyle Pamela L. , Hicks Donna J. , Bozon Viviana , Glaspy John A. , Rosen Neal , Solit David B. , Netterville James L. , Vnencak-Jones Cindy L. , Sosman Jeffrey A. , Ribas Antoni , Zhao Zhongming , Pao William
Published: April 2023

PDF file - 105K, Tables describing the somatic SNPs and indels identified by WGS, SV validation results, PCR primers used for validation, and tumor measurements from the patient treated with TAK-733
Supplementary Figures 1-11 from BRAFL597 Mutations in Melanoma Are Associated with Sensitivity to MEK Inhibitors
Authors: Dahlman Kimberly Brown , Xia Junfeng , Hutchinson Katherine , Ng Charles , Hucks Donald , Jia Peilin , Atefi Mohammad , Su Zengliu , Branch Suzanne , Lyle Pamela L. , Hicks Donna J. , Bozon Viviana , Glaspy John A. , Rosen Neal , Solit David B. , Netterville James L. , Vnencak-Jones Cindy L. , Sosman Jeffrey A. , Ribas Antoni , Zhao Zhongming , Pao William
Published: April 2023

PDF file - 480K
Supplementary Figure 10 from Coordinate Direct Input of Both KRAS and IGF1 Receptor to Activation of PI3 kinase in KRAS-Mutant Lung Cancer
Authors: Molina-Arcas Miriam , Hancock David C. , Sheridan Clare , Kumar Madhu S. , Downward Julian
Published: April 2023

Supplementary Figure 10 - PDF file 115K, Acute oncogenic RAS signaling in MCF10A epithelial cells
Supplementary Figure 1 from Coordinate Direct Input of Both KRAS and IGF1 Receptor to Activation of PI3 kinase in KRAS-Mutant Lung Cancer
Authors: Molina-Arcas Miriam , Hancock David C. , Sheridan Clare , Kumar Madhu S. , Downward Julian
Published: April 2023

Supplementary Figure 1 - PDF file 152K, Single agent drug effects in NSCLC cell lines
Supplementary Tables 1-7, 9 from Genotype-Selective Combination Therapies for Melanoma Identified by High-Throughput Drug Screening
Authors: Held Matthew A. , Langdon Casey G. , Platt James T. , Graham-Steed Tisheeka , Liu Zongzhi , Chakraborty Ashok , Bacchiocchi Antonella , Koo Andrew , Haskins Jonathan W. , Bosenberg Marcus W. , Stern David F.
Published: April 2023

PDF file - 169K, Table S1. Agents used in single-agent HTS; Table S2. Melanoma cell lines and mutation status; Table S3. Concentrations required to inhibit 50% of cell growth (GI50) in single-agent screens; Table S4. Single agents with significant genotype-selective efficacy; Table S5. Agents and concentrations chosen for cHTS; Table S6. Partial list of drug pairs showing genotype selectivity; Table S7. Genotype-selective combinations with simvastatin; Table S9. Combination index (CI) values for select drug combinations
Supplementary Tables 1-2 from ATM Mutations in Patients with Hereditary Pancreatic Cancer
Authors: Roberts Nicholas J. , Jiao Yuchen , Yu Jun , Kopelovich Levy , Petersen Gloria M. , Bondy Melissa L. , Gallinger Steven , Schwartz Ann G. , Syngal Sapna , Cote Michele L. , Axilbund Jennifer , Schulick Richard , Ali Syed Z. , Eshleman James R. , Velculescu Victor E. , Goggins Michael , Vogelstein Bert , Papadopoulos Nickolas , Hruban Ralph H. , Kinzler Kenneth W. , Klein Alison P.
Published: April 2023

PDF file - 67K
Supplementary Table 1 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 - 23K, Quantitative determination of the binding affinities of the parent and modified STAT3 decoys
Supplementary Figure 5 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 - 524K, Soft agar colony formation assay on MCF10A-HER2 mutant or WT cells
Supplementary Figure 3 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 - 2.2MB, Modified STAT3 decoys demonstrate enhanced resistance to thermal denaturation
Supplementary Figures 1-12, Tables 5-8, Methods from ERα-Dependent E2F Transcription Can Mediate Resistance to Estrogen Deprivation in Human Breast Cancer
Authors: Miller Todd W. , Balko Justin M. , Fox Emily M. , Ghazoui Zara , Dunbier Anita , Anderson Helen , Dowsett Mitch , Jiang Aixiang , Smith R. Adam , Maira Sauveur-Michel , Manning H. Charles , González-Angulo Ana M. , Mills Gordon B. , Higham Catherine , Chanthaphaychith Siprachanh , Kuba Maria G. , Miller William R. , Shyr Yu , Arteaga Carlos L.
Published: April 2023

PDF file - 2340K
Supplementary Table 3 from Janus Kinase 3–Activating Mutations Identified in Natural Killer/T-cell Lymphoma
Authors: Koo Ghee Chong , Tan Soo Yong , Tang Tiffany , Poon Song Ling , Allen George E. , Tan Leonard , Chong Soo Ching , Ong Whee Sze , Tay Kevin , Tao Miriam , Quek Richard , Loong Susan , Yeoh Kheng-Wei , Yap Swee Peng , Lee Kuo Ann , Lim Lay Cheng , Tan Daryl , Goh Christopher , Cutcutache Ioana , Yu Willie , Young Ng Cedric Chuan , Rajasegaran Vikneswari , Heng Hong Lee , Gan Anna , Ong Choon Kiat , Rozen Steve , Tan Patrick , Teh Bin Tean , Lim Soon Thye
Published: April 2023

PDF file - 83K, JAK1 and JAK3 mutation status in NKTCL cases
Supplementary Movie Legends 1-12 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

Supplementary Movie Legends 1-12 from Ovarian Cancer Spheroids Use Myosin-Generated Force to Clear the Mesothelium
Supplementary Movie 7 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 Figures 1-4 from A High-Throughput Functional Complementation Assay for Classification of BRCA1 Missense Variants
Authors: Bouwman Peter , van der Gulden Hanneke , van der Heijden Ingrid , Drost Rinske , Klijn Christiaan N. , Prasetyanti Pramudita , Pieterse Mark , Wientjens Ellen , Seibler Jost , Hogervorst Frans B.L. , Jonkers Jos
Published: April 2023

Supplementary Figures 1-4 - PDF 213K, This file contains additional data on the generation of R26CreERT2/RMCE;Brca1SCo/{delta} ES cells and analysis of Rosa26 targeted human BRCA1 cDNA expression (Fig. S1), analysis of BRCA1 VUS protein and mRNA expression (Fig. S2 and S3) and growth curves supplementary to Figure 6 (Fig. S4)
Supplementary Movie 4B 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: 6 MB.
Supplementary Table 2 from The Transcription Factor ZNF217 Is a Prognostic Biomarker and Therapeutic Target during Breast Cancer Progression
Authors: Littlepage Laurie E. , Adler Adam S. , Kouros-Mehr Hosein , Huang Guiqing , Chou Jonathan , Krig Sheryl R. , Griffith Obi L. , Korkola James E. , Qu Kun , Lawson Devon A. , Xue Qing , Sternlicht Mark D. , Dijkgraaf Gerrit J.P. , Yaswen Paul , Rugo Hope S. , Sweeney Colleen A. , Collins Colin C. , Gray Joe W. , Chang Howard Y. , Werb Zena
Published: April 2023

PDF file - 46K, Gene ontology for microarray gene sets. List of gene ontology (GO) terms from the microarray gene expression datasets of primary MECs � Znf217 using DAVID software
Supplementary Figure 5 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 - 273K, Confirmation of CD3 expression on OP9 DL1 outgrowth cells.
Supplementary Figure 2 from Increased Levels of COX-2 and Prostaglandin E2 Contribute to Elevated Aromatase Expression in Inflamed Breast Tissue of Obese Women
Authors: Subbaramaiah Kotha , Morris Patrick G. , Zhou Xi Kathy , Morrow Monica , Du Baoheng , Giri Dilip , Kopelovich Levy , Hudis Clifford A. , Dannenberg Andrew J.
Published: April 2023

PDF file - 98K
Supplementary Figure Legends 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 Figure Legends 1-7 from Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer
Supplementary Table 2 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 - 138K
Supplementary Methods, Figure Legends 1-4 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 - 73K
Supplementary Figure 2 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 - 104K
Supplementary Figure 1 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 - 141K
Supplementary Figures S2 and S3 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figures S2 and S3 - PDF file 2332K, Figure S2:SG3 tumors are positive for beta-catenin and Myf5 Figure S3:Normal development of Myf5 myoblasts in beta-catenin knockout mice
Interview with Dr. Weinstock 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

mp3 file (7.8 MB). In the January edition of the Cancer Discovery podcast, Executive Editor Mark Landis talks with David Weinstock about his paper, in which analysis of a donor-recipient pair of sisters with follicular lymphoma reveals the time-course of somatic mutations acquired during lymphomagenesis.
Supplementary Figure S8 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figure S8 - PDF file 1084K, Figure S8: Effects of SSTC-104 on Wnt-regulated tissues
Supplementary Methods from Androgen Receptor Signaling in Circulating Tumor Cells as a Marker of Hormonally Responsive Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Stott Shannon L. , Ting David T. , Wittner Ben S. , Ulman Matthew , Smas Malgorzata E. , Lord Jenna B. , Brannigan Brian W. , Trautwein Julie , Bander Neil H. , Wu Chin-Lee , Sequist Lecia V. , Smith Matthew R. , Ramaswamy Sridhar , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

PDF file - 49K, Supplemental Methods for (a) single molecule sequencing and AR transcriptional signature, (b) HB CTC-chip fabrication, (c) HB CTC-chip blood processing, and (d) automated fluorescence microscopy.
Supplementary Figure S10 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figure S10 4882K, Figure S10a and S10b: Nuclear beta-catenin accumulation in human synovial sarcoma tumors
Supplementary Figure S1 from Targeting the Wnt Pathway in Synovial Sarcoma Models
Authors: Barham Whitney , Frump Andrea L. , Sherrill Taylor P. , Garcia Christina B. , Saito-Diaz Kenyi , VanSaun Michael N. , Fingleton Barbara , Gleaves Linda , Orton Darren , Capecchi Mario R. , Blackwell Timothy S. , Lee Ethan , Yull Fiona , Eid Josiane E.
Published: April 2023

Supplementary Figure S1 - PDF file 554K, Breeding strategy used to generate beta-catenin-null SYT-SSX2 transgenic mice
Supplementary Table 1 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 - 23K, Summary of Interactions for sterol pathway genes
Supplementary Figures 1-10 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 - 1.2MB, Fig. S1. Validation of the sterol pathway targeting siRNA. Fig. S2. Silencing of SC4MOL increased erlotinib-induced apoptosis. Fig. S3. Metabolic effects of SC4MOL silencing and sterols supplementation. Fig. S4. Sterol pathway interactions. Fig. S5. Effects of SC4MOL silencing on EGFR synthesis and I-125 EGF internalization and degradation. Fig. S6. Effects of sterol pathway genes silencing on EGFR endosomal traffic. Fig. S7. Effects of SC4MOL silencing on EGFR ubiquitin conjugation and accumulation in late endosomes. Fig. S8. Supporting data for Figure 5. Fig. S9. Supporting data for Figure 7A. Fig. S10. Analysis of NSDHL expression in malignant and benign epithelial tissues
Supplementary Table 5 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

XLSX file - 13K, shRNA, siRNA, and qPCR primer sequences used.
Supplementary Table 3 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

XLSX file - 487K, Pancreatic sample kinome compendium by RNA-Seq.
Supplementary Materials and Methods, Tables 1-2 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 - 120K
Supplementary Figures 1 - 4 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 - 1133K, This file contains supplemental figures validating RNA-Seq method for measuring gene expression and nominating outlier kinases in individual cancer samples.
Supplementary Figure 4 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 - 237K, Pharmacological MEK inhibition sensitizes RAS mutant cancer cells to acute EGFR activation
Supplementary Figure 3 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 - 206K, Wild-type Ras isoforms are required to mediate the suppression of MAPK signaling by ephrin-A1-Fc
Supplementary Figure 9 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 - 69K
Supplementary Figure 8 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 - 57K
Supplementary Figure 4 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 - 48K
Supplementary Figures 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 - 1.5MB
Supplementary Figure 2 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 - 62K
Supplementary Figure 2 from De-Repression of PDGFRβ Transcription Promotes Acquired Resistance to EGFR Tyrosine Kinase Inhibitors in Glioblastoma Patients
Authors: Akhavan David , Pourzia Alexandra L. , Nourian Alex A. , Williams Kevin J. , Nathanson David , Babic Ivan , Villa Genaro R. , Tanaka Kazuhiro , Nael Ali , Yang Huijun , Dang Julie , Vinters Harry V. , Yong William H. , Flagg Mitchell , Tamanoi Fuyuhiko , Sasayama Takashi , James C. David , Kornblum Harley I. , Cloughesy Tim F. , Cavenee Webster K. , Bensinger Steven J. , Mischel Paul S.
Published: April 2023

PDF file - 212K, Fig. S2. Ligand-dependent PDGFRβ stimulation promotes the proliferation of erlotinib-treated glioblastoma cells.
Supplementary Figure 1 from De-Repression of PDGFRβ Transcription Promotes Acquired Resistance to EGFR Tyrosine Kinase Inhibitors in Glioblastoma Patients
Authors: Akhavan David , Pourzia Alexandra L. , Nourian Alex A. , Williams Kevin J. , Nathanson David , Babic Ivan , Villa Genaro R. , Tanaka Kazuhiro , Nael Ali , Yang Huijun , Dang Julie , Vinters Harry V. , Yong William H. , Flagg Mitchell , Tamanoi Fuyuhiko , Sasayama Takashi , James C. David , Kornblum Harley I. , Cloughesy Tim F. , Cavenee Webster K. , Bensinger Steven J. , Mischel Paul S.
Published: April 2023

PDF file - 199K, Fig. S1. EGFRvIII and wild type EGFR signaling regulate PDGFRβ in vitro.
Supplementary Table 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

XLS file - 303K
Supplementary Data from PTEN Loss Mediates Clinical Cross-Resistance to CDK4/6 and PI3Kα Inhibitors in Breast Cancer
Authors: Costa Carlotta , Wang Ye , Ly Amy , Hosono Yasuyuki , Murchie Ellen , Walmsley Charlotte S. , Huynh Tiffany , Healy Christopher , Peterson Rachel , Yanase Shogo , Jakubik Charles T. , Henderson Laura E. , Damon Leah J. , Timonina Daria , Sanidas Ioannis , Pinto Christopher J. , Mino-Kenudson Mari , Stone James R. , Dyson Nicholas J. , Ellisen Leif W. , Bardia Aditya , Ebi Hiromichi , Benes Cyril H. , Engelman Jeffrey A. , Juric Dejan
Published: April 2023

Supplementary Figures
Supplementary Figure 5 from Combining a PI3K Inhibitor with a PARP Inhibitor Provides an Effective Therapy for BRCA1-Related Breast Cancer
Authors: Juvekar Ashish , Burga Laura N. , Hu Hai , Lunsford Elaine P. , Ibrahim Yasir H. , Balmañà Judith , Rajendran Anbazhagan , Papa Antonella , Spencer Katherine , Lyssiotis Costas A. , Nardella Caterina , Pandolfi Pier Paolo , Baselga José , Scully Ralph , Asara John M. , Cantley Lewis C. , Wulf Gerburg M.
Published: April 2023

PDF file - 71K, Standard Curve for the quantitation of NVP-BKM120 in tumor cell lysates. Counts were measured from the peaks of the total ion current for NVP-BKM-120, integrated using MultiQuant v2.0 software (AB/SCIEX). For the concentration curve data, BKM-120 was prepared at concentrations of 1 nM, 10 nM, 100 nM, 500 nM, 1 muM and 10 muM in 40% methanol
Supplementary Figure 4 from Combining a PI3K Inhibitor with a PARP Inhibitor Provides an Effective Therapy for BRCA1-Related Breast Cancer
Authors: Juvekar Ashish , Burga Laura N. , Hu Hai , Lunsford Elaine P. , Ibrahim Yasir H. , Balmañà Judith , Rajendran Anbazhagan , Papa Antonella , Spencer Katherine , Lyssiotis Costas A. , Nardella Caterina , Pandolfi Pier Paolo , Baselga José , Scully Ralph , Asara John M. , Cantley Lewis C. , Wulf Gerburg M.
Published: April 2023

PDF file - 71K, In vitro responses of BRCA1-mutant breast cancer cell lines to treatments with NVP-BKM120 (1 muM), Olaparib (10 muM) or their combination. Cells were seeded in quadruplicate in 96-well plates and treated for 7 days as indicated. A. HCC1937 parental cells, B. SUM149 cells, C. HCC1937 cells stably transfected with vector control or a PTEN expression construct (D)
Supplementary Table 2 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 - 55K
Supplementary Table 1 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

XLS file - 71K, This file contains supplementary Table 1 that contains results from the shRNA screen, including the proliferation assay, plasmid stability assay, and plasmid stability ratios.
Supplementary Methods 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 - 106K, This file contains supplementary information and methods, including sequences of all siRNAs employed.
Supplementary Figures 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

PDF file 287K, contains 12 supplementary figures in PDF format
Supplementary Figure 1 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 1 - PDF file 87K, Cul3 catalyzes the ubiquitination of Nrf2 in vitro
Supplementary Methods 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

PDF file - 266KB
Supplementary Table S2 from A Large-Scale RNAi-Based Mouse Tumorigenesis Screen Identifies New Lung Cancer Tumor Suppressors That Repress FGFR Signaling
Authors: Lin Ling , Chamberlain Lynn , Pak Magnolia L. , Nagarajan Arvindhan , Gupta Romi , Zhu Lihua J. , Wright Casey M. , Fong Kwun M. , Wajapeyee Narendra , Green Michael R.
Published: April 2023

Intensity ratios of methylated to unmethylated DNA for TSG promoters in paired primary hLSCC (LC) and normal lung squamous cell (NL) samples from 18 individuals.
Supplementary Figures 1 - 10 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

PDF file - 2923KB, Supplementary Figure 1. Discordant pairs from whole-genome sequencing indicating the presence of multiple distinct EGFR rearrangements co-existing in individual TCGA samples. Supplementary Figure 2. Evaluation of the quality of whole-genome amplifications in SNS libraries. Supplementary Figure 3. EGFR amplification and rearrangements in BT325 and BT340. Supplementary Figure 4. Clonality analysis of BT325. Supplementary Figure 5. Detection of loss-of-heterozygosity in single nuclei by haplotype clustering. Supplementary Figure 6. Constructing the clonal hierarchy of 48 single nuclei derived from BT340. Supplementary Figure 7. Clonal alterations in BT325. Supplementary Figure 8. Complex rearrangements in BT340. Supplementary Figure 9. Interrogation of clonal alterations in single nuclei derived from BT325. Supplementary Figure 10. EGFRvII deletion mutant expressing Ba/F3 cells are sensitive to EGFR inhibitors.
Supplementary Figure Legends, Table Legends 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

PDF file - 110KB
Supplementary Tables 1 - 3 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 - 84K, Supplementary Table 1. NF1 and BRAF mutations identified in human melanoma cell lines. Data were generated in this study when specified and collected from publicly available databases. (CCLE: Cancer Cell Line Encyclopedia, COSMIC: Catalogue of Somatic Mutations in Cancer, WT: wild-type, n/a: not analyzed). Supplementary Table 2. Somatic NF1 mutations detected in human primary melanomas.Supplementary Table 3. NF1 expression is lost in malignant and metastatic melanomas. Quantification of complete NF1 loss of the human melanoma tissue micorarray ME804a (US Biomax Inc)
Supplementary Figure Legend 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 - 78K
Supplementary Table S5 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

XLSX file 12K, Accounting of frequencies of detecting core resistance pathway mechanisms
Supplementary Table 3 from Prospective Blinded Study of BRAFV600E Mutation Detection in Cell-Free DNA of Patients with Systemic Histiocytic Disorders
Authors: Hyman David M. , Diamond Eli L. , Vibat Cecile Rose T. , Hassaine Latifa , Poole Jason C. , Patel Minal , Holley Veronica R. , Cabrilo Goran , Lu Timothy T. , Arcila Maria E. , Chung Young Rock , Rampal Raajit , Lacouture Mario E. , Rosen Neal , Meric-Bernstam Funda , Baselga José , Kurzrock Razelle , Erlander Mark G. , Janku Filip , Abdel-Wahab Omar
Published: April 2023

Supplemental Table 3: Plasma and urine cfDNA mutation detection zscores for KRAS (G12A, G12C, G12D, G12R, G12S, G12V, G13D) with tissue biopsy KRASG12 genotyping from patient with Erdheim-Chester Disease (ECD).
Supplementary Figure 2 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 - 220K, Response to the Pro-Tumorigenic TNBC Environment is Not Oncotype Specific.
Supplementary Figure 1 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 - 181K, Instigating Tumors Facilitate Responder Growth in the Absence of "Self-seeding".
Supplementary Table S5 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Table S5. Quantification of peptides identified bound to dasatinib by mass spectrometry.
Supplementary Table S4 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Table S4. List of 664 cancer cell lines and sensitivity to dasatinib as determined by area under the curve (AUC) in this study.
Supplementary Table S1 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Table S1. List of constructs used to generate stable cell lines.
Supplementary Methods, Table Legends, Figures 1 - 7 from Linking Tumor Mutations to Drug Responses via a Quantitative Chemical–Genetic Interaction Map
Authors: Martins Maria M. , Zhou Alicia Y. , Corella Alexandra , Horiuchi Dai , Yau Christina , Rakhshandehroo Taha , Gordan John D. , Levin Rebecca S. , Johnson Jeff , Jascur John , Shales Mike , Sorrentino Antonio , Cheah Jaime , Clemons Paul A. , Shamji Alykhan F. , Schreiber Stuart L. , Krogan Nevan J. , Shokat Kevan M. , McCormick Frank , Goga Andrei , Bandyopadhyay Sourav
Published: April 2023

Supplementary Figure 1. Distribution of gene alterations in Breast TCGA and verification of expression of MCF10A cells. Supplementary Figure 2. Analysis of the MCF10A drug screen. Supplementary Figure 3. Significance of overlap between interactions found in this study and in the CGP. Supplementary Figure 4. Response of isogenic engineered cells to dasatinib. Supplementary Figure 5. Dasatinib sensitivity of CML versus AML cancer cell lines. Supplementary Figure 6. Verification of LYN knockdown via siRNA and response of LYN T319I to dasatinib. Supplementary Figure 7. Co-Â­â€�expression of MYC and LYN in breast cancer cell lines.
Supplementary Figure 4 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 - 3743K, TAK1 inhibition alters cell cycle regulation. Panc-1 cells were treated with TAK1 inhibitor, 5Z-7-oxozaenol or vehicle control, DMSO for 24 hours. Cells were fixed and stained with Propidium Iodide and analyzed by Flow cytometry.
Supplementary Figure S5 from Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma
Authors: Ryan Russell J.H. , Drier Yotam , Whitton Holly , Cotton M. Joel , Kaur Jasleen , Issner Robbyn , Gillespie Shawn , Epstein Charles B. , Nardi Valentina , Sohani Aliyah R. , Hochberg Ephraim P. , Bernstein Bradley E.
Published: April 2023

Supplementary Figure S5. Additional details regarding candidate MYC enhancers identified in B cell lymphomas.
Supplementary Movie E 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 1064K, Cell undergoing a normal mitosis followed by cell cell cycle arrest in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplementary Figure S2 from Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma
Authors: Ryan Russell J.H. , Drier Yotam , Whitton Holly , Cotton M. Joel , Kaur Jasleen , Issner Robbyn , Gillespie Shawn , Epstein Charles B. , Nardi Valentina , Sohani Aliyah R. , Hochberg Ephraim P. , Bernstein Bradley E.
Published: April 2023

Supplementary Figure S2. Quantitative RT-PCR evaluation of lymphoma samples.
Supplementary Figure S1 from Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma
Authors: Ryan Russell J.H. , Drier Yotam , Whitton Holly , Cotton M. Joel , Kaur Jasleen , Issner Robbyn , Gillespie Shawn , Epstein Charles B. , Nardi Valentina , Sohani Aliyah R. , Hochberg Ephraim P. , Bernstein Bradley E.
Published: April 2023

Supplementary Figure S1. H3K27ac ChIP-Seq tracks and position of rearrangements of possible oncogenic significance detected by PEAR-ChIP. Red bars join discordant intra-chromosomal read pairs.
Supplementary Movie A 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 1070K, Cell undergoing a segregation error followed by mitosis in the daughter cell (see Supplementary Figure 4 for movie stills)
Supplementary Figure 8 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 45K, Supplementary Figure 8: A) Full survival curves for TCGA cohort and B) full survival curves for the validation cohort. C) Diploid only tumour survival curves from validation cohort
Supplementary Figures 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 Figures - PDF file 441K, Four figures as follows: SF1: decreased PTEN expression in HNSCC with PTEN loss. SFs 2-4: PIK3CA mutant HNSCC tumorgrafts treatment response characterization; PI3K inhibitors +/- cetuximab, tumor measurements and western blotting for PI3K signaling
Supplementary Figures 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 1227K, This file contains Supplemental Figures 1-7, which provide additional supporting information for each of the main figures
Supplementary Table 5 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 90K, Alterations in Each Patient in Genes that Scored in Functional Screens
Supplementary Table 4 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 12K, Candidate Resistance Genes from RNAi and ORF Functional Screens
Supplementary Table 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 Table S3. Primers/probes used for Taqman PCR array.
Supplementary Table 1 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

XLS file 6188K, Annotated SNVs and Indels in All Samples