bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S4 from Suppression of CHK1 by ETS Family Members Promotes DNA Damage Response Bypass and Tumorigenesis
Authors: Lunardi Andrea , Varmeh Shohreh , Chen Ming , Taulli Riccardo , Guarnerio Jlenia , Ala Ugo , Seitzer Nina , Ishikawa Tomoki , Carver Brett S. , Hobbs Robin M. , Quarantotti Valentina , Ng Christopher , Berger Alice H. , Nardella Caterina , Poliseno Laura , Montironi Rodolfo , Castillo-Martin Mireia , Cordon-Cardo Carlos , Signoretti Sabina , Pandolfi Pier Paolo
Published: April 2023

Supplementary Figure S4. Chk1 heterozygosity accelerates classical Pten+/- driven phenotypes.
Table S4 from PDK1 Signaling Toward PLK1–MYC Activation Confers Oncogenic Transformation, Tumor-Initiating Cell Activation, and Resistance to mTOR-Targeted Therapy
Authors: Tan Jing , Li Zhimei , Lee Puay Leng , Guan Peiyong , Aau Mei Yee , Lee Shuet Theng , Feng Min , Lim Cheryl Zihui , Lee Eric Yong Jing , Wee Zhen Ning , Lim Yaw Chyn , Karuturi R.K. Murthy , Yu Qiang
Published: April 2023

Table S4 - XLS file 55K, Supplementary table 4 shows the list of PDK1-regulated genes significantly different from Myc-regulated genes
Supplementary Tables S1-S2 from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors
Authors: Konieczkowski David J. , Johannessen Cory M. , Abudayyeh Omar , Kim Jong Wook , Cooper Zachary A. , Piris Adriano , Frederick Dennie T. , Barzily-Rokni Michal , Straussman Ravid , Haq Rizwan , Fisher David E. , Mesirov Jill P. , Hahn William C. , Flaherty Keith T. , Wargo Jennifer A. , Tamayo Pablo , Garraway Levi A.
Published: April 2023

PDF file 89K, This file contains a table listing the top 75 genes correlated with RAF-inhibitor sensitivity in BRAFV600E-mutant cell lines as well as a table describing the IHC results summarized in Main Figure 2b and 2c
Supplementary Movie Legends from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Supplementary Movie Legends
Supplementary Movie 3 from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Real-time intravital two-photon microscopy showing pinocytosis of bisphosphonate by a single tumour-associated macrophage.
Supplementary Methods from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: April 2023

Supplementary Methods
Supplementary Figure S7 from Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid–Induced 2
Authors: Werner Stefan , Brors Benedikt , Eick Julia , Marques Elsa , Pogenberg Vivian , Parret Annabel , Kemming Dirk , Wood Antony W. , Edgren Henrik , Neubauer Hans , Streichert Thomas , Riethdorf Sabine , Bedi Upasana , Baccelli Irène , Jücker Manfred , Eils Roland , Fehm Tanja , Trumpp Andreas , Johnsen Steven A. , Klefström Juha , Wilmanns Matthias , Müller Volkmar , Pantel Klaus , Wikman Harriet
Published: April 2023

Supplementary Figure S7. Gene expression profiling of MDA-MD-231 cells over expressing wild type and CtBP binding deficient RAI2 proteins.
Supplementary Figure S6 from Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid–Induced 2
Authors: Werner Stefan , Brors Benedikt , Eick Julia , Marques Elsa , Pogenberg Vivian , Parret Annabel , Kemming Dirk , Wood Antony W. , Edgren Henrik , Neubauer Hans , Streichert Thomas , Riethdorf Sabine , Bedi Upasana , Baccelli Irène , Jücker Manfred , Eils Roland , Fehm Tanja , Trumpp Andreas , Johnsen Steven A. , Klefström Juha , Wilmanns Matthias , Müller Volkmar , Pantel Klaus , Wikman Harriet
Published: April 2023

Supplementary Figure S6. Analysis of adherents junction formation following RAI2 depletion in MCF-7 and KPL-1.
Supplementary Figure S2 from Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid–Induced 2
Authors: Werner Stefan , Brors Benedikt , Eick Julia , Marques Elsa , Pogenberg Vivian , Parret Annabel , Kemming Dirk , Wood Antony W. , Edgren Henrik , Neubauer Hans , Streichert Thomas , Riethdorf Sabine , Bedi Upasana , Baccelli Irène , Jücker Manfred , Eils Roland , Fehm Tanja , Trumpp Andreas , Johnsen Steven A. , Klefström Juha , Wilmanns Matthias , Müller Volkmar , Pantel Klaus , Wikman Harriet
Published: April 2023

Supplementary Figure S2. Survival analysis in extreme quartiles of RERG and RLN2 mRNA expression in breast cancer data sets.
Supplementary Figures S1 - S4 from PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in BRAF-Mutated Melanoma
Authors: Deuker Marian M. , Marsh Durban Victoria , Phillips Wayne A. , McMahon Martin
Published: April 2023

Supplementary Figure S1. BP2C mouse melanoma-derived cells are sensitive to PI3Kalpha-selective inhibition. Supplementary Figure S2. BRAFV600E/PTENNull melanoma-derived cells are sensitive to PI3Kalpha-sparing PI3'-kinase. Supplementary Figure S3. PI3Kalpha-sparing PI3K inhibition enhances the effects of MEK inhibition on BRAFV600E/PTENNull melanoma-derived cells inhibition. Supplementary Figure S4. BRAFV600E/PTENWT melanoma cells are sensitive to PI3Kalpha-sparing PI3'-kinase inhibition, and PI3Kalpha-sparing PI3K inhibition enhances the effects of MEK inhibition on BRAFV600E/ PTENWT melanoma cells.
Supplementary Figures and Tables from Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis
Authors: Parmenter Tiffany J. , Kleinschmidt Margarete , Kinross Kathryn M. , Bond Simon T. , Li Jason , Kaadige Mohan R. , Rao Aparna , Sheppard Karen E. , Hugo Willy , Pupo Gulietta M. , Pearson Richard B. , McGee Sean L. , Long Georgina V. , Scolyer Richard A. , Rizos Helen , Lo Roger S. , Cullinane Carleen , Ayer Donald E. , Ribas Antoni , Johnstone Ricky W. , Hicks Rodney J. , McArthur Grant A.
Published: April 2023

PDF file 3260K, Supplementary figures and tables
Supplementary Material from An In Vivo Functional Screen Identifies ST6GalNAc2 Sialyltransferase as a Breast Cancer Metastasis Suppressor
Authors: Murugaesu Nirupa , Iravani Marjan , van Weverwijk Antoinette , Ivetic Aleksandar , Johnson Damian A. , Antonopoulos Aristotelis , Fearns Antony , Jamal-Hanjani Mariam , Sims David , Fenwick Kerry , Mitsopoulos Costas , Gao Qiong , Orr Nick , Zvelebil Marketa , Haslam Stuart M. , Dell Anne , Yarwood Helen , Lord Christopher J. , Ashworth Alan , Isacke Clare M.
Published: April 2023

PDF file 107K, Inventory of supplementary material. Supplementary Table S1 listing primers and siRNAs. Legends for Supplementary Fig. S1 - S7 Legends for Supplementary Movies S1 and S2 Supplementary Figures S1 - S6 legends Supplementary Movies S1 and S2 legends
Supplementary Figure 6 from RHOA-FAK Is a Required Signaling Axis for the Maintenance of KRAS-Driven Lung Adenocarcinomas
Authors: Konstantinidou Georgia , Ramadori Giorgio , Torti Francesca , Kangasniemi Kim , Ramirez Rachel E. , Cai Yiran , Behrens Carmen , Dellinger Michael T. , Brekken Rolf A. , Wistuba Ignacio I. , Heguy Adriana , Teruya-Feldstein Julie , Scaglioni Pier Paolo
Published: April 2023

Supplementary Figure 6 PDF file - 141K, This Figure shows that FAK is co-expressed with RHOA in lung adenocarcinomas. In addition, we provide the validation of RHOA-GTP antibody on human specimens by IHC
Supplementary Figure 4 from RHOA-FAK Is a Required Signaling Axis for the Maintenance of KRAS-Driven Lung Adenocarcinomas
Authors: Konstantinidou Georgia , Ramadori Giorgio , Torti Francesca , Kangasniemi Kim , Ramirez Rachel E. , Cai Yiran , Behrens Carmen , Dellinger Michael T. , Brekken Rolf A. , Wistuba Ignacio I. , Heguy Adriana , Teruya-Feldstein Julie , Scaglioni Pier Paolo
Published: April 2023

Supplementary Figure 4 PDF file - 169K, This Figure shows that RHOA activation is essential for the survival of NSCLC expressing mutant KRAS in association with INK4a/ARF or p53 deficiency
Supplementary Figure 1 from RHOA-FAK Is a Required Signaling Axis for the Maintenance of KRAS-Driven Lung Adenocarcinomas
Authors: Konstantinidou Georgia , Ramadori Giorgio , Torti Francesca , Kangasniemi Kim , Ramirez Rachel E. , Cai Yiran , Behrens Carmen , Dellinger Michael T. , Brekken Rolf A. , Wistuba Ignacio I. , Heguy Adriana , Teruya-Feldstein Julie , Scaglioni Pier Paolo
Published: April 2023

Supplementary Figure 1 PDF file - 311K, This Figure shows that the KrasG12D;Ink4a/Arf -/- mice show increased tumor burden, increased Ki-67, Cyclin D1 expression and decreased survival compared to KrasG12D;Ink4a/Arf +/+ mice
Supplementary Figure 6 from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: April 2023

A, Immunoblots of control RPE1 cells and cells depleted for Chk2 using Chk2 siRNA stained using anti-Chk2 antibody and anti-actin antibody as a loading control. B, Chromosome mis-segregation in control RPE1 cells and cells depleted for Chk2 using Chk2 siRNA in the presence or absence of Doxorubicin. Bars represent mean, n = 150 cells, 3 experiments, **, p<0.01. C, Chromosome mis-segregation in AT22IJE-T fibroblasts and AT22IJE-T fibroblasts expressing FLAG-ATM in the presence or absence of either Chloroquine (31Î¼g ml-1) or Doxorubicin (0.5 Î¼M). Bars represent mean, n = 150 cells, 3 experiments, **, p<0.01.
Supplementary Figure 3 from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: April 2023

IR does not significantly affect sister chromatid cohesion. A, Experimental schema of assessing sister chromatid cohesion after IR exposure. Noc, Nocodazole. Bar graphs show percentage of mitotic spreads containing chromosomes with intact sister-chromatid cohesion or uncohesed chromosomes as a function of IR dose. n>300 mitotic spreads, p>0.14, Ï‡2-test for all cell lines B, Experimental schema of assessing sister chromatid cohesion after Doxorubicin exposure. Noc, Nocodazole; Doxo, Doxorubicin. Graphs depicting the percentage of mitotic spreads with intact sister chromatid cohesion over time. n>300 spreads, 3 experiments. C, Examples of mitotic spreads from control (left) and irradiated (middle) cells and spreads containing uncohesed chromosomes (right). Scale bar, 25-Î¼m.
Supplementary Figure 2 from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: April 2023

IR does not dramatically alter spindle geometry of irradiated mitotic cells. Examples of monopolar (A) and multipolar (B) Spindles of U251 cells stained for kinetochores (green), DNA (blue), and microtubules (red). Scale bar, 5-Î¼m. Graphs represent the percentage of monopolar (A) and multipolar (B) spindles as a function of IR dose. Circles represent mean {plus minus} s.e.m, n = 150 cells, 3 experiments.
Supplementary Figure 3 from Phase IB Study of Vemurafenib in Combination with Irinotecan and Cetuximab in Patients with Metastatic Colorectal Cancer with BRAFV600E Mutation
Authors: Hong David S. , Morris Van K. , El Osta Badi , Sorokin Alexey V. , Janku Filip , Fu Siqing , Overman Michael J. , Piha-Paul Sarina , Subbiah Vivek , Kee Bryan , Tsimberidou Apostolia M. , Fogelman David , Bellido Jorge , Shureiqi Imad , Huang Helen , Atkins Johnique , Tarcic Gabi , Sommer Nicolas , Lanman Richard , Meric-Bernstam Funda , Kopetz Scott
Published: April 2023

Analysis of BRAFV600E allele fraction by cfDNA was validated using two separate methodologies.
Supplementary Table S1 from CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions
Authors: Munoz Diana M. , Cassiani Pamela J. , Li Li , Billy Eric , Korn Joshua M. , Jones Michael D. , Golji Javad , Ruddy David A. , Yu Kristine , McAllister Gregory , DeWeck Antoine , Abramowski Dorothee , Wan Jessica , Shirley Matthew D. , Neshat Sarah Y. , Rakiec Daniel , de Beaumont Rosalie , Weber Odile , Kauffmann Audrey , McDonald E. Robert , Keen Nicholas , Hofmann Francesco , Sellers William R. , Schmelzle Tobias , Stegmeier Frank , Schlabach Michael R.
Published: April 2023

Correlation analysis matrix displaying features that correlate most strongly with sgRNA's having off target effects.
Supplementary Figures 1-12, Tables 1-11, Methods from MYC Is Activated by USP2a-Mediated Modulation of MicroRNAs in Prostate Cancer
Authors: Benassi Barbara , Flavin Richard , Marchionni Luigi , Zanata Silvio , Pan Yunfeng , Chowdhury Dipanjan , Marani Marina , Strano Sabrina , Muti Paola , Blandino Giovanni , Loda Massimo
Published: April 2023

PDF file - 643K
Supplementary Figures from A Preexisting Rare PIK3CAE545K Subpopulation Confers Clinical Resistance to MEK plus CDK4/6 Inhibition in NRAS Melanoma and Is Dependent on S6K1 Signaling
Authors: Romano Gabriele , Chen Pei-Ling , Song Ping , McQuade Jennifer L. , Liang Roger J. , Liu Mingguang , Roh Whijae , Duose Dzifa Y. , Carapeto Fernando C.L. , Li Jun , Teh Jessica L.F. , Aplin Andrew E. , Chen Merry , Zhang Jianhua , Lazar Alexander J. , Davies Michael A. , Futreal P. Andrew , Amaria Rodabe N. , Zhang David Y. , Wargo Jennifer A. , Kwong Lawrence N.
Published: April 2023

Supplementary Figures S1-S13
Supplementary Table S1 from NRG1 Fusions in KRAS Wild-Type Pancreatic Cancer
Authors: Heining Christoph , Horak Peter , Uhrig Sebastian , Codo Paula L. , Klink Barbara , Hutter Barbara , Fröhlich Martina , Bonekamp David , Richter Daniela , Steiger Katja , Penzel Roland , Endris Volker , Ehrenberg Karl Roland , Frank Stephanie , Kleinheinz Kortine , Toprak Umut H. , Schlesner Matthias , Mandal Ranadip , Schulz Lothar , Lambertz Helmut , Fetscher Sebastian , Bitzer Michael , Malek Nisar P. , Horger Marius , Giese Nathalia A. , Strobel Oliver , Hackert Thilo , Springfeld Christoph , Feuerbach Lars , Bergmann Frank , Schröck Evelin , von Kalle Christof , Weichert Wilko , Scholl Claudia , Ball Claudia R. , Stenzinger Albrecht , Brors Benedikt , Fröhling Stefan , Glimm Hanno
Published: April 2023

Supplementary Table S1 lists potentially clinically relevant somatic alterations in the PDAC patient cohort.
Supplementary Patient Data from NRG1 Fusions in KRAS Wild-Type Pancreatic Cancer
Authors: Heining Christoph , Horak Peter , Uhrig Sebastian , Codo Paula L. , Klink Barbara , Hutter Barbara , Fröhlich Martina , Bonekamp David , Richter Daniela , Steiger Katja , Penzel Roland , Endris Volker , Ehrenberg Karl Roland , Frank Stephanie , Kleinheinz Kortine , Toprak Umut H. , Schlesner Matthias , Mandal Ranadip , Schulz Lothar , Lambertz Helmut , Fetscher Sebastian , Bitzer Michael , Malek Nisar P. , Horger Marius , Giese Nathalia A. , Strobel Oliver , Hackert Thilo , Springfeld Christoph , Feuerbach Lars , Bergmann Frank , Schröck Evelin , von Kalle Christof , Weichert Wilko , Scholl Claudia , Ball Claudia R. , Stenzinger Albrecht , Brors Benedikt , Fröhling Stefan , Glimm Hanno
Published: April 2023

Supplementary patient data provides a summary on the clinical course of patient 16.
Merged Supplementary Figures from The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression
Authors: Pushalkar Smruti , Hundeyin Mautin , Daley Donnele , Zambirinis Constantinos P. , Kurz Emma , Mishra Ankita , Mohan Navyatha , Aykut Berk , Usyk Mykhaylo , Torres Luisana E. , Werba Gregor , Zhang Kevin , Guo Yuqi , Li Qianhao , Akkad Neha , Lall Sarah , Wadowski Benjamin , Gutierrez Johana , Kochen Rossi Juan Andres , Herzog Jeremy W. , Diskin Brian , Torres-Hernandez Alejandro , Leinwand Josh , Wang Wei , Taunk Pardeep S. , Savadkar Shivraj , Janal Malvin , Saxena Anjana , Li Xin , Cohen Deirdre , Sartor R. Balfour , Saxena Deepak , Miller George
Published: April 2023

Supplementary Figures 1-8.
Chemical Methods from A Unified Approach to Targeting the Lysosome's Degradative and Growth Signaling Roles
Authors: Rebecca Vito W. , Nicastri Michael C. , McLaughlin Noel , Fennelly Colin , McAfee Quentin , Ronghe Amruta , Nofal Michel , Lim Chun-Yan , Witze Eric , Chude Cynthia I. , Zhang Gao , Alicea Gretchen M. , Piao Shengfu , Murugan Sengottuvelan , Ojha Rani , Levi Samuel M. , Wei Zhi , Barber-Rotenberg Julie S. , Murphy Maureen E. , Mills Gordon B. , Lu Yiling , Rabinowitz Joshua , Marmorstein Ronen , Liu Qin , Liu Shujing , Xu Xiaowei , Herlyn Meenhard , Zoncu Roberto , Brady Donita C. , Speicher David W. , Winkler Jeffrey D. , Amaravadi Ravi K.
Published: April 2023

Supplemental Chemical Methods
Supplementary Table S13 from Tissue-Specific Oncogenic Activity of KRASA146T
Authors: Poulin Emily J. , Bera Asim K. , Lu Jia , Lin Yi-Jang , Strasser Samantha Dale , Paulo Joao A. , Huang Tannie Q. , Morales Carolina , Yan Wei , Cook Joshua , Nowak Jonathan A. , Brubaker Douglas K. , Joughin Brian A. , Johnson Christian W. , DeStefanis Rebecca A. , Ghazi Phaedra C. , Gondi Sudershan , Wales Thomas E. , Iacob Roxana E. , Bogdanova Lana , Gierut Jessica J. , Li Yina , Engen John R. , Perez-Mancera Pedro A. , Braun Benjamin S. , Gygi Steven P. , Lauffenburger Douglas A. , Westover Kenneth D. , Haigis Kevin M.
Published: April 2023

GSEA analysis of spleens expressing WT or mutant K-Ras.
Supplementary Table S12 from Tissue-Specific Oncogenic Activity of KRASA146T
Authors: Poulin Emily J. , Bera Asim K. , Lu Jia , Lin Yi-Jang , Strasser Samantha Dale , Paulo Joao A. , Huang Tannie Q. , Morales Carolina , Yan Wei , Cook Joshua , Nowak Jonathan A. , Brubaker Douglas K. , Joughin Brian A. , Johnson Christian W. , DeStefanis Rebecca A. , Ghazi Phaedra C. , Gondi Sudershan , Wales Thomas E. , Iacob Roxana E. , Bogdanova Lana , Gierut Jessica J. , Li Yina , Engen John R. , Perez-Mancera Pedro A. , Braun Benjamin S. , Gygi Steven P. , Lauffenburger Douglas A. , Westover Kenneth D. , Haigis Kevin M.
Published: April 2023

GSEA analysis of pancreata expressing WT or mutant K-Ras.
Supplementary Figures S1-S18 from Tissue-Specific Oncogenic Activity of KRASA146T
Authors: Poulin Emily J. , Bera Asim K. , Lu Jia , Lin Yi-Jang , Strasser Samantha Dale , Paulo Joao A. , Huang Tannie Q. , Morales Carolina , Yan Wei , Cook Joshua , Nowak Jonathan A. , Brubaker Douglas K. , Joughin Brian A. , Johnson Christian W. , DeStefanis Rebecca A. , Ghazi Phaedra C. , Gondi Sudershan , Wales Thomas E. , Iacob Roxana E. , Bogdanova Lana , Gierut Jessica J. , Li Yina , Engen John R. , Perez-Mancera Pedro A. , Braun Benjamin S. , Gygi Steven P. , Lauffenburger Douglas A. , Westover Kenneth D. , Haigis Kevin M.
Published: April 2023

Supplementary Figures S1-S18
Figure S6 from Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation
Authors: Song Chunying , Piva Marco , Sun Lu , Hong Aayoung , Moriceau Gatien , Kong Xiangju , Zhang Hong , Lomeli Shirley , Qian Jin , Yu Clarissa C. , Damoiseaux Robert , Kelley Mark C. , Dahlman Kimberley B. , Scumpia Philip O. , Sosman Jeffrey A. , Johnson Douglas B. , Ribas Antoni , Hugo Willy , Lo Roger S.
Published: April 2023

Figure S6
Figure S4 from Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation
Authors: Song Chunying , Piva Marco , Sun Lu , Hong Aayoung , Moriceau Gatien , Kong Xiangju , Zhang Hong , Lomeli Shirley , Qian Jin , Yu Clarissa C. , Damoiseaux Robert , Kelley Mark C. , Dahlman Kimberley B. , Scumpia Philip O. , Sosman Jeffrey A. , Johnson Douglas B. , Ribas Antoni , Hugo Willy , Lo Roger S.
Published: April 2023

Figure S4
Figure S2 from Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation
Authors: Song Chunying , Piva Marco , Sun Lu , Hong Aayoung , Moriceau Gatien , Kong Xiangju , Zhang Hong , Lomeli Shirley , Qian Jin , Yu Clarissa C. , Damoiseaux Robert , Kelley Mark C. , Dahlman Kimberley B. , Scumpia Philip O. , Sosman Jeffrey A. , Johnson Douglas B. , Ribas Antoni , Hugo Willy , Lo Roger S.
Published: April 2023

Figure S2
Supplementary Materials from Targeting DNA Damage Response Promotes Antitumor Immunity through STING-Mediated T-cell Activation in Small Cell Lung Cancer
Authors: Sen Triparna , Rodriguez B. Leticia , Chen Limo , Corte Carminia M. Della , Morikawa Naoto , Fujimoto Junya , Cristea Sandra , Nguyen Thuyen , Diao Lixia , Li Lerong , Fan Youhong , Yang Yongbin , Wang Jing , Glisson Bonnie S. , Wistuba Ignacio I. , Sage Julien , Heymach John V. , Gibbons Don L. , Byers Lauren A.
Published: April 2023

This file contains supplementary materials and methods; figures and figure legends and Tables.
Table S1 from BRCA Reversion Mutations in Circulating Tumor DNA Predict Primary and Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma
Authors: Lin Kevin K. , Harrell Maria I. , Oza Amit M. , Oaknin Ana , Ray-Coquard Isabelle , Tinker Anna V. , Helman Elena , Radke Marc R. , Say Carmen , Vo Lan-Thanh , Mann Elaina , Isaacson Jeffrey D. , Maloney Lara , O'Malley David M. , Chambers Setsuko K. , Kaufmann Scott H. , Scott Clare L. , Konecny Gottfried E. , Coleman Robert L. , Sun James X. , Giordano Heidi , Brenton James D. , Harding Thomas C. , McNeish Iain A. , Swisher Elizabeth M.
Published: April 2023

Table S1 is an Excel sheet that provides a detailed listing of primary BRCA and TP53 mutations as well as BRCA reversion mutations detected in pretreatment and postprogression circulating cell-free DNA and tumor biopsy samples
Supp. Tables S16-S19 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Authors: Grasso Catherine S. , Giannakis Marios , Wells Daniel K. , Hamada Tsuyoshi , Mu Xinmeng Jasmine , Quist Michael , Nowak Jonathan A. , Nishihara Reiko , Qian Zhi Rong , Inamura Kentaro , Morikawa Teppei , Nosho Katsuhiko , Abril-Rodriguez Gabriel , Connolly Charles , Escuin-Ordinas Helena , Geybels Milan S. , Grady William M. , Hsu Li , Hu-Lieskovan Siwen , Huyghe Jeroen R. , Kim Yeon Joo , Krystofinski Paige , Leiserson Mark D.M. , Montoya Dennis J. , Nadel Brian B. , Pellegrini Matteo , Pritchard Colin C. , Puig-Saus Cristina , Quist Elleanor H. , Raphael Ben J. , Salipante Stephen J. , Shin Daniel Sanghoon , Shinbrot Eve , Shirts Brian , Shukla Sachet , Stanford Janet L. , Sun Wei , Tsoi Jennifer , Upfill-Brown Alexander , Wheeler David A. , Wu Catherine J. , Yu Ming , Zaidi Syed H. , Zaretsky Jesse M. , Gabriel Stacey B. , Lander Eric S. , Garraway Levi A. , Hudson Thomas J. , Fuchs Charles S. , Ribas Antoni , Ogino Shuji , Peters Ulrike
Published: April 2023

Supplementary Tables S16-S19, describing IHC results on NHS/HPFS data
Supp. Tables S1, S3-S15, S20, and S23 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Authors: Grasso Catherine S. , Giannakis Marios , Wells Daniel K. , Hamada Tsuyoshi , Mu Xinmeng Jasmine , Quist Michael , Nowak Jonathan A. , Nishihara Reiko , Qian Zhi Rong , Inamura Kentaro , Morikawa Teppei , Nosho Katsuhiko , Abril-Rodriguez Gabriel , Connolly Charles , Escuin-Ordinas Helena , Geybels Milan S. , Grady William M. , Hsu Li , Hu-Lieskovan Siwen , Huyghe Jeroen R. , Kim Yeon Joo , Krystofinski Paige , Leiserson Mark D.M. , Montoya Dennis J. , Nadel Brian B. , Pellegrini Matteo , Pritchard Colin C. , Puig-Saus Cristina , Quist Elleanor H. , Raphael Ben J. , Salipante Stephen J. , Shin Daniel Sanghoon , Shinbrot Eve , Shirts Brian , Shukla Sachet , Stanford Janet L. , Sun Wei , Tsoi Jennifer , Upfill-Brown Alexander , Wheeler David A. , Wu Catherine J. , Yu Ming , Zaidi Syed H. , Zaretsky Jesse M. , Gabriel Stacey B. , Lander Eric S. , Garraway Levi A. , Hudson Thomas J. , Fuchs Charles S. , Ribas Antoni , Ogino Shuji , Peters Ulrike
Published: April 2023

Supplementary Tables S1, S3 through S15, S20, and S23
Supp. Table S22 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Authors: Grasso Catherine S. , Giannakis Marios , Wells Daniel K. , Hamada Tsuyoshi , Mu Xinmeng Jasmine , Quist Michael , Nowak Jonathan A. , Nishihara Reiko , Qian Zhi Rong , Inamura Kentaro , Morikawa Teppei , Nosho Katsuhiko , Abril-Rodriguez Gabriel , Connolly Charles , Escuin-Ordinas Helena , Geybels Milan S. , Grady William M. , Hsu Li , Hu-Lieskovan Siwen , Huyghe Jeroen R. , Kim Yeon Joo , Krystofinski Paige , Leiserson Mark D.M. , Montoya Dennis J. , Nadel Brian B. , Pellegrini Matteo , Pritchard Colin C. , Puig-Saus Cristina , Quist Elleanor H. , Raphael Ben J. , Salipante Stephen J. , Shin Daniel Sanghoon , Shinbrot Eve , Shirts Brian , Shukla Sachet , Stanford Janet L. , Sun Wei , Tsoi Jennifer , Upfill-Brown Alexander , Wheeler David A. , Wu Catherine J. , Yu Ming , Zaidi Syed H. , Zaretsky Jesse M. , Gabriel Stacey B. , Lander Eric S. , Garraway Levi A. , Hudson Thomas J. , Fuchs Charles S. , Ribas Antoni , Ogino Shuji , Peters Ulrike
Published: April 2023

Supplementary Table S22: Segmented b-allele deficits
Supp. Table S21 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Authors: Grasso Catherine S. , Giannakis Marios , Wells Daniel K. , Hamada Tsuyoshi , Mu Xinmeng Jasmine , Quist Michael , Nowak Jonathan A. , Nishihara Reiko , Qian Zhi Rong , Inamura Kentaro , Morikawa Teppei , Nosho Katsuhiko , Abril-Rodriguez Gabriel , Connolly Charles , Escuin-Ordinas Helena , Geybels Milan S. , Grady William M. , Hsu Li , Hu-Lieskovan Siwen , Huyghe Jeroen R. , Kim Yeon Joo , Krystofinski Paige , Leiserson Mark D.M. , Montoya Dennis J. , Nadel Brian B. , Pellegrini Matteo , Pritchard Colin C. , Puig-Saus Cristina , Quist Elleanor H. , Raphael Ben J. , Salipante Stephen J. , Shin Daniel Sanghoon , Shinbrot Eve , Shirts Brian , Shukla Sachet , Stanford Janet L. , Sun Wei , Tsoi Jennifer , Upfill-Brown Alexander , Wheeler David A. , Wu Catherine J. , Yu Ming , Zaidi Syed H. , Zaretsky Jesse M. , Gabriel Stacey B. , Lander Eric S. , Garraway Levi A. , Hudson Thomas J. , Fuchs Charles S. , Ribas Antoni , Ogino Shuji , Peters Ulrike
Published: April 2023

Supplementary Table S21: Segmented copy-number ratios
Table S3 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Pharmacokinetic properties of JBJ-02-112-05 and JBJ-04-125-02.
Figure S4 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Not all tyrosine kinase inhibitors (TKIs) can enhance or bind at the same time as an allosteric inhibitor (AI) and co-binding of TKIs and AIs do not necessarily translate into increased drug potency.
Supplementary Video S5 from E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer
Authors: Bajrami Ilirjana , Marlow Rebecca , van de Ven Marieke , Brough Rachel , Pemberton Helen N. , Frankum Jessica , Song Feifei , Rafiq Rumana , Konde Asha , Krastev Dragomir B. , Menon Malini , Campbell James , Gulati Aditi , Kumar Rahul , Pettitt Stephen J. , Gurden Mark D. , Cardenosa Marta Llorca , Chong Irene , Gazinska Patrycja , Wallberg Fredrik , Sawyer Elinor J. , Martin Lesley-Ann , Dowsett Mitch , Linardopoulos Spiros , Natrajan Rachael , Ryan Colm J. , Derksen Patrick W.B. , Jonkers Jos , Tutt Andrew N.J. , Ashworth Alan , Lord Christopher J.
Published: April 2023

Membrane oscillation in E-cadherin defective cell exposed to crizotinib leading to failed cytokinesis
Supplementary Video S4 from E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer
Authors: Bajrami Ilirjana , Marlow Rebecca , van de Ven Marieke , Brough Rachel , Pemberton Helen N. , Frankum Jessica , Song Feifei , Rafiq Rumana , Konde Asha , Krastev Dragomir B. , Menon Malini , Campbell James , Gulati Aditi , Kumar Rahul , Pettitt Stephen J. , Gurden Mark D. , Cardenosa Marta Llorca , Chong Irene , Gazinska Patrycja , Wallberg Fredrik , Sawyer Elinor J. , Martin Lesley-Ann , Dowsett Mitch , Linardopoulos Spiros , Natrajan Rachael , Ryan Colm J. , Derksen Patrick W.B. , Jonkers Jos , Tutt Andrew N.J. , Ashworth Alan , Lord Christopher J.
Published: April 2023

Lagging chromosomes followed by membrane oscillation in E-cadherin defective cell exposed to crizotinib leading to failed cytokinesis
Supplementary Video S3 from E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer
Authors: Bajrami Ilirjana , Marlow Rebecca , van de Ven Marieke , Brough Rachel , Pemberton Helen N. , Frankum Jessica , Song Feifei , Rafiq Rumana , Konde Asha , Krastev Dragomir B. , Menon Malini , Campbell James , Gulati Aditi , Kumar Rahul , Pettitt Stephen J. , Gurden Mark D. , Cardenosa Marta Llorca , Chong Irene , Gazinska Patrycja , Wallberg Fredrik , Sawyer Elinor J. , Martin Lesley-Ann , Dowsett Mitch , Linardopoulos Spiros , Natrajan Rachael , Ryan Colm J. , Derksen Patrick W.B. , Jonkers Jos , Tutt Andrew N.J. , Ashworth Alan , Lord Christopher J.
Published: April 2023

Lagging chromosomes in E-cadherin defective cell exposed to foretinib leading to failed cytokinesis
Supplementary Video S1 from E-Cadherin/ROS1 Inhibitor Synthetic Lethality in Breast Cancer
Authors: Bajrami Ilirjana , Marlow Rebecca , van de Ven Marieke , Brough Rachel , Pemberton Helen N. , Frankum Jessica , Song Feifei , Rafiq Rumana , Konde Asha , Krastev Dragomir B. , Menon Malini , Campbell James , Gulati Aditi , Kumar Rahul , Pettitt Stephen J. , Gurden Mark D. , Cardenosa Marta Llorca , Chong Irene , Gazinska Patrycja , Wallberg Fredrik , Sawyer Elinor J. , Martin Lesley-Ann , Dowsett Mitch , Linardopoulos Spiros , Natrajan Rachael , Ryan Colm J. , Derksen Patrick W.B. , Jonkers Jos , Tutt Andrew N.J. , Ashworth Alan , Lord Christopher J.
Published: April 2023

Normal cytokinesis in E-cadherin defective cell exposed to vehicle
Figure S6 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S6
Figure S5 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S5
Figure S4 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S4
Figure S1 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S1
Tables S1-S5 from Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer
Authors: Janjigian Yelena Y. , Sanchez-Vega Francisco , Jonsson Philip , Chatila Walid K. , Hechtman Jaclyn F. , Ku Geoffrey Y. , Riches Jamie C. , Tuvy Yaelle , Kundra Ritika , Bouvier Nancy , Vakiani Efsevia , Gao Jianjiong , Heins Zachary J. , Gross Benjamin E. , Kelsen David P. , Zhang Liying , Strong Vivian E. , Schattner Mark , Gerdes Hans , Coit Daniel G. , Bains Manjit , Stadler Zsofia K. , Rusch Valerie W. , Jones David R. , Molena Daniela , Shia Jinru , Robson Mark E. , Capanu Marinela , Middha Sumit , Zehir Ahmet , Hyman David M. , Scaltriti Maurizio , Ladanyi Marc , Rosen Neal , Ilson David H. , Berger Michael F. , Tang Laura , Taylor Barry S. , Solit David B. , Schultz Nikolaus
Published: April 2023

Supplementary Table 1: Comprehensive clinical data and sample IDs. Supplementary Table 2: Summary of baseline patient and sample characteristics. Supplementary Table 3: List of somatic mutations identified in all samples. Supplementary Table 4: Detailed data for assesment of ERBB2 amplification. Supplementary Table 5: Genes included on MSK-IMPACT platform
Figure S4 from Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer
Authors: Janjigian Yelena Y. , Sanchez-Vega Francisco , Jonsson Philip , Chatila Walid K. , Hechtman Jaclyn F. , Ku Geoffrey Y. , Riches Jamie C. , Tuvy Yaelle , Kundra Ritika , Bouvier Nancy , Vakiani Efsevia , Gao Jianjiong , Heins Zachary J. , Gross Benjamin E. , Kelsen David P. , Zhang Liying , Strong Vivian E. , Schattner Mark , Gerdes Hans , Coit Daniel G. , Bains Manjit , Stadler Zsofia K. , Rusch Valerie W. , Jones David R. , Molena Daniela , Shia Jinru , Robson Mark E. , Capanu Marinela , Middha Sumit , Zehir Ahmet , Hyman David M. , Scaltriti Maurizio , Ladanyi Marc , Rosen Neal , Ilson David H. , Berger Michael F. , Tang Laura , Taylor Barry S. , Solit David B. , Schultz Nikolaus
Published: April 2023

CONSORT diagram of sample flow and sequencing success rates.
Figure S3 from Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer
Authors: Janjigian Yelena Y. , Sanchez-Vega Francisco , Jonsson Philip , Chatila Walid K. , Hechtman Jaclyn F. , Ku Geoffrey Y. , Riches Jamie C. , Tuvy Yaelle , Kundra Ritika , Bouvier Nancy , Vakiani Efsevia , Gao Jianjiong , Heins Zachary J. , Gross Benjamin E. , Kelsen David P. , Zhang Liying , Strong Vivian E. , Schattner Mark , Gerdes Hans , Coit Daniel G. , Bains Manjit , Stadler Zsofia K. , Rusch Valerie W. , Jones David R. , Molena Daniela , Shia Jinru , Robson Mark E. , Capanu Marinela , Middha Sumit , Zehir Ahmet , Hyman David M. , Scaltriti Maurizio , Ladanyi Marc , Rosen Neal , Ilson David H. , Berger Michael F. , Tang Laura , Taylor Barry S. , Solit David B. , Schultz Nikolaus
Published: April 2023

Alteration patterns of paired pre- vs post-treatment samples from HER2 positive patients treated with trastuzumab.
Figure S1 from Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer
Authors: Janjigian Yelena Y. , Sanchez-Vega Francisco , Jonsson Philip , Chatila Walid K. , Hechtman Jaclyn F. , Ku Geoffrey Y. , Riches Jamie C. , Tuvy Yaelle , Kundra Ritika , Bouvier Nancy , Vakiani Efsevia , Gao Jianjiong , Heins Zachary J. , Gross Benjamin E. , Kelsen David P. , Zhang Liying , Strong Vivian E. , Schattner Mark , Gerdes Hans , Coit Daniel G. , Bains Manjit , Stadler Zsofia K. , Rusch Valerie W. , Jones David R. , Molena Daniela , Shia Jinru , Robson Mark E. , Capanu Marinela , Middha Sumit , Zehir Ahmet , Hyman David M. , Scaltriti Maurizio , Ladanyi Marc , Rosen Neal , Ilson David H. , Berger Michael F. , Tang Laura , Taylor Barry S. , Solit David B. , Schultz Nikolaus
Published: April 2023

Comparison of mutation frequencies in non-MSI-H tumors in the MSK cohort vs. TCGA and comparison of mutation frequencies in primary vs. metastatic samples in the MSK cohort.
Supplementary Methods from Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition
Authors: Harding James J. , Lowery Maeve A. , Shih Alan H. , Schvartzman Juan M. , Hou Shengqi , Famulare Christopher , Patel Minal , Roshal Mikhail , Do Richard K. , Zehir Ahmet , You Daoqi , Selcuklu S. Duygu , Viale Agnes , Tallman Martin S. , Hyman David M. , Reznik Ed , Finley Lydia W.S. , Papaemmanuil Elli , Tosolini Alessandra , Frattini Mark G. , MacBeth Kyle J. , Liu Guowen , Fan Bin , Choe Sung , Wu Bin , Janjigian Yelena Y. , Mellinghoff Ingo K. , Diaz Luis A. , Levine Ross L. , Abou-Alfa Ghassan K. , Stein Eytan M. , Intlekofer Andrew M.
Published: April 2023

Supplemental Methods. DNA constructs, Gel electrophoresis and western blotting, Metabolite extraction and analysis
Supplementary Table 2 from Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor
Authors: Zhang Xiaoyang , Choi Peter S. , Francis Joshua M. , Gao Galen F. , Campbell Joshua D. , Ramachandran Aruna , Mitsuishi Yoichiro , Ha Gavin , Shih Juliann , Vazquez Francisca , Tsherniak Aviad , Taylor Alison M. , Zhou Jin , Wu Zhong , Berger Ashton C. , Giannakis Marios , Hahn William C. , Cherniack Andrew D. , Meyerson Matthew
Published: April 2023

Table S2: Oligos used in the study
Supplementary Figures from Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor
Authors: Zhang Xiaoyang , Choi Peter S. , Francis Joshua M. , Gao Galen F. , Campbell Joshua D. , Ramachandran Aruna , Mitsuishi Yoichiro , Ha Gavin , Shih Juliann , Vazquez Francisca , Tsherniak Aviad , Taylor Alison M. , Zhou Jin , Wu Zhong , Berger Ashton C. , Giannakis Marios , Hahn William C. , Cherniack Andrew D. , Meyerson Matthew
Published: April 2023

Figure S1. Super-enhancers near the KLF5 gene are focally amplified in cancer cell lines;Figure S2. The regulatory potential of the KLF5/KLF12 intervening region;Figure S3. Expression level of KLF12, DIS3 and PIBF1 after repression of KLF5 superenhancers;Figure S4. Genomic analysis of KLF5 binding sites in BICR31 cells;Figure S5. Target genes of KLF5 in head and neck squamous cell carcinomas;Figure S6. The effect of KLF5 silencing on H3K27ac profile;Figure S7. Mutation hotspots in KLF5;Figure S8. Mutation profile in FBXW7 in colorectal cancers; Figure S9. Ectopic expression of KLF5 mutants in HEK293T cells; Figure S10. Ectopic expression of KLF5 E419Q in HCC95 cells
Figure S2 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Quality controls performed to validate the in vivo screening platform
Figure S17 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Secondary clustering of T cells
Figure S15 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Primary clustering of tumor cells and immune cell populations
Supplementary File Table All (excel) from Lower Airway Dysbiosis Affects Lung Cancer Progression
Authors: Tsay Jun-Chieh J. , Wu Benjamin G. , Sulaiman Imran , Gershner Katherine , Schluger Rosemary , Li Yonghua , Yie Ting-An , Meyn Peter , Olsen Evan , Perez Luisannay , Franca Brendan , Carpenito Joseph , Iizumi Tadasu , El-Ashmawy Mariam , Badri Michelle , Morton James T. , Shen Nan , He Linchen , Michaud Gaetane , Rafeq Samaan , Bessich Jamie L. , Smith Robert L. , Sauthoff Harald , Felner Kevin , Pillai Ray , Zavitsanou Anastasia-Maria , Koralov Sergei B. , Mezzano Valeria , Loomis Cynthia A. , Moreira Andre L. , Moore William , Tsirigos Aristotelis , Heguy Adriana , Rom William N. , Sterman Daniel H. , Pass Harvey I. , Clemente Jose C. , Li Huilin , Bonneau Richard , Wong Kwok-Kin , Papagiannakopoulos Thales , Segal Leopoldo N.
Published: April 2023

Supplementary File Table 1-10
Figure S1 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Library and cells used for in vivo CRISPR screen
Supplementary Table S8 (xlsx) from Circulating Tumor Cells Exhibit Metastatic Tropism and Reveal Brain Metastasis Drivers
Authors: Klotz Remi , Thomas Amal , Teng Teng , Han Sung Min , Iriondo Oihana , Li Lin , Restrepo-Vassalli Sara , Wang Alan , Izadian Negeen , MacKay Matthew , Moon Byoung-San , Liu Kevin J. , Ganesan Sathish Kumar , Lee Grace , Kang Diane S. , Walmsley Charlotte S. , Pinto Christopher , Press Michael F. , Lu Wange , Lu Janice , Juric Dejan , Bardia Aditya , Hicks James , Salhia Bodour , Attenello Frank , Smith Andrew D. , Yu Min
Published: April 2023

List of upregulated genes associated with brain tropism in CTCs
Supplementary Figure S3. from Efficacy and Determinants of Response to HER Kinase Inhibition in HER2-Mutant Metastatic Breast Cancer
Authors: Smyth Lillian M. , Piha-Paul Sarina A. , Won Helen H. , Schram Alison M. , Saura Cristina , Loi Sherene , Lu Janice , Shapiro Geoffrey I. , Juric Dejan , Mayer Ingrid A. , Arteaga Carlos L. , de la Fuente Macarena I. , Brufksy Adam M. , Spanggaard Iben , Mau-Sørensen Morten , Arnedos Monica , Moreno Victor , Boni Valentina , Sohn Joohyuk , Schwartzberg Lee S. , Gonzàlez-Farré Xavier , Cervantes Andrés , Bidard François-Clement , Gorelick Alexander N. , Lanman Richard B. , Nagy Rebecca J. , Ulaner Gary A. , Chandarlapaty Sarat , Jhaveri Komal , Gavrila Elena I. , Zimel Catherine , Selcuklu S. Duygu , Melcer Myra , Samoila Aliaksandra , Cai Yanyan , Scaltriti Maurizio , Mann Grace , Xu Feng , Eli Lisa D. , Dujka Melanie , Lalani Alshad S. , Bryce Richard , Baselga José , Taylor Barry S. , Solit David B. , Meric-Bernstam Funda , Hyman David M.
Published: April 2023

Comprehensive OncoPrint of nine patients with paired pre- and post-treatment tissue sequencing showing acquired alterations in the post-treatment tumor.
Supplementary Data from Regulatory T-cell Depletion Alters the Tumor Microenvironment and Accelerates Pancreatic Carcinogenesis
Authors: Zhang Yaqing , Lazarus Jenny , Steele Nina G. , Yan Wei , Lee Ho-Joon , Nwosu Zeribe C. , Halbrook Christopher J. , Menjivar Rosa E. , Kemp Samantha B. , Sirihorachai Veerin R. , Velez-Delgado Ashley , Donahue Katelyn , Carpenter Eileen S. , Brown Kristee L. , Irizarry-Negron Valerie , Nevison Anna C. , Vinta Alekya , Anderson Michelle A. , Crawford Howard C. , Lyssiotis Costas A. , Frankel Timothy L. , Bednar Filip , Pasca di Magliano Marina
Published: April 2023

Supplemental figure 5 with legend
Table S2 from Loss of EZH2 Reprograms BCAA Metabolism to Drive Leukemic Transformation
Authors: Gu Zhimin , Liu Yuxuan , Cai Feng , Patrick McKenzie , Zmajkovic Jakub , Cao Hui , Zhang Yuannyu , Tasdogan Alpaslan , Chen Mingyi , Qi Le , Liu Xin , Li Kailong , Lyu Junhua , Dickerson Kathryn E. , Chen Weina , Ni Min , Merritt Matthew E. , Morrison Sean J. , Skoda Radek C. , DeBerardinis Ralph J. , Xu Jian
Published: April 2023

Table S2 shows differentially expressed genes by RNA-seq
Table S5 from The Phenotypes of Proliferating Glioblastoma Cells Reside on a Single Axis of Variation
Authors: Wang Lin , Babikir Husam , Müller Sören , Yagnik Garima , Shamardani Karin , Catalan Francisca , Kohanbash Gary , Alvarado Beatriz , Di Lullo Elizabeth , Kriegstein Arnold , Shah Sumedh , Wadhwa Harsh , Chang Susan M. , Phillips Joanna J. , Aghi Manish K. , Diaz Aaron A.
Published: April 2023

Table S5: ScATAC-seq cluster-specific gene-body activities and pair-wise inter-cluster differentially enriched transcription-factor motifs.
Table S4 from The Phenotypes of Proliferating Glioblastoma Cells Reside on a Single Axis of Variation
Authors: Wang Lin , Babikir Husam , Müller Sören , Yagnik Garima , Shamardani Karin , Catalan Francisca , Kohanbash Gary , Alvarado Beatriz , Di Lullo Elizabeth , Kriegstein Arnold , Shah Sumedh , Wadhwa Harsh , Chang Susan M. , Phillips Joanna J. , Aghi Manish K. , Diaz Aaron A.
Published: April 2023

Table S4: Antibodies used for IHC.
Table S2 from The Phenotypes of Proliferating Glioblastoma Cells Reside on a Single Axis of Variation
Authors: Wang Lin , Babikir Husam , Müller Sören , Yagnik Garima , Shamardani Karin , Catalan Francisca , Kohanbash Gary , Alvarado Beatriz , Di Lullo Elizabeth , Kriegstein Arnold , Shah Sumedh , Wadhwa Harsh , Chang Susan M. , Phillips Joanna J. , Aghi Manish K. , Diaz Aaron A.
Published: April 2023

Table S2: Gene-loadings of the neoplastic-cell PCAs for 10x and C1 data.
Supplementary Table S6 from Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML
Authors: Duy Cihangir , Teater Matt , Garrett-Bakelman Francine E. , Lee Tak C. , Meydan Cem , Glass Jacob L. , Li Meng , Hellmuth Johannes C. , Mohammad Helai P. , Smitheman Kimberly N. , Shih Alan H. , Abdel-Wahab Omar , Tallman Martin S. , Guzman Monica L. , Muench David , Grimes H. Leighton , Roboz Gail J. , Kruger Ryan G. , Creasy Caretha L. , Paietta Elisabeth M. , Levine Ross L. , Carroll Martin , Melnick Ari M.
Published: April 2023

GEO data sets