bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures S1 - S11 from Co-occurring Genomic Alterations Define Major Subsets of KRAS-Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and Therapeutic Vulnerabilities
Authors: Skoulidis Ferdinandos , Byers Lauren A. , Diao Lixia , Papadimitrakopoulou Vassiliki A. , Tong Pan , Izzo Julie , Behrens Carmen , Kadara Humam , Parra Edwin R. , Canales Jaime Rodriguez , Zhang Jianjun , Giri Uma , Gudikote Jayanthi , Cortez Maria A. , Yang Chao , Fan Youhong , Peyton Michael , Girard Luc , Coombes Kevin R. , Toniatti Carlo , Heffernan Timothy P. , Choi Murim , Frampton Garrett M. , Miller Vincent , Weinstein John N. , Herbst Roy S. , Wong Kwok-Kin , Zhang Jianhua , Sharma Padmanee , Mills Gordon B. , Hong Waun K. , Minna John D. , Allison James P. , Futreal Andrew , Wang Jing , Wistuba Ignacio I. , Heymach John V.
Published: April 2023

Supplementary Figure S1. Functional modules among 384 genes selected for the NMF algorithm. Supplementary Figure S2. Co-occurring somatic mutations in KRAS-mutant LUAC subgroups. Supplementary Figure S3. Distribution of bi-allelic deletion/amplification events in the three KRAS-mutant LUAC subsets. Supplementary Figure S4. Alterations in genes involved in G1/S transition in the three KRAS-mutant LUAC subgroups. Supplementary Figure S5. Clonal fractions for somatically mutated genes in the 68 KRAS-mutant LUACs (TCGA). Supplementary Figure S6. Co-mutation plot for the combined PROSPECT/CHITALE validation dataset of chemotherapy -naïve KRAS-mutant LUACs. Supplementary Figure S7. Co-occurring genetic events in PI3K-AKT-MTOR pathway genes in the three KRAS-mutant LUAC subsets. Supplementary Figure S8. LKB1-loss-dependent up-regulation of adaptive branches of the unfolded protein response in KRAS-mutant LUAC cell lines. Supplementary Figure S9. Enumeration of distinct immune cell populations in the KRAS LUAC sub-groups from PROSPECT. Supplementary Figure S10. Analysis of overall survival (OS) in KRAS-mutant LUAC subsets. Supplementary Figure S11. Integrated analyses for a higher pre-determined number of KRAS-mutant LUAC subsets.
Supplementary Figure Legends 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 Legends
Supplementary Materials and Methods, Figure Legends from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 116K, Supplementary Materials and Methods and Supplementary Figure Legends.
Supplementary Movie 5 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

3D reconstruction of 4T1 mammary tumour 24 hours after injection of bisphosphonate.
Supplementary Figure 6 from Vulnerabilities of PTEN–TP53-Deficient Prostate Cancers to Compound PARP–PI3K Inhibition
Authors: González-Billalabeitia Enrique , Seitzer Nina , Song Su Jung , Song Min Sup , Patnaik Akash , Liu Xue-Song , Epping Mirjam T. , Papa Antonella , Hobbs Robin M. , Chen Ming , Lunardi Andrea , Ng Christopher , Webster Kaitlyn A. , Signoretti Sabina , Loda Massimo , Asara John M. , Nardella Caterina , Clohessy John G. , Cantley Lewis C. , Pandolfi Pier Paolo
Published: April 2023

PDF - 69095K, Supporting histology for the in vivo treatment of Olaparib and BKM120.
Supplementary Figure 3 from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: April 2023

PDF file 348K, Digital PCR validation graphs
Supplementary Table 1 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

Demographic information for patients on study.
Supplementary Table S3 from Infection Exposure Is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility
Authors: Martín-Lorenzo Alberto , Hauer Julia , Vicente-Dueñas Carolina , Auer Franziska , González-Herrero Inés , García-Ramírez Idoia , Ginzel Sebastian , Thiele Ralf , Constantinescu Stefan N. , Bartenhagen Christoph , Dugas Martin , Gombert Michael , Schäfer Daniel , Blanco Oscar , Mayado Andrea , Orfao Alberto , Alonso-López Diego , Rivas Javier De Las , Cobaleda César , García-Cenador Maria Begoña , García-Criado Francisco Javier , Sánchez-García Isidro , Borkhardt Arndt
Published: April 2023

Pax5 target genes differentially express in p-BALL bearing Pax5+/- mice according to Delogu A. et al 2006, Schebesta A. et al 2007, and Revilla-i-Domingo R. et al 2012.
Supplementary Figure 1 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

Trends in various mutation allele frequencies tracked serially over treatment course for two patients on study.
Supplementary Figure S1 - S3 from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

Supplementary Figure S1. IGV visualization for whole exome sequencing of codon Q61 of NRAS in the pre-treatment tumor vs. the relapsed tumor in patient 1. The red color indicates the A>G for the p.Q61R mutation in the tumor. Supplementary Figure S2. A. IGV visualization for the targeted sequencing of BRAF and PI3KCA in patient 6. B. IGV visualization for the targeted sequencing of BRAF and NRAS in patient 7. Supplementary Figure S3. Response of patient 5 PDX to PLX4720.
Supplementary Figure S2. Genetic tools used for dissecting Il6/Stat3/Myc signaling. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S2. Genetic tools used for dissecting Il6/Stat3/Myc signaling. (A) Scheme of conditional alleles and PCR primers used for assessing the recombination of Pten/ Trp53 genes. (B) Senescence-specific ÃŸ-gal staining is detected after Pten loss but not after Pten/Trp53 co-deletion. Scale Bar, 200 Î¼m.
Supplementary Methods from Acquired METD1228V Mutation and Resistance to MET Inhibition in Lung Cancer
Authors: Bahcall Magda , Sim Taebo , Paweletz Cloud P. , Patel Jyoti D. , Alden Ryan S. , Kuang Yanan , Sacher Adrian G. , Kim Nam Doo , Lydon Christine A. , Awad Mark M. , Jaklitsch Michael T. , Sholl Lynette M. , Jänne Pasi A. , Oxnard Geoffrey R.
Published: April 2023

Supplementary methods, including croplet digital PCR for MET D1228V; molecular docking study; Molecular Dynamics Simulations.
Supplementary Table S6 from Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Authors: Eckhardt Manon , Zhang Wei , Gross Andrew M. , Von Dollen John , Johnson Jeffrey R. , Franks-Skiba Kathleen E. , Swaney Danielle L. , Johnson Tasha L. , Jang Gwendolyn M. , Shah Priya S. , Brand Toni M. , Archambault Jacques , Kreisberg Jason F. , Grandis Jennifer R. , Ideker Trey , Krogan Nevan J.
Published: April 2023

Differentially Expressed Genes upon L2 Overexpression. Related to Figure 5.
Table S1 from Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer
Authors: Gettinger Scott , Choi Jungmin , Hastings Katherine , Truini Anna , Datar Ila , Sowell Ryan , Wurtz Anna , Dong Weilai , Cai Guoping , Melnick Mary Ann , Du Victor Y. , Schlessinger Joseph , Goldberg Sarah B. , Chiang Anne , Sanmamed Miguel F. , Melero Ignacio , Agorreta Jackeline , Montuenga Luis M. , Lifton Richard , Ferrone Soldano , Kavathas Paula , Rimm David L. , Kaech Susan M. , Schalper Kurt , Herbst Roy S. , Politi Katerina
Published: April 2023

Table with Details of Patient Characteristics
Supplementary Figures from Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer
Authors: Gettinger Scott , Choi Jungmin , Hastings Katherine , Truini Anna , Datar Ila , Sowell Ryan , Wurtz Anna , Dong Weilai , Cai Guoping , Melnick Mary Ann , Du Victor Y. , Schlessinger Joseph , Goldberg Sarah B. , Chiang Anne , Sanmamed Miguel F. , Melero Ignacio , Agorreta Jackeline , Montuenga Luis M. , Lifton Richard , Ferrone Soldano , Kavathas Paula , Rimm David L. , Kaech Susan M. , Schalper Kurt , Herbst Roy S. , Politi Katerina
Published: April 2023

Supplementary Figures S1-S8
Supplementary Table 3 from Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion–Driven Cancer
Authors: Slotkin Emily K. , Diolaiti Daniel , Shukla Neerav N. , Dela Cruz Filemon S. , Clark Jennifer J. , Gundem Gunes , Yellapantula Venkata D. , Levine Max F. , You Daoqi , Ma Peilin , Pachhal Sagarika , Ibanez Sanchez Glorymar , Benayed Ryma , Jungbluth Achim A. , Smyth Lillian M. , Mauguen Audrey , Gushterova Irena , Ding Hongxu , Spraggon Lee , Darnell Robert , Califano Andrea , Ladanyi Marc , Papaemmanuil Elli , Kung Andrew L. , Hyman David M. , Roberts Stephen S.
Published: April 2023

Supplementary Table 3
Supplementary Table 1 from Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion–Driven Cancer
Authors: Slotkin Emily K. , Diolaiti Daniel , Shukla Neerav N. , Dela Cruz Filemon S. , Clark Jennifer J. , Gundem Gunes , Yellapantula Venkata D. , Levine Max F. , You Daoqi , Ma Peilin , Pachhal Sagarika , Ibanez Sanchez Glorymar , Benayed Ryma , Jungbluth Achim A. , Smyth Lillian M. , Mauguen Audrey , Gushterova Irena , Ding Hongxu , Spraggon Lee , Darnell Robert , Califano Andrea , Ladanyi Marc , Papaemmanuil Elli , Kung Andrew L. , Hyman David M. , Roberts Stephen S.
Published: April 2023

Supplementary Table 1
Supplementary Material from Combined BRAF, EGFR, and MEK Inhibition in Patients with BRAFV600E-Mutant Colorectal Cancer
Authors: Corcoran Ryan B. , André Thierry , Atreya Chloe E. , Schellens Jan H.M. , Yoshino Takayuki , Bendell Johanna C. , Hollebecque Antoine , McRee Autumn J. , Siena Salvatore , Middleton Gary , Muro Kei , Gordon Michael S. , Tabernero Josep , Yaeger Rona , O'Dwyer Peter J. , Humblet Yves , De Vos Filip , Jung A. Scott , Brase Jan C. , Jaeger Savina , Bettinger Severine , Mookerjee Bijoyesh , Rangwala Fatima , Van Cutsem Eric
Published: April 2023

Supplementary Material
Table S6 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Authors: Rajbhandari Presha , Lopez Gonzalo , Capdevila Claudia , Salvatori Beatrice , Yu Jiyang , Rodriguez-Barrueco Ruth , Martinez Daniel , Yarmarkovich Mark , Weichert-Leahey Nina , Abraham Brian J. , Alvarez Mariano J. , Iyer Archana , Harenza Jo Lynne , Oldridge Derek , De Preter Katleen , Koster Jan , Asgharzadeh Shahab , Seeger Robert C. , Wei Jun S. , Khan Javed , Vandesompele Jo , Mestdagh Pieter , Versteeg Rogier , Look A. Thomas , Young Richard A. , Iavarone Antonio , Lasorella Anna , Silva Jose M. , Maris John M. , Califano Andrea
Published: April 2023

TEAD4 ChIP-seq results
Table S3 from Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma
Authors: Rajbhandari Presha , Lopez Gonzalo , Capdevila Claudia , Salvatori Beatrice , Yu Jiyang , Rodriguez-Barrueco Ruth , Martinez Daniel , Yarmarkovich Mark , Weichert-Leahey Nina , Abraham Brian J. , Alvarez Mariano J. , Iyer Archana , Harenza Jo Lynne , Oldridge Derek , De Preter Katleen , Koster Jan , Asgharzadeh Shahab , Seeger Robert C. , Wei Jun S. , Khan Javed , Vandesompele Jo , Mestdagh Pieter , Versteeg Rogier , Look A. Thomas , Young Richard A. , Iavarone Antonio , Lasorella Anna , Silva Jose M. , Maris John M. , Califano Andrea
Published: April 2023

ARACNe-AP transcriptional network from gene expression profiles
Table S1 from Allele-Specific Mechanisms of Activation of MEK1 Mutants Determine Their Properties
Authors: Gao Yijun , Chang Matthew T. , McKay Daniel , Na Na , Zhou Bing , Yaeger Rona , Torres Neilawattie M. , Muniz Keven , Drosten Matthias , Barbacid Mariano , Caponigro Giordano , Stuart Darrin , Moebitz Henrik , Solit David B. , Abdel-Wahab Omar , Taylor Barry S. , Yao Zhan , Rosen Neal
Published: April 2023

Supplemental Table
Table S5 from Deletion 6q Drives T-cell Leukemia Progression by Ribosome Modulation
Authors: Gachet Stéphanie , El-Chaar Tiama , Avran David , Genesca Eulalia , Catez Frédéric , Quentin Samuel , Delord Marc , Thérizols Gabriel , Briot Delphine , Meunier Godelieve , Hernandez Lucie , Pla Marika , Smits Willem K. , Buijs-Gladdines Jessica G. , Van Loocke Wouter , Menschaert Gerben , André-Schmutz Isabelle , Taghon Tom , Van Vlierberghe Pieter , Meijerink Jules P. , Baruchel André , Dombret Hervé , Clappier Emmanuelle , Diaz Jean-Jacques , Gazin Claude , de Thé Hugues , Sigaux François , Soulier Jean
Published: April 2023

Differentially expressed genes in Xenograted T-ALL shSYNCRIP-SNHG5 versus ShCtrl
Supplementary Figures from Landscape of Acquired Resistance to Osimertinib in EGFR-Mutant NSCLC and Clinical Validation of Combined EGFR and RET Inhibition with Osimertinib and BLU-667 for Acquired RET Fusion
Authors: Piotrowska Zofia , Isozaki Hideko , Lennerz Jochen K. , Gainor Justin F. , Lennes Inga T. , Zhu Viola W. , Marcoux Nicolas , Banwait Mandeep K. , Digumarthy Subba R. , Su Wenjia , Yoda Satoshi , Riley Amanda K. , Nangia Varuna , Lin Jessica J. , Nagy Rebecca J. , Lanman Richard B. , Dias-Santagata Dora , Mino-Kenudson Mari , Iafrate A. John , Heist Rebecca S. , Shaw Alice T. , Evans Erica K. , Clifford Corinne , Ou Sai-Hong I. , Wolf Beni , Hata Aaron N. , Sequist Lecia V.
Published: April 2023

Supplementary Figures
Supplementary Table S7 from Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs
Authors: Dobson Stephanie M. , García-Prat Laura , Vanner Robert J. , Wintersinger Jeffrey , Waanders Esmé , Gu Zhaohui , McLeod Jessica , Gan Olga I. , Grandal Ildiko , Payne-Turner Debbie , Edmonson Michael N. , Ma Xiaotu , Fan Yiping , Voisin Veronique , Chan-Seng-Yue Michelle , Xie Stephanie Z. , Hosseini Mohsen , Abelson Sagi , Gupta Pankaj , Rusch Michael , Shao Ying , Olsen Scott R. , Neale Geoffrey , Chan Steven M. , Bader Gary , Easton John , Guidos Cynthia J. , Danska Jayne S. , Zhang Jinghui , Minden Mark D. , Morris Quaid , Mullighan Charles G. , Dick John E.
Published: April 2023

RNA-sequencing, pathway enrichment (GSEA) reports and GSVA results (including gene list HSC vs B) of PDX and paired patient samples
Supplementary Table S6 from Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs
Authors: Dobson Stephanie M. , García-Prat Laura , Vanner Robert J. , Wintersinger Jeffrey , Waanders Esmé , Gu Zhaohui , McLeod Jessica , Gan Olga I. , Grandal Ildiko , Payne-Turner Debbie , Edmonson Michael N. , Ma Xiaotu , Fan Yiping , Voisin Veronique , Chan-Seng-Yue Michelle , Xie Stephanie Z. , Hosseini Mohsen , Abelson Sagi , Gupta Pankaj , Rusch Michael , Shao Ying , Olsen Scott R. , Neale Geoffrey , Chan Steven M. , Bader Gary , Easton John , Guidos Cynthia J. , Danska Jayne S. , Zhang Jinghui , Minden Mark D. , Morris Quaid , Mullighan Charles G. , Dick John E.
Published: April 2023

dPDX and dRI-PDX leukemia-initiating cell frequencies
Supplementary Table S4 from Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs
Authors: Dobson Stephanie M. , García-Prat Laura , Vanner Robert J. , Wintersinger Jeffrey , Waanders Esmé , Gu Zhaohui , McLeod Jessica , Gan Olga I. , Grandal Ildiko , Payne-Turner Debbie , Edmonson Michael N. , Ma Xiaotu , Fan Yiping , Voisin Veronique , Chan-Seng-Yue Michelle , Xie Stephanie Z. , Hosseini Mohsen , Abelson Sagi , Gupta Pankaj , Rusch Michael , Shao Ying , Olsen Scott R. , Neale Geoffrey , Chan Steven M. , Bader Gary , Easton John , Guidos Cynthia J. , Danska Jayne S. , Zhang Jinghui , Minden Mark D. , Morris Quaid , Mullighan Charles G. , Dick John E.
Published: April 2023

RNA-sequencing data from Patient 9 PDX
Supplementary Data from Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification
Authors: Clarke Thomas L. , Tang Ran , Chakraborty Damayanti , Van Rechem Capucine , Ji Fei , Mishra Sweta , Ma Anqi , Kaniskan H. Ümit , Jin Jian , Lawrence Michael S. , Sadreyev Ruslan I. , Whetstine Johnathan R.
Published: April 2023

Supplemental Data and legends and tables.
Supplementary Data from The Evolutionary Origins of Recurrent Pancreatic Cancer
Authors: Sakamoto Hitomi , Attiyeh Marc A. , Gerold Jeffrey M. , Makohon-Moore Alvin P. , Hayashi Akimasa , Hong Jungeui , Kappagantula Rajya , Zhang Lance , Melchor Jerry P. , Reiter Johannes G. , Heyde Alexander , Bielski Craig M. , Penson Alexander V. , Gönen Mithat , Chakravarty Debyani , O'Reilly Eileen M. , Wood Laura D. , Hruban Ralph H. , Nowak Martin A. , Socci Nicholas D. , Taylor Barry S. , Iacobuzio-Donahue Christine A.
Published: April 2023

Figures S1-S3
Supplementary Table S3 from An In Vivo Kras Allelic Series Reveals Distinct Phenotypes of Common Oncogenic Variants
Authors: Zafra Maria Paz , Parsons Marie J. , Kim Jangkyung , Alonso-Curbelo Direna , Goswami Sukanya , Schatoff Emma M. , Han Teng , Katti Alyna , Fernandez Maria Teresa Calvo , Wilkinson John E. , Piskounova Elena , Dow Lukas E.
Published: April 2023

Differential gene expression analysis of RNAseq from MEFs
Supplementary Figures 1-11 from An In Vivo Kras Allelic Series Reveals Distinct Phenotypes of Common Oncogenic Variants
Authors: Zafra Maria Paz , Parsons Marie J. , Kim Jangkyung , Alonso-Curbelo Direna , Goswami Sukanya , Schatoff Emma M. , Han Teng , Katti Alyna , Fernandez Maria Teresa Calvo , Wilkinson John E. , Piskounova Elena , Dow Lukas E.
Published: April 2023

Supplementary Figures and legends
Data S2 from Single-Cell Analysis Reveals Fibroblast Clusters Linked to Immunotherapy Resistance in Cancer
Authors: Kieffer Yann , Hocine Hocine R. , Gentric Géraldine , Pelon Floriane , Bernard Charles , Bourachot Brigitte , Lameiras Sonia , Albergante Luca , Bonneau Claire , Guyard Alice , Tarte Karin , Zinovyev Andrei , Baulande Sylvain , Zalcman Gerard , Vincent-Salomon Anne , Mechta-Grigoriou Fatima
Published: April 2023

Data S2
Supplementary Table 1 from Myeloid-Derived Suppressor Cell Subsets Drive Glioblastoma Growth in a Sex-Specific Manner
Authors: Bayik Defne , Zhou Yadi , Park Chihyun , Hong Changjin , Vail Daniel , Silver Daniel J. , Lauko Adam , Roversi Gustavo , Watson Dionysios C. , Lo Alice , Alban Tyler J. , McGraw Mary , Sorensen Mia , Grabowski Matthew M. , Otvos Balint , Vogelbaum Michael A. , Horbinski Craig , Kristensen Bjarne Winther , Khalil Ahmad M. , Hwang Tae Hyun , Ahluwalia Manmeet S. , Cheng Feixiong , Lathia Justin D.
Published: April 2023

Gene list for network medicine
Supplementary Figures and Methods from Selective Inhibition of HDAC3 Targets Synthetic Vulnerabilities and Activates Immune Surveillance in Lymphoma
Authors: Mondello Patrizia , Tadros Saber , Teater Matt , Fontan Lorena , Chang Aaron Y. , Jain Neeraj , Yang Haopeng , Singh Shailbala , Ying Hsia-Yuan , Chu Chi-Shuen , Ma Man Chun John , Toska Eneda , Alig Stefan , Durant Matthew , de Stanchina Elisa , Ghosh Sreejoyee , Mottok Anja , Nastoupil Loretta , Neelapu Sattva S. , Weigert Oliver , Inghirami Giorgio , Baselga José , Younes Anas , Yee Cassian , Dogan Ahmet , Scheinberg David A. , Roeder Robert G. , Melnick Ari M. , Green Michael R.
Published: April 2023

Figures S1 - S16 Supplementary Methods
Supplementary information from EZH2-Deficient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress
Authors: León Theresa E. , Rapoz-D'Silva Tanya , Bertoli Cosetta , Rahman Sunniyat , Magnussen Michael , Philip Brian , Farah Nadine , Richardson Simon E. , Ahrabi Sara , Guerra-Assunção José Afonso , Gupta Rajeev , Nacheva Elisabeth P. , Henderson Stephen , Herrero Javier , Linch David C. , de Bruin Robertus A.M. , Mansour Marc R.
Published: April 2023

Supplementary information provided in this work.
Supplementary Table 3 from EZH2-Deficient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress
Authors: León Theresa E. , Rapoz-D'Silva Tanya , Bertoli Cosetta , Rahman Sunniyat , Magnussen Michael , Philip Brian , Farah Nadine , Richardson Simon E. , Ahrabi Sara , Guerra-Assunção José Afonso , Gupta Rajeev , Nacheva Elisabeth P. , Henderson Stephen , Herrero Javier , Linch David C. , de Bruin Robertus A.M. , Mansour Marc R.
Published: April 2023

Supplementary Table 3: Mutations identified by exome sequencing in Liu et al., 2017 T-ALL cohort (related to Fig. 5G)
Supplemental Table 8 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 8
Supplemental Table 7 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 7
Supplemental Table 6 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 6
Supplemental Table 2 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 2
Supplemental Figure 7 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

Figure S7
Supplemental Figure 6 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

Figure S6
Supplemental Figure 10 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

Figure S10
Supplementary Data from Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma
Authors: Aoki Tomohiro , Chong Lauren C. , Takata Katsuyoshi , Milne Katy , Hav Monirath , Colombo Anthony , Chavez Elizabeth A. , Nissen Michael , Wang Xuehai , Miyata-Takata Tomoko , Lam Vivian , Viganò Elena , Woolcock Bruce W. , Telenius Adèle , Li Michael Y. , Healy Shannon , Ghesquiere Chanel , Kos Daniel , Goodyear Talia , Veldman Johanna , Zhang Allen W. , Kim Jubin , Saberi Saeed , Ding Jiarui , Farinha Pedro , Weng Andrew P. , Savage Kerry J. , Scott David W. , Krystal Gerald , Nelson Brad H. , Mottok Anja , Merchant Akil , Shah Sohrab P. , Steidl Christian
Published: April 2023

Supplementary Table 1-5
Supplementary Table S5 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

Primer sequences used in this study
Figure S6 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

Progression free survival by baseline ESR1
Figure S6 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 6 shows schematics for experimental set-up, tumor volume at the start of treatment, and graphs showing individual tumor growth for figure 6
Table S7 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

MC2vsMC1 DMRs
Table S4 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

PDACvsNP DMRs
Movie S4 from Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy
Authors: Driehuis Else , Kolders Sigrid , Spelier Sacha , Lõhmussaar Kadi , Willems Stefan M. , Devriese Lot A. , de Bree Remco , de Ruiter Emma J. , Korving Jeroen , Begthel Harry , van Es Johan H. , Geurts Veerle , He Gui-Wei , van Jaarsveld Richard H. , Oka Rurika , Muraro Mauro J. , Vivié Judith , Zandvliet Maurice M.J.M. , Hendrickx Antoni P.A. , Iakobachvili Nino , Sridevi Priya , Kranenburg Onno , van Boxtel Ruben , Kops Geert J.P.L. , Tuveson David A. , Peters Peter J. , van Oudenaarden Alexander , Clevers Hans
Published: April 2023

Movie S4
Table S3 from Machine-Learning and Chemicogenomics Approach Defines and Predicts Cross-Talk of Hippo and MAPK Pathways
Authors: Pham Trang H. , Hagenbeek Thijs J. , Lee Ho-June , Li Jason , Rose Christopher M. , Lin Eva , Yu Mamie , Martin Scott E. , Piskol Robert , Lacap Jennifer A. , Sampath Deepak , Pham Victoria C. , Modrusan Zora , Lill Jennie R. , Klijn Christiaan , Malek Shiva , Chang Matthew T. , Dey Anwesha
Published: April 2023

Four consensus gene clusters from YAP1/WWTR1 knockdown
Figure S5 from Machine-Learning and Chemicogenomics Approach Defines and Predicts Cross-Talk of Hippo and MAPK Pathways
Authors: Pham Trang H. , Hagenbeek Thijs J. , Lee Ho-June , Li Jason , Rose Christopher M. , Lin Eva , Yu Mamie , Martin Scott E. , Piskol Robert , Lacap Jennifer A. , Sampath Deepak , Pham Victoria C. , Modrusan Zora , Lill Jennie R. , Klijn Christiaan , Malek Shiva , Chang Matthew T. , Dey Anwesha
Published: April 2023

Supplementary Figure 5
Table S8 from The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis
Authors: Hong Xin , Roh Whijae , Sullivan Ryan J. , Wong Keith H.K. , Wittner Ben S. , Guo Hongshan , Dubash Taronish D. , Sade-Feldman Moshe , Wesley Benjamin , Horwitz Elad , Boland Genevieve M. , Marvin Dieuwke L. , Bonesteel Todd , Lu Chenyue , Aguet François , Burr Risa , Freeman Samuel S. , Parida Laxmi , Calhoun Katherine , Jewett Michelle K. , Nieman Linda T. , Hacohen Nir , Näär Anders M. , Ting David T. , Toner Mehmet , Stott Shannon L. , Getz Gad , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Table S8
Table S6 from The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis
Authors: Hong Xin , Roh Whijae , Sullivan Ryan J. , Wong Keith H.K. , Wittner Ben S. , Guo Hongshan , Dubash Taronish D. , Sade-Feldman Moshe , Wesley Benjamin , Horwitz Elad , Boland Genevieve M. , Marvin Dieuwke L. , Bonesteel Todd , Lu Chenyue , Aguet François , Burr Risa , Freeman Samuel S. , Parida Laxmi , Calhoun Katherine , Jewett Michelle K. , Nieman Linda T. , Hacohen Nir , Näär Anders M. , Ting David T. , Toner Mehmet , Stott Shannon L. , Getz Gad , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Table S6
Table S2 from Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis
Authors: Halbritter Florian , Farlik Matthias , Schwentner Raphaela , Jug Gunhild , Fortelny Nikolaus , Schnöller Thomas , Pisa Hanja , Schuster Linda C. , Reinprecht Andrea , Czech Thomas , Gojo Johannes , Holter Wolfgang , Minkov Milen , Bauer Wolfgang M. , Simonitsch-Klupp Ingrid , Bock Christoph , Hutter Caroline
Published: April 2023

Marker genes and genomic regions. Lists of differentially expressed genes between LCH cells and non-LCH immune cells, marker genes for each LCH cell subset, and differentially accessible genomic regions between LCH cell subsets.
Supplementary File 1 from Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis
Authors: Halbritter Florian , Farlik Matthias , Schwentner Raphaela , Jug Gunhild , Fortelny Nikolaus , Schnöller Thomas , Pisa Hanja , Schuster Linda C. , Reinprecht Andrea , Czech Thomas , Gojo Johannes , Holter Wolfgang , Minkov Milen , Bauer Wolfgang M. , Simonitsch-Klupp Ingrid , Bock Christoph , Hutter Caroline
Published: April 2023

Gene regulatory networks. Interactive diagrams for the web-browser-based exploration of LCH-subset-specific gene regulatory networks.
Supplementary Figures from Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis
Authors: Halbritter Florian , Farlik Matthias , Schwentner Raphaela , Jug Gunhild , Fortelny Nikolaus , Schnöller Thomas , Pisa Hanja , Schuster Linda C. , Reinprecht Andrea , Czech Thomas , Gojo Johannes , Holter Wolfgang , Minkov Milen , Bauer Wolfgang M. , Simonitsch-Klupp Ingrid , Bock Christoph , Hutter Caroline
Published: April 2023

Supplementary Figures
Supplementary Table S1 from A Critical Role for Fas-Mediated Off-Target Tumor Killing in T-cell Immunotherapy
Authors: Upadhyay Ranjan , Boiarsky Jonathan A. , Pantsulaia Gvantsa , Svensson-Arvelund Judit , Lin Matthew J. , Wroblewska Aleksandra , Bhalla Sherry , Scholler Nathalie , Bot Adrian , Rossi John M. , Sadek Norah , Parekh Samir , Lagana Alessandro , Baccarini Alessia , Merad Miriam , Brown Brian D. , Brody Joshua D.
Published: April 2023

Supplementary Table S1
Supplementary Tables S1, S2, S3, S5, S7, S9, S11, S12, S17, S19, S21 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Authors: Elyada Ela , Bolisetty Mohan , Laise Pasquale , Flynn William F. , Courtois Elise T. , Burkhart Richard A. , Teinor Jonathan A. , Belleau Pascal , Biffi Giulia , Lucito Matthew S. , Sivajothi Santhosh , Armstrong Todd D. , Engle Dannielle D. , Yu Kenneth H. , Hao Yuan , Wolfgang Christopher L. , Park Youngkyu , Preall Jonathan , Jaffee Elizabeth M. , Califano Andrea , Robson Paul , Tuveson David A.
Published: April 2023

Supplementary Table S1 shows patient information, Supplementary Table S2 shows cell numbers analyzed from each human PDAC sample, Supplementary Table S3 shows statistics of the clustering analysis of the human PDAC single cell RNA sequencing, Supplementary Table S5 shows statistics of the human PDAC ductal cell analysis, Supplementary Table S7 shows statistics of the human PDAC myeloid cell analysis, Supplementary Table S9 shows statistics of the human PDAC T & NK cell analysis, Supplementary Table S11 shows cell numbers analyzed for fibroblast subtypes from each human PDAC sample, Supplementary Table S12 shows statistics of the human PDAC fibroblast analysis, Supplementary Table S17 shows statistics of all viable KPC mouse cell analysis, Supplementary Table S19 shows statistics of the KPC mouse fibroblast-enriched fraction analysis, Supplementary Table S21 shows statistics of the fibroblasts from KPC mouse fibroblast-enriched population
Supplementary Figures S1-S8 from Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts
Authors: Elyada Ela , Bolisetty Mohan , Laise Pasquale , Flynn William F. , Courtois Elise T. , Burkhart Richard A. , Teinor Jonathan A. , Belleau Pascal , Biffi Giulia , Lucito Matthew S. , Sivajothi Santhosh , Armstrong Todd D. , Engle Dannielle D. , Yu Kenneth H. , Hao Yuan , Wolfgang Christopher L. , Park Youngkyu , Preall Jonathan , Jaffee Elizabeth M. , Califano Andrea , Robson Paul , Tuveson David A.
Published: April 2023

Supplementary Figure S1 shows the data quality and clustering metrics of the human PDAC single cell transcriptomes, Supplementary Figure S2 shows the distribution of sub-clusters of cells throughout the human dataset, Supplementary Figure S3 shows pathway analysis in human PDAC iCAFs and myCAFs, Supplementary Figure S4 shows the data quality and clustering metrics of the KPC mouse PDAC single cell transcriptomes, Supplementary Figure S5 shows pathway analysis in different KPC CAFs, Supplementary Figure S6 shows that Podoplanin is a pan-fibroblast marker in murine PDAC, Supplementary Figure S7 shows the validation of apCAFs in human PDAC, Supplementary Figure S8 shows the characterization of apCAFs in KPC and orthotopic transplantation models
Supplementary Tables S1-S7 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 Tables
Supplementary Figure S3 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

Exposure-response relationship between CX-5461 levels and rDNA transcription rate in normal PBMCs
Supplementary Figure S1 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

Significant dermatological toxicities associated with CX-5461 treatment
Table S3 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 S3. List of reagents, software and deposited data
Supplementary Table S7 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 S7 - Antibody list
Supplementary Data 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

Supplementary Figures and methods
Supplementary Table 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

Logistic Regression Results
Figure S5 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

Impact of Arid1a, Arid2 and Smarcb1 loss on thyroid lineage TF expression and chromatin accessibility.
Figure S13 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

Schema of redifferentiation trials.
Supplementary Data from Tumor Immunity and Immunotherapy for HPV-Related Cancers
Authors: Shamseddine Achraf A. , Burman Bharat , Lee Nancy Y. , Zamarin Dmitriy , Riaz Nadeem
Published: April 2023

Supplementary data (Table S1 and Figure S1)
TableS1.xlsx from CDK4/6 Inhibition Promotes Antitumor Immunity through the Induction of T-cell Memory
Authors: Lelliott Emily J. , Kong Isabella Y. , Zethoven Magnus , Ramsbottom Kelly M. , Martelotto Luciano G. , Meyran Deborah , Zhu Joe Jiang , Costacurta Matteo , Kirby Laura , Sandow Jarrod J. , Lim Lydia , Dominguez Pilar M. , Todorovski Izabela , Haynes Nicole M. , Beavis Paul A. , Neeson Paul J. , Hawkins Edwin D. , McArthur Grant A. , Parish Ian A. , Johnstone Ricky W. , Oliaro Jane , Sheppard Karen E. , Kearney Conor J. , Vervoort Stephin J.
Published: April 2023

Supplementary Table S1