bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S10 from The Folate Cycle Enzyme MTHFR Is a Critical Regulator of Cell Response to MYC-Targeting Therapies
Authors: Su Angela , Ling Frank , Vaganay Camille , Sodaro Gaetano , Benaksas Chaïma , Dal Bello Reinaldo , Forget Antoine , Pardieu Bryann , Lin Kevin H. , Rutter Justine C. , Bassil Christopher F. , Fortin Gael , Pasanisi Justine , Antony-Debré Iléana , Alexe Gabriela , Benoist Jean-François , Pruvost Alain , Pikman Yana , Qi Jun , Schlageter Marie-Hélène , Micol Jean-Baptiste , Roti Giovanni , Cluzeau Thomas , Dombret Hervé , Preudhomme Claude , Fenouille Nina , Benajiba Lina , Golan Hava M. , Stegmaier Kimberly , Lobry Camille , Wood Kris C. , Itzykson Raphael , Puissant Alexandre
Published: April 2023

Metabolic perturbations induced by folate starvation in AML cells.
Figure S1 from The Folate Cycle Enzyme MTHFR Is a Critical Regulator of Cell Response to MYC-Targeting Therapies
Authors: Su Angela , Ling Frank , Vaganay Camille , Sodaro Gaetano , Benaksas Chaïma , Dal Bello Reinaldo , Forget Antoine , Pardieu Bryann , Lin Kevin H. , Rutter Justine C. , Bassil Christopher F. , Fortin Gael , Pasanisi Justine , Antony-Debré Iléana , Alexe Gabriela , Benoist Jean-François , Pruvost Alain , Pikman Yana , Qi Jun , Schlageter Marie-Hélène , Micol Jean-Baptiste , Roti Giovanni , Cluzeau Thomas , Dombret Hervé , Preudhomme Claude , Fenouille Nina , Benajiba Lina , Golan Hava M. , Stegmaier Kimberly , Lobry Camille , Wood Kris C. , Itzykson Raphael , Puissant Alexandre
Published: April 2023

CDK7 inhibitor, THZ-1, decreases MYC expression in AML cells.
Supplementary Data from Selective Alanine Transporter Utilization Creates a Targetable Metabolic Niche in Pancreatic Cancer
Authors: Parker Seth J. , Amendola Caroline R. , Hollinshead Kate E.R. , Yu Qijia , Yamamoto Keisuke , Encarnación-Rosado Joel , Rose Rebecca E. , LaRue Madeleine M. , Sohn Albert S.W. , Biancur Doug E. , Paulo Joao A. , Gygi Steven P. , Jones Drew R. , Wang Huamin , Philips Mark R. , Bar-Sagi Dafna , Mancias Joseph D. , Kimmelman Alec C.
Published: April 2023

contains supplementary methods, figures, legends, and table
Supplementary Table S4 (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 differentially expressed genes in brain stromal cells after tumor formation
Supplementary Data from Tumor Microenvironment Is Critical for the Maintenance of Cellular States Found in Primary Glioblastomas
Authors: Pine Allison R. , Cirigliano Stefano M. , Nicholson James G. , Hu Yang , Linkous Amanda , Miyaguchi Ken , Edwards Lincoln , Singhania Richa , Schwartz Theodore H. , Ramakrishna Rohan , Pisapia David J. , Snuderl Matija , Elemento Olivier , Fine Howard A.
Published: April 2023

Supplementary figures and tables with Figure legends.
Supplemental Table 5 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Authors: Wander Seth A. , Cohen Ofir , Gong Xueqian , Johnson Gabriela N. , Buendia-Buendia Jorge E. , Lloyd Maxwell R. , Kim Dewey , Luo Flora , Mao Pingping , Helvie Karla , Kowalski Kailey J. , Nayar Utthara , Waks Adrienne G. , Parsons Stephen H. , Martinez Ricardo , Litchfield Lacey M. , Ye Xiang S. , Yu Chunping , Jansen Valerie M. , Stille John R. , Smith Patricia S. , Oakley Gerard J. , Chu Quincy S. , Batist Gerald , Hughes Melissa E. , Kremer Jill D. , Garraway Levi A. , Winer Eric P. , Tolaney Sara M. , Lin Nancy U. , Buchanan Sean G. , Wagle Nikhil
Published: April 2023

Supplemental Table 5
Supplemental Table 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Authors: Wander Seth A. , Cohen Ofir , Gong Xueqian , Johnson Gabriela N. , Buendia-Buendia Jorge E. , Lloyd Maxwell R. , Kim Dewey , Luo Flora , Mao Pingping , Helvie Karla , Kowalski Kailey J. , Nayar Utthara , Waks Adrienne G. , Parsons Stephen H. , Martinez Ricardo , Litchfield Lacey M. , Ye Xiang S. , Yu Chunping , Jansen Valerie M. , Stille John R. , Smith Patricia S. , Oakley Gerard J. , Chu Quincy S. , Batist Gerald , Hughes Melissa E. , Kremer Jill D. , Garraway Levi A. , Winer Eric P. , Tolaney Sara M. , Lin Nancy U. , Buchanan Sean G. , Wagle Nikhil
Published: April 2023

Supplemental Table 3
Supplementary Table S2 from Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis
Authors: Kato Shinichiro , Weng Qing Yu , Insco Megan L. , Chen Kevin Y. , Muralidhar Sathya , Pozniak Joanna , Diaz Joey Mark S. , Drier Yotam , Nguyen Nhu , Lo Jennifer A. , van Rooijen Ellen , Kemeny Lajos V. , Zhan Yao , Feng Yang , Silkworth Whitney , Powell C. Thomas , Liau Brian B. , Xiong Yan , Jin Jian , Newton-Bishop Julia , Zon Leonard I. , Bernstein Bradley E. , Fisher David E.
Published: April 2023

IC50 values of G9a inhibitors (UNC0638 and BIX01294) in melanoma cell lines carrying different G9a copy number and H3K9me2 status
Supplementary Table S1 from Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis
Authors: Kato Shinichiro , Weng Qing Yu , Insco Megan L. , Chen Kevin Y. , Muralidhar Sathya , Pozniak Joanna , Diaz Joey Mark S. , Drier Yotam , Nguyen Nhu , Lo Jennifer A. , van Rooijen Ellen , Kemeny Lajos V. , Zhan Yao , Feng Yang , Silkworth Whitney , Powell C. Thomas , Liau Brian B. , Xiong Yan , Jin Jian , Newton-Bishop Julia , Zon Leonard I. , Bernstein Bradley E. , Fisher David E.
Published: April 2023

Whole exome sequence datasets used to discover G9a recurrent mutations
Supplementary Figure S1-S10 from Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis
Authors: Kato Shinichiro , Weng Qing Yu , Insco Megan L. , Chen Kevin Y. , Muralidhar Sathya , Pozniak Joanna , Diaz Joey Mark S. , Drier Yotam , Nguyen Nhu , Lo Jennifer A. , van Rooijen Ellen , Kemeny Lajos V. , Zhan Yao , Feng Yang , Silkworth Whitney , Powell C. Thomas , Liau Brian B. , Xiong Yan , Jin Jian , Newton-Bishop Julia , Zon Leonard I. , Bernstein Bradley E. , Fisher David E.
Published: April 2023

Supplementary figures and legends
Figure S5 from Triplet Therapy with Palbociclib, Taselisib, and Fulvestrant in PIK3CA-Mutant Breast Cancer and Doublet Palbociclib and Taselisib in Pathway-Mutant Solid Cancers
Authors: Pascual Javier , Lim Joline S.J. , Macpherson Iain R. , Armstrong Anne C. , Ring Alistair , Okines Alicia F.C. , Cutts Rosalind J. , Herrera-Abreu Maria Teresa , Garcia-Murillas Isaac , Pearson Alex , Hrebien Sarah , Gevensleben Heidrun , Proszek Paula Z. , Hubank Michael , Hills Margaret , King Jenny , Parmar Mona , Prout Toby , Finneran Laura , Malia Jason , Swales Karen E. , Ruddle Ruth , Raynaud Florence I. , Turner Alison , Hall Emma , Yap Timothy A. , Lopez Juanita S. , Turner Nicholas C.
Published: April 2023

Circulating tumor DNA dynamics as a surrogate of efficacy
Figure S4 from Triplet Therapy with Palbociclib, Taselisib, and Fulvestrant in PIK3CA-Mutant Breast Cancer and Doublet Palbociclib and Taselisib in Pathway-Mutant Solid Cancers
Authors: Pascual Javier , Lim Joline S.J. , Macpherson Iain R. , Armstrong Anne C. , Ring Alistair , Okines Alicia F.C. , Cutts Rosalind J. , Herrera-Abreu Maria Teresa , Garcia-Murillas Isaac , Pearson Alex , Hrebien Sarah , Gevensleben Heidrun , Proszek Paula Z. , Hubank Michael , Hills Margaret , King Jenny , Parmar Mona , Prout Toby , Finneran Laura , Malia Jason , Swales Karen E. , Ruddle Ruth , Raynaud Florence I. , Turner Alison , Hall Emma , Yap Timothy A. , Lopez Juanita S. , Turner Nicholas C.
Published: April 2023

Baseline tissue biomarker analysis
Supplementary Figures from Golgi Acidification by NHE7 Regulates Cytosolic pH Homeostasis in Pancreatic Cancer Cells
Authors: Galenkamp Koen M.O. , Sosicka Paulina , Jung Michael , Recouvreux M. Victoria , Zhang Yijuan , Moldenhauer Matthew R. , Brandi Giovanni , Freeze Hudson H. , Commisso Cosimo
Published: April 2023

Supplementary Figures
Figure S2 from Triplet Therapy with Palbociclib, Taselisib, and Fulvestrant in PIK3CA-Mutant Breast Cancer and Doublet Palbociclib and Taselisib in Pathway-Mutant Solid Cancers
Authors: Pascual Javier , Lim Joline S.J. , Macpherson Iain R. , Armstrong Anne C. , Ring Alistair , Okines Alicia F.C. , Cutts Rosalind J. , Herrera-Abreu Maria Teresa , Garcia-Murillas Isaac , Pearson Alex , Hrebien Sarah , Gevensleben Heidrun , Proszek Paula Z. , Hubank Michael , Hills Margaret , King Jenny , Parmar Mona , Prout Toby , Finneran Laura , Malia Jason , Swales Karen E. , Ruddle Ruth , Raynaud Florence I. , Turner Alison , Hall Emma , Yap Timothy A. , Lopez Juanita S. , Turner Nicholas C.
Published: April 2023

Pharmacokinetics
Supplementary Methods from Poly(ADP-ribose) Glycohydrolase Inhibition Sequesters NAD+ to Potentiate the Metabolic Lethality of Alkylating Chemotherapy in IDH-Mutant Tumor Cells
Authors: Nagashima Hiroaki , Lee Christine K. , Tateishi Kensuke , Higuchi Fumi , Subramanian Megha , Rafferty Seamus , Melamed Lisa , Miller Julie J. , Wakimoto Hiroaki , Cahill Daniel P.
Published: April 2023

shRNA and Control shRNA Cell Lines, Molecular Analyses, 2-HG Quantitation, Western blot analysis, Immunohistochemistry, TUNEL assay, In Vivo Studies
Figure S3 from Interferon Signaling Is Diminished with Age and Is Associated with Immune Checkpoint Blockade Efficacy in Triple-Negative Breast Cancer
Authors: Sceneay Jaclyn , Goreczny Gregory J. , Wilson Kristin , Morrow Sara , DeCristo Molly J. , Ubellacker Jessalyn M. , Qin Yuanbo , Laszewski Tyler , Stover Daniel G. , Barrera Victor , Hutchinson John N. , Freedman Rachel A. , Mittendorf Elizabeth A. , McAllister Sandra S.
Published: April 2023

Supplementary Figure 3 shows the gating strategy and absolute numbers of CD8 cell subsets in the blood, spleen, and tumor to generate the heatmaps in figure 3
Supplementary Table S1-S6 from The TP53 Apoptotic Network Is a Primary Mediator of Resistance to BCL2 Inhibition in AML Cells
Authors: Nechiporuk Tamilla , Kurtz Stephen E. , Nikolova Olga , Liu Tingting , Jones Courtney L. , D'Alessandro Angelo , Culp-Hill Rachel , d'Almeida Amanda , Joshi Sunil K. , Rosenberg Mara , Tognon Cristina E. , Danilov Alexey V. , Druker Brian J. , Chang Bill H. , McWeeney Shannon K , Tyner Jeffrey W.
Published: April 2023

Supplementary Data Tables
Table S8 from Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin
Authors: Espinet Elisa , Gu Zuguang , Imbusch Charles D. , Giese Nathalia A. , Büscher Magdalena , Safavi Mariam , Weisenburger Silke , Klein Corinna , Vogel Vanessa , Falcone Mattia , Insua-Rodríguez Jacob , Reitberger Manuel , Thiel Vera , Kossi Steffi O. , Muckenhuber Alexander , Sarai Karnjit , Lee Alex Y.L. , Backx Elyne , Zarei Soheila , Gaida Matthias M. , Rodríguez-Paredes Manuel , Donato Elisa , Yen Hsi-Yu , Eils Roland , Schlesner Matthias , Pfarr Nicole , Hackert Thilo , Plass Christoph , Brors Benedikt , Steiger Katja , Weichenhan Dieter , Arda H. Efsun , Rooman Ilse , Kopp Janel L. , Strobel Oliver , Weichert Wilko , Sprick Martin R. , Trumpp Andreas
Published: April 2023

Genesets used in the study
Supplementary Methods Figure from Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin
Authors: Espinet Elisa , Gu Zuguang , Imbusch Charles D. , Giese Nathalia A. , Büscher Magdalena , Safavi Mariam , Weisenburger Silke , Klein Corinna , Vogel Vanessa , Falcone Mattia , Insua-Rodríguez Jacob , Reitberger Manuel , Thiel Vera , Kossi Steffi O. , Muckenhuber Alexander , Sarai Karnjit , Lee Alex Y.L. , Backx Elyne , Zarei Soheila , Gaida Matthias M. , Rodríguez-Paredes Manuel , Donato Elisa , Yen Hsi-Yu , Eils Roland , Schlesner Matthias , Pfarr Nicole , Hackert Thilo , Plass Christoph , Brors Benedikt , Steiger Katja , Weichenhan Dieter , Arda H. Efsun , Rooman Ilse , Kopp Janel L. , Strobel Oliver , Weichert Wilko , Sprick Martin R. , Trumpp Andreas
Published: April 2023

Supplementary Methods Figure 1
Extended Data from Aggressive PDACs Show Hypomethylation of Repetitive Elements and the Execution of an Intrinsic IFN Program Linked to a Ductal Cell of Origin
Authors: Espinet Elisa , Gu Zuguang , Imbusch Charles D. , Giese Nathalia A. , Büscher Magdalena , Safavi Mariam , Weisenburger Silke , Klein Corinna , Vogel Vanessa , Falcone Mattia , Insua-Rodríguez Jacob , Reitberger Manuel , Thiel Vera , Kossi Steffi O. , Muckenhuber Alexander , Sarai Karnjit , Lee Alex Y.L. , Backx Elyne , Zarei Soheila , Gaida Matthias M. , Rodríguez-Paredes Manuel , Donato Elisa , Yen Hsi-Yu , Eils Roland , Schlesner Matthias , Pfarr Nicole , Hackert Thilo , Plass Christoph , Brors Benedikt , Steiger Katja , Weichenhan Dieter , Arda H. Efsun , Rooman Ilse , Kopp Janel L. , Strobel Oliver , Weichert Wilko , Sprick Martin R. , Trumpp Andreas
Published: April 2023

Extended Data Figures 1-3
Supplementary Table S1 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

Mutational frequency in patient-derived AML specimens
Supplementary Video4 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes
Authors: Miyabayashi Koji , Baker Lindsey A. , Deschênes Astrid , Traub Benno , Caligiuri Giuseppina , Plenker Dennis , Alagesan Brinda , Belleau Pascal , Li Siran , Kendall Jude , Jang Gun Ho , Kawaguchi Risa Karakida , Somerville Tim D.D. , Tiriac Hervé , Hwang Chang-Il , Burkhart Richard A. , Roberts Nicholas J. , Wood Laura D. , Hruban Ralph H. , Gillis Jesse , Krasnitz Alexander , Vakoc Christopher R. , Wigler Michael , Notta Faiyaz , Gallinger Steven , Park Youngkyu , Tuveson David A.
Published: April 2023

Confocal z-stack imaging of immunofluorescent (IF) images of mStrawberry-hM1A grafts 4 weeks after IGO transplantation
Figure S6 from Oncogenic KRAS Induces NIX-Mediated Mitophagy to Promote Pancreatic Cancer
Authors: Humpton Timothy J. , Alagesan Brinda , DeNicola Gina M. , Lu Dan , Yordanov Georgi N. , Leonhardt Carl S. , Yao Melissa A. , Alagesan Priya , Zaatari Maya N. , Park Youngkyu , Skepper Jeremy N. , Macleod Kay F. , Perez-Mancera Pedro A. , Murphy Michael P. , Evan Gerard I. , Vousden Karen H. , Tuveson David A.
Published: April 2023

Supp figure 6
Supplementary Video3 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes
Authors: Miyabayashi Koji , Baker Lindsey A. , Deschênes Astrid , Traub Benno , Caligiuri Giuseppina , Plenker Dennis , Alagesan Brinda , Belleau Pascal , Li Siran , Kendall Jude , Jang Gun Ho , Kawaguchi Risa Karakida , Somerville Tim D.D. , Tiriac Hervé , Hwang Chang-Il , Burkhart Richard A. , Roberts Nicholas J. , Wood Laura D. , Hruban Ralph H. , Gillis Jesse , Krasnitz Alexander , Vakoc Christopher R. , Wigler Michael , Notta Faiyaz , Gallinger Steven , Park Youngkyu , Tuveson David A.
Published: April 2023

Confocal z-stack imaging of immunofluorescent (IF) images of mStrawberry-hT3 grafts 4 weeks after IGO transplantation
Supplementary Table S4 from Extracellular ATP and CD39 Activate cAMP-Mediated Mitochondrial Stress Response to Promote Cytarabine Resistance in Acute Myeloid Leukemia
Authors: Aroua Nesrine , Boet Emeline , Ghisi Margherita , Nicolau-Travers Marie-Laure , Saland Estelle , Gwilliam Ryan , de Toni Fabienne , Hosseini Mohsen , Mouchel Pierre-Luc , Farge Thomas , Bosc Claudie , Stuani Lucille , Sabatier Marie , Mazed Fetta , Larrue Clément , Jarrou Latifa , Gandarillas Sarah , Bardotti Massimiliano , Picard Muriel , Syrykh Charlotte , Laurent Camille , Gotanègre Mathilde , Bonnefoy Nathalie , Bellvert Floriant , Portais Jean-Charles , Nicot Nathalie , Azuaje Francisco , Kaoma Tony , Joffre Carine , Tamburini Jérome , Récher Christian , Vergez François , Sarry Jean-Emmanuel
Published: April 2023

Table S4
Supplementary Table 3 from Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance
Authors: Pettitt Stephen J. , Frankum Jessica R. , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Yap Timothy A. , Haider Syed , Tutt Andrew N.J. , Lord Christopher J.
Published: April 2023

Cases not explained by reversion
Supplementary Table 2 from Clinical BRCA1/2 Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance
Authors: Pettitt Stephen J. , Frankum Jessica R. , Punta Marco , Lise Stefano , Alexander John , Chen Yi , Yap Timothy A. , Haider Syed , Tutt Andrew N.J. , Lord Christopher J.
Published: April 2023

Full list of reversions
Supplementary Table 3 from Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade
Authors: Gstalder Cécile , Liu David , Miao Diana , Lutterbach Bart , DeVine Alexander L. , Lin Chenyu , Shettigar Megha , Pancholi Priya , Buchbinder Elizabeth I. , Carter Scott L. , Manos Michael P. , Rojas-Rudilla Vanesa , Brennick Ryan , Gjini Evisa , Chen Pei-Hsuan , Lako Ana , Rodig Scott , Yoon Charles H. , Freeman Gordon J. , Barbie David A. , Hodi F. Stephen , Miles Wayne , Van Allen Eliezer M. , Haq Rizwan
Published: April 2023

Comparison of mRNA expression of immune-related genes in tumors derived from control and Fbxw7-deficient tumors
Supplementary Figures and Legends from Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade
Authors: Gstalder Cécile , Liu David , Miao Diana , Lutterbach Bart , DeVine Alexander L. , Lin Chenyu , Shettigar Megha , Pancholi Priya , Buchbinder Elizabeth I. , Carter Scott L. , Manos Michael P. , Rojas-Rudilla Vanesa , Brennick Ryan , Gjini Evisa , Chen Pei-Hsuan , Lako Ana , Rodig Scott , Yoon Charles H. , Freeman Gordon J. , Barbie David A. , Hodi F. Stephen , Miles Wayne , Van Allen Eliezer M. , Haq Rizwan
Published: April 2023

Supplementary Figures 1-10, Supplementary Legends 1-10, Supplementary Legends to Tables 1-7
Supplementary Data from Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site
Authors: Fowler Joanna C. , King Charlotte , Bryant Christopher , Hall Michael W.J. , Sood Roshan , Ong Swee Hoe , Earp Eleanor , Fernandez-Antoran David , Koeppel Jonas , Dentro Stefan C. , Shorthouse David , Durrani Amer , Fife Kate , Rytina Edward , Milne Doreen , Roshan Amit , Mahububani Krishnaa , Saeb-Parsy Kourosh , Hall Benjamin A. , Gerstung Moritz , Jones Philip H.
Published: April 2023

Supplementary Tables S3 to S8
Supplementary Data from Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site
Authors: Fowler Joanna C. , King Charlotte , Bryant Christopher , Hall Michael W.J. , Sood Roshan , Ong Swee Hoe , Earp Eleanor , Fernandez-Antoran David , Koeppel Jonas , Dentro Stefan C. , Shorthouse David , Durrani Amer , Fife Kate , Rytina Edward , Milne Doreen , Roshan Amit , Mahububani Krishnaa , Saeb-Parsy Kourosh , Hall Benjamin A. , Gerstung Moritz , Jones Philip H.
Published: April 2023

Supplementary Figures S1-S7 and Tables S1 and S2
Supplemental Table 3 from Netrin G1 Promotes Pancreatic Tumorigenesis through Cancer-Associated Fibroblast–Driven Nutritional Support and Immunosuppression
Authors: Francescone Ralph , Barbosa Vendramini-Costa Débora , Franco-Barraza Janusz , Wagner Jessica , Muir Alexander , Lau Allison N. , Gabitova Linara , Pazina Tatiana , Gupta Sapna , Luong Tiffany , Rollins Dustin , Malik Ruchi , Thapa Roshan J. , Restifo Diana , Zhou Yan , Cai Kathy Q. , Hensley Harvey H. , Tan Yinfei , Kruger Warren D. , Devarajan Karthik , Balachandran Siddharth , Klein-Szanto Andres J. , Wang Huamin , El-Deiry Wafik S. , Vander Heiden Matthew G. , Peri Suraj , Campbell Kerry S. , Astsaturov Igor , Cukierman Edna
Published: April 2023

TMA IHC Scores
Supplemental Table 1 from Netrin G1 Promotes Pancreatic Tumorigenesis through Cancer-Associated Fibroblast–Driven Nutritional Support and Immunosuppression
Authors: Francescone Ralph , Barbosa Vendramini-Costa Débora , Franco-Barraza Janusz , Wagner Jessica , Muir Alexander , Lau Allison N. , Gabitova Linara , Pazina Tatiana , Gupta Sapna , Luong Tiffany , Rollins Dustin , Malik Ruchi , Thapa Roshan J. , Restifo Diana , Zhou Yan , Cai Kathy Q. , Hensley Harvey H. , Tan Yinfei , Kruger Warren D. , Devarajan Karthik , Balachandran Siddharth , Klein-Szanto Andres J. , Wang Huamin , El-Deiry Wafik S. , Vander Heiden Matthew G. , Peri Suraj , Campbell Kerry S. , Astsaturov Igor , Cukierman Edna
Published: April 2023

Microarray
Supplementary Data from First-in-Human Trial of the Oral Ataxia Telangiectasia and RAD3-Related (ATR) Inhibitor BAY 1895344 in Patients with Advanced Solid Tumors
Authors: Yap Timothy A. , Tan David S.P. , Terbuch Angelika , Caldwell Reece , Guo Christina , Goh Boon Cher , Heong Valerie , Haris Noor R. Md. , Bashir Saira , Drew Yvette , Hong David S. , Meric-Bernstam Funda , Wilkinson Gary , Hreiki Joseph , Wengner Antje M. , Bladt Friedhelm , Schlicker Andreas , Ludwig Matthias , Zhou Yinghui , Liu Li , Bordia Sonal , Plummer Ruth , Lagkadinou Eleni , de Bono Johann S.
Published: April 2023

Supplementary Data
Supplementary Data from Infiltrating Myeloid Cells Drive Osteosarcoma Progression via GRM4 Regulation of IL23
Authors: Kansara Maya , Thomson Kristian , Pang Puiyi , Dutour Aurelie , Mirabello Lisa , Acher Francine , Pin Jean-Philippe , Demicco Elizabeth G. , Yan Juming , Teng Michele W.L. , Smyth Mark J. , Thomas David M.
Published: April 2023

Figures S1-S16 Tables S1 to S2
Figure S5 from Antitumor T-cell Homeostatic Activation Is Uncoupled from Homeostatic Inhibition by Checkpoint Blockade
Authors: Marshall Netonia , Hutchinson Keino , Marron Thomas U. , Aleynick Mark , Hammerich Linda , Upadhyay Ranjan , Svensson-Arvelund Judit , Brown Brian D. , Merad Miriam , Brody Joshua D.
Published: April 2023

Homeostatic activation and inhibition require JAK3-signaling
Figure S4 from Antitumor T-cell Homeostatic Activation Is Uncoupled from Homeostatic Inhibition by Checkpoint Blockade
Authors: Marshall Netonia , Hutchinson Keino , Marron Thomas U. , Aleynick Mark , Hammerich Linda , Upadhyay Ranjan , Svensson-Arvelund Judit , Brown Brian D. , Merad Miriam , Brody Joshua D.
Published: April 2023

Immunotransplant modulates serum cytokines levels
Supplementary Methods from First-in-Human RNA Polymerase I Transcription Inhibitor CX-5461 in Patients with Advanced Hematologic Cancers: Results of a Phase I Dose-Escalation Study
Authors: Khot Amit , Brajanovski Natalie , Cameron Donald P. , Hein Nadine , Maclachlan Kylee H. , Sanij Elaine , Lim John , Soong John , Link Emma , Blombery Piers , Thompson Ella R. , Fellowes Andrew , Sheppard Karen E. , McArthur Grant A. , Pearson Richard B. , Hannan Ross D. , Poortinga Gretchen , Harrison Simon J.
Published: April 2023

All Supplementary Methods and associated references
Supplementary Table 1 from The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells
Authors: Dixit Deobrat , Prager Briana C. , Gimple Ryan C. , Poh Hui Xian , Wang Yang , Wu Qiulian , Qiu Zhixin , Kidwell Reilly L. , Kim Leo J.Y. , Xie Qi , Vitting-Seerup Kristoffer , Bhargava Shruti , Dong Zhen , Jiang Li , Zhu Zhe , Hamerlik Petra , Jaffrey Samie R. , Zhao Jing Crystal , Wang Xiuxing , Rich Jeremy N.
Published: April 2023

Supplementary Table
Supplementary Data from The RNA m6A Reader YTHDF2 Maintains Oncogene Expression and Is a Targetable Dependency in Glioblastoma Stem Cells
Authors: Dixit Deobrat , Prager Briana C. , Gimple Ryan C. , Poh Hui Xian , Wang Yang , Wu Qiulian , Qiu Zhixin , Kidwell Reilly L. , Kim Leo J.Y. , Xie Qi , Vitting-Seerup Kristoffer , Bhargava Shruti , Dong Zhen , Jiang Li , Zhu Zhe , Hamerlik Petra , Jaffrey Samie R. , Zhao Jing Crystal , Wang Xiuxing , Rich Jeremy N.
Published: April 2023

Supplementary figures and legends
Supplementary Data from Targeting CD39 in Cancer Reveals an Extracellular ATP- and Inflammasome-Driven Tumor Immunity
Authors: Li Xian-Yang , Moesta Achim K. , Xiao Christos , Nakamura Kyohei , Casey Mika , Zhang Haiyan , Madore Jason , Lepletier Ailin , Aguilera Amelia Roman , Sundarrajan Ashmitha , Jacoberger-Foissac Celia , Wong Clifford , dela Cruz Tracy , Welch Megan , Lerner Alana G. , Spatola Bradley N. , Soros Vanessa B. , Corbin John , Anderson Ana C. , Effern Maike , Hölzel Michael , Robson Simon C. , Johnston Rebecca L. , Waddell Nicola , Smith Corey , Bald Tobias , Geetha Nishamol , Beers Courtney , Teng Michele W. L. , Smyth Mark J.
Published: April 2023

Supplementary Methods, Figures, Legends and Tables
Table S2 from Phenotypic Mapping of Pathologic Cross-Talk between Glioblastoma and Innate Immune Cells by Synthetic Genetic Tracing
Authors: Schmitt Matthias Jürgen , Company Carlos , Dramaretska Yuliia , Barozzi Iros , Göhrig Andreas , Kertalli Sonia , Großmann Melanie , Naumann Heike , Sanchez-Bailon Maria Pilar , Hulsman Danielle , Glass Rainer , Squatrito Massimo , Serresi Michela , Gargiulo Gaetano
Published: April 2023

Supplementary Table S2. Phenotypic CRISPR-screen data analysis
Supplementary Table S6 from Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas
Authors: Zheng Tuyu , Ghasemi David R. , Okonechnikov Konstantin , Korshunov Andrey , Sill Martin , Maass Kendra K. , Benites Goncalves da Silva Patricia , Ryzhova Marina , Gojo Johannes , Stichel Damian , Arabzade Amir , Kupp Robert , Benzel Julia , Taya Shinichiro , Adachi Toma , Shiraishi Ryo , Gerber Nicolas U. , Sturm Dominik , Ecker Jonas , Sievers Philipp , Selt Florian , Chapman Rebecca , Haberler Christine , Figarella-Branger Dominique , Reifenberger Guido , Fleischhack Gudrun , Rutkowski Stefan , Donson Andrew M. , Ramaswamy Vijay , Capper David , Ellison David W. , Herold-Mende Christel C. , Schüller Ulrich , Brandner Sebastian , Driever Pablo Hernáiz , Kros Johan M. , Snuderl Matija , Milde Till , Grundy Richard G. , Hoshino Mikio , Mack Stephen C. , Gilbertson Richard J. , Jones David T.W. , Kool Marcel , von Deimling Andreas , Pfister Stefan M. , Sahm Felix , Kawauchi Daisuke , Pajtler Kristian W.
Published: April 2023

Suppl. Table S6 - Primer list
Supplementary Table S5 from Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas
Authors: Zheng Tuyu , Ghasemi David R. , Okonechnikov Konstantin , Korshunov Andrey , Sill Martin , Maass Kendra K. , Benites Goncalves da Silva Patricia , Ryzhova Marina , Gojo Johannes , Stichel Damian , Arabzade Amir , Kupp Robert , Benzel Julia , Taya Shinichiro , Adachi Toma , Shiraishi Ryo , Gerber Nicolas U. , Sturm Dominik , Ecker Jonas , Sievers Philipp , Selt Florian , Chapman Rebecca , Haberler Christine , Figarella-Branger Dominique , Reifenberger Guido , Fleischhack Gudrun , Rutkowski Stefan , Donson Andrew M. , Ramaswamy Vijay , Capper David , Ellison David W. , Herold-Mende Christel C. , Schüller Ulrich , Brandner Sebastian , Driever Pablo Hernáiz , Kros Johan M. , Snuderl Matija , Milde Till , Grundy Richard G. , Hoshino Mikio , Mack Stephen C. , Gilbertson Richard J. , Jones David T.W. , Kool Marcel , von Deimling Andreas , Pfister Stefan M. , Sahm Felix , Kawauchi Daisuke , Pajtler Kristian W.
Published: April 2023

Suppl. Table S5 - GO analysis for C11orf95-target models specific DEGs
Supplementary Table S2 from Cross-Species Genomics Reveals Oncogenic Dependencies in ZFTA/C11orf95 Fusion–Positive Supratentorial Ependymomas
Authors: Zheng Tuyu , Ghasemi David R. , Okonechnikov Konstantin , Korshunov Andrey , Sill Martin , Maass Kendra K. , Benites Goncalves da Silva Patricia , Ryzhova Marina , Gojo Johannes , Stichel Damian , Arabzade Amir , Kupp Robert , Benzel Julia , Taya Shinichiro , Adachi Toma , Shiraishi Ryo , Gerber Nicolas U. , Sturm Dominik , Ecker Jonas , Sievers Philipp , Selt Florian , Chapman Rebecca , Haberler Christine , Figarella-Branger Dominique , Reifenberger Guido , Fleischhack Gudrun , Rutkowski Stefan , Donson Andrew M. , Ramaswamy Vijay , Capper David , Ellison David W. , Herold-Mende Christel C. , Schüller Ulrich , Brandner Sebastian , Driever Pablo Hernáiz , Kros Johan M. , Snuderl Matija , Milde Till , Grundy Richard G. , Hoshino Mikio , Mack Stephen C. , Gilbertson Richard J. , Jones David T.W. , Kool Marcel , von Deimling Andreas , Pfister Stefan M. , Sahm Felix , Kawauchi Daisuke , Pajtler Kristian W.
Published: April 2023

Suppl. Table S2 - Copy number alterations for all 613 tumors
Supplementary Table S3 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

HER2 counting at a single cell level
Supplementary Table S1 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

List of all AEs
Supplementary Fig. S4 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

Relationship between ERBB2 copy number and pCR. A, Median HER2/CEP17 ratio for the overall population acording to pCR results. P-value is from a Wilcoxon test. B, Median HER2/CEP17 ratio for the hormone receptor-positive and hormone receptor-negative subsets according to pCR results. P-value is from a Wilcoxon test. C, Median HER2/CEP17 ratio for each of the six core biopsy areas from each tumor and association with pCR. A-C, Red represents patients without pCR, and blue represents patients with pCR.
Supplementary Fig. S2 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

Assessment of HER2 copy number dispersion. A, The Gini coefficient measuring the dispersion of HER2/CEP17 ratio in each patient. P-value is from a Kolmogorov-Smirnov test. B, Association between the Gini coefficient and Shan-non equitability index in each patient. R and p-value are from a Pearson correlation test of association. C, Association between the Gini coefficient and percent of HER2 non-amplified cells in each patient. R and p-value are from a Pearson correlation test of association. A-C, Red represents patients without pCR and blue represents patients with pCR.
Supplementary Fig. S1 from Impact of HER2 Heterogeneity on Treatment Response of Early-Stage HER2-Positive Breast Cancer: Phase II Neoadjuvant Clinical Trial of T-DM1 Combined with Pertuzumab
Authors: Filho Otto Metzger , Viale Giuseppe , Stein Shayna , Trippa Lorenzo , Yardley Denise A. , Mayer Ingrid A. , Abramson Vandana G. , Arteaga Carlos L. , Spring Laura M. , Waks Adrienne G. , Wrabel Eileen , DeMeo Michelle K. , Bardia Aditya , Dell'Orto Patrizia , Russo Leila , King Tari A. , Polyak Kornelia , Michor Franziska , Winer Eric P. , Krop Ian E.
Published: April 2023

Pattern of HER2 amplification in the subset of HER2 heterogeneous tumors. Heatmap generated using data from central pathology evaluation of HER2 heterogeneity. The graphic includes patients classified as HER2 heterogeneous depicted in each row. The color code to the right of the heatmap refers to the percentage of HER2 amplified cells per core biopsy tumor area. Core biopsy tumor areas, A, B and C were obtained from core biopsy site 1 and D, E and F from core biopsy site 2.
Supplementary Table 3 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

List of Primers for qRT-PCR
Figure S9 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Effects of MEK inhibition on chromatin accessibility and thyroid differentiated gene expression in Braf-mutant cancers with homozygous loss of Swi/Snf subunit genes.
Supplementary Figure from Surface Proteomics Reveals CD72 as a Target for In Vitro–Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL
Authors: Nix Matthew A. , Mandal Kamal , Geng Huimin , Paranjape Neha , Lin Yu-Hsiu T. , Rivera Jose M. , Marcoulis Makeba , White Kristie L. , Whitman Jeffrey D. , Bapat Sagar P. , Parker Kevin R. , Ramirez Jonathan , Deucher Anne , Phojanokong Paul , Steri Veronica , Fattahi Faranak , Hann Byron C. , Satpathy Ansuman T. , Manglik Aashish , Stieglitz Elliot , Wiita Arun P.
Published: April 2023

Supplementary Figure from Surface Proteomics Reveals CD72 as a Target for In Vitro–Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL
Figure S11 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Smarcb1 loss is associated with active enhancer/promoter marks at CTCF motif.
Figure S10 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

Loss of Arid1a or Smarcb1 promotes increased accessibility to binding motifs for non-canonical BAF complexes.
Figure S1 from SWI/SNF Complex Mutations Promote Thyroid Tumor Progression and Insensitivity to Redifferentiation Therapies
Authors: Saqcena Mahesh , Leandro-Garcia Luis Javier , Maag Jesper L.V. , Tchekmedyian Vatche , Krishnamoorthy Gnana P. , Tamarapu Prasanna P. , Tiedje Vera , Reuter Vincent , Knauf Jeffrey A. , de Stanchina Elisa , Xu Bin , Liao Xiao-Hui , Refetoff Samuel , Ghossein Ronald , Chi Ping , Ho Alan L. , Koche Richard P. , Fagin James A.
Published: April 2023

SWI/SNF alterations in human thyroid cancers.
Supplementary Data from Surface Proteomics Reveals CD72 as a Target for In Vitro–Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL
Authors: Nix Matthew A. , Mandal Kamal , Geng Huimin , Paranjape Neha , Lin Yu-Hsiu T. , Rivera Jose M. , Marcoulis Makeba , White Kristie L. , Whitman Jeffrey D. , Bapat Sagar P. , Parker Kevin R. , Ramirez Jonathan , Deucher Anne , Phojanokong Paul , Steri Veronica , Fattahi Faranak , Hann Byron C. , Satpathy Ansuman T. , Manglik Aashish , Stieglitz Elliot , Wiita Arun P.
Published: April 2023

Supplementary Data from Surface Proteomics Reveals CD72 as a Target for In Vitro–Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL
Supplementary Data from A Procarcinogenic Colon Microbe Promotes Breast Tumorigenesis and Metastatic Progression and Concomitantly Activates Notch and β-Catenin Axes
Authors: Parida Sheetal , Wu Shaoguang , Siddharth Sumit , Wang Guannan , Muniraj Nethaji , Nagalingam Arumugam , Hum Christina , Mistriotis Panagiotis , Hao Haiping , Talbot C. Conover , Konstantopoulos Konstantinos , Gabrielson Kathleen L. , Sears Cynthia L. , Sharma Dipali
Published: April 2023

Supplementary Figures and Legends
Supplementary Table from Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti–PD-1 Refractory Melanoma
Authors: Haymaker Cara , Johnson Daniel H. , Murthy Ravi , Bentebibel Salah-Eddine , Uemura Marc I. , Hudgens Courtney W. , Safa Houssein , James Marihella , Andtbacka Robert H.I. , Johnson Douglas B. , Shaheen Montaser , Davies Michael A. , Rahimian Shah , Chunduru Srinivas K. , Milton Denái R. , Tetzlaff Michael T. , Overwijk Willem W. , Hwu Patrick , Gabrail Nashat , Agrawal Sudhir , Doolittle Gary , Puzanov Igor , Markowitz Joseph , Bernatchez Chantale , Diab Adi
Published: April 2023

Supplementary Table from Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti–PD-1 Refractory Melanoma
Figures S1-S5 and Tables S1-S3 from Preexisting and Post–COVID-19 Immune Responses to SARS-CoV-2 in Patients with Cancer
Authors: Bilich Tatjana , Roerden Malte , Maringer Yacine , Nelde Annika , Heitmann Jonas S. , Dubbelaar Marissa L. , Peter Andreas , Hörber Sebastian , Bauer Jens , Rieth Jonas , Wacker Marcel , Berner Fiamma , Flatz Lukas , Held Stefanie , Brossart Peter , Märklin Melanie , Wagner Philipp , Erne Eva , Klein Reinhild , Rammensee Hans-Georg , Salih Helmut R. , Walz Juliane S.
Published: April 2023

Supplementary Figures S1-S5 Supplementary Tables S1-S3 revised
Figure S4 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 4: Non-negative matrix factorization rank survey in TCGA COAD/READ Quality measures for Non-negative matrix factorization in TCGA COAD/READ, as described in the R package "NMF". Arrows indicate the estimated rank of mutational signatures.
Figure S3 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 3: Comparison between NHS/ HPFS CRC and COSMIC signatures Cosine similarity heat map between de novo signatures found in NHS/ HPFS (y axis) and COSMIC signatures (x axis). NHS/ HPFS signatures were named after their closest COSMIC mutational process match (in bold)
Figure S16 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 16: Impact of VAF on NMF rank selection The cophenetic score after NMF in NHS/HPFS was computed for different ranks (2 to 10, on the x axis) and different variant allele fraction thresholds (0 to 20).
Figure S14 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 14: Variant calling pipeline Overview of the variant calling pipeline as described in CGA WES Characterization pipeline (https://github.com/broadinstitute/CGA_Production_Analysis_Pipeline) developed at the Broad Institute of MIT and Harvard.
Figure S12 from Discovery and Features of an Alkylating Signature in Colorectal Cancer
Authors: Gurjao Carino , Zhong Rong , Haruki Koichiro , Li Yvonne Y. , Spurr Liam F. , Lee-Six Henry , Reardon Brendan , Ugai Tomotaka , Zhang Xuehong , Cherniack Andrew D. , Song Mingyang , Van Allen Eliezer M. , Meyerhardt Jeffrey A. , Nowak Jonathan A. , Giovannucci Edward L. , Fuchs Charles S. , Wu Kana , Ogino Shuji , Giannakis Marios
Published: April 2023

Supplemental Figure 12: MGMT promoter methylation status and red meat intake Red meat intake for NHS/ HPFS patients, stratified by MGMT promoter methylation status. The two-sided Mann Whitney U test p-value is indicated.
Supplementary Table S6 from Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity
Authors: Mahadevan Navin R. , Knelson Erik H. , Wolff Jacquelyn O. , Vajdi Amir , Saigí Maria , Campisi Marco , Hong Deli , Thai Tran C. , Piel Brandon , Han Saemi , Reinhold Bruce B. , Duke-Cohan Jonathan S. , Poitras Michael J. , Taus Luke J. , Lizotte Patrick H. , Portell Andrew , Quadros Victor , Santucci Alison D. , Murayama Takahiko , Cañadas Israel , Kitajima Shunsuke , Akitsu Aoi , Fridrikh Maya , Watanabe Hideo , Reardon Brendan , Gokhale Prafulla C. , Paweletz Cloud P. , Awad Mark M. , Van Allen Eliezer M. , Lako Ana , Wang Xi-Tao , Chen Benjamin , Hong Fangxin , Sholl Lynette M. , Tolstorukov Michael Y. , Pfaff Kathleen , Jänne Pasi A. , Gjini Evisa , Edwards Robin , Rodig Scott , Reinherz Ellis L. , Oser Matthew G. , Barbie David A.
Published: April 2023

Supplementary Table S6
Table S4 from Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Authors: Derosa Lisa , Routy Bertrand , Desilets Antoine , Daillère Romain , Terrisse Safae , Kroemer Guido , Zitvogel Laurence
Published: April 2023

Supplementary Table S4
Table S1 from Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Authors: Derosa Lisa , Routy Bertrand , Desilets Antoine , Daillère Romain , Terrisse Safae , Kroemer Guido , Zitvogel Laurence
Published: April 2023

Supplementary Table S1
Supplementary Data from Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Authors: Derosa Lisa , Routy Bertrand , Desilets Antoine , Daillère Romain , Terrisse Safae , Kroemer Guido , Zitvogel Laurence
Published: April 2023

Supplementary material
Supplementary Table S3 from Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia
Authors: Yang Zhaolin , Wu Xiaoli S. , Wei Yiliang , Polyanskaya Sofya A. , Iyer Shruti V. , Jung Moonjung , Lach Francis P. , Adelman Emmalee R. , Klingbeil Olaf , Milazzo Joseph P. , Kramer Melissa , Demerdash Osama E. , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Smogorzewska Agata , Vakoc Christopher R.
Published: April 2023

Sequences of additional sgRNA and primers.
Table S2 from Obesity-Dependent Adipokine Chemerin Suppresses Fatty Acid Oxidation to Confer Ferroptosis Resistance
Authors: Tan Sze Kiat , Mahmud Iqbal , Fontanesi Flavia , Puchowicz Michelle , Neumann Chase K.A. , Griswold Anthony J. , Patel Rutulkumar , Dispagna Marco , Ahmed Hamzah H. , Gonzalgo Mark L. , Brown J. Mark , Garrett Timothy J. , Welford Scott M.
Published: April 2023

Differential expression of genes between ccRCC cluster and normal cluster
Supplementary Table S3 from Pharmacologic Activation of p53 Triggers Viral Mimicry Response Thereby Abolishing Tumor Immune Evasion and Promoting Antitumor Immunity
Authors: Zhou Xiaolei , Singh Madhurendra , Sanz Santos Gema , Guerlavais Vincent , Carvajal Luis A. , Aivado Manuel , Zhan Yue , Oliveira Mariana M.S. , Westerberg Lisa S. , Annis D. Allen , Johnsen John Inge , Selivanova Galina
Published: April 2023

Primers, siRNAs and CRISPR guide RNAs
Supplementary Table S1 from Pharmacologic Activation of p53 Triggers Viral Mimicry Response Thereby Abolishing Tumor Immune Evasion and Promoting Antitumor Immunity
Authors: Zhou Xiaolei , Singh Madhurendra , Sanz Santos Gema , Guerlavais Vincent , Carvajal Luis A. , Aivado Manuel , Zhan Yue , Oliveira Mariana M.S. , Westerberg Lisa S. , Annis D. Allen , Johnsen John Inge , Selivanova Galina
Published: April 2023

P53 CHIP-SEQ
Supplementary References from Pharmacologic Activation of p53 Triggers Viral Mimicry Response Thereby Abolishing Tumor Immune Evasion and Promoting Antitumor Immunity
Authors: Zhou Xiaolei , Singh Madhurendra , Sanz Santos Gema , Guerlavais Vincent , Carvajal Luis A. , Aivado Manuel , Zhan Yue , Oliveira Mariana M.S. , Westerberg Lisa S. , Annis D. Allen , Johnsen John Inge , Selivanova Galina
Published: April 2023

References for supplementary methods file
Supplementary Figure from Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis
Authors: Schaettler Maximilian O. , Richters Megan M. , Wang Anthony Z. , Skidmore Zachary L. , Fisk Bryan , Miller Katherine E. , Vickery Tammi L. , Kim Albert H. , Chicoine Michael R. , Osbun Joshua W. , Leuthardt Eric C. , Dowling Joshua L. , Zipfel Gregory J. , Dacey Ralph G. , Lu Hsiang-Chih , Johanns Tanner M. , Griffith Obi L. , Mardis Elaine R. , Griffith Malachi , Dunn Gavin P.
Published: April 2023

Supplementary Figure from Characterization of the Genomic and Immunologic Diversity of Malignant Brain Tumors through Multisector Analysis