bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S2 from Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma
Authors: Hong Aayoung , Moriceau Gatien , Sun Lu , Lomeli Shirley , Piva Marco , Damoiseaux Robert , Holmen Sheri L. , Sharpless Norman E. , Hugo Willy , Lo Roger S.
Published: April 2023

Supplementary Figure S2. Gene expression and signaling responses underlying the slow-cycling predominant, MAPKi-addiction phenotype
Figure S1 from Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma
Authors: Hong Aayoung , Moriceau Gatien , Sun Lu , Lomeli Shirley , Piva Marco , Damoiseaux Robert , Holmen Sheri L. , Sharpless Norman E. , Hugo Willy , Lo Roger S.
Published: April 2023

Supplementary Figure S1. The magnitude of p-ERK rebound induced by MAPKi-withdrawal determines the cellular response of drug-resistant melanoma
Supplementary Tables 1-8 from Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma
Authors: Pectasides Eirini , Stachler Matthew D. , Derks Sarah , Liu Yang , Maron Steven , Islam Mirazul , Alpert Lindsay , Kwak Heewon , Kindler Hedy , Polite Blase , Sharma Manish R. , Allen Kenisha , O'Day Emily , Lomnicki Samantha , Maranto Melissa , Kanteti Rajani , Fitzpatrick Carrie , Weber Christopher , Setia Namrata , Xiao Shu-Yuan , Hart John , Nagy Rebecca J. , Kim Kyoung-Mee , Choi Min-Gew , Min Byung-Hoon , Nason Katie S. , O'Keefe Lea , Watanabe Masayuki , Baba Hideo , Lanman Rick , Agoston Agoston T. , Oh David J. , Dunford Andrew , Thorner Aaron R. , Ducar Matthew D. , Wollison Bruce M. , Coleman Haley A. , Ji Yuan , Posner Mitchell C. , Roggin Kevin , Turaga Kiran , Chang Paul , Hogarth Kyle , Siddiqui Uzma , Gelrud Andres , Ha Gavin , Freeman Samuel S. , Rhoades Justin , Reed Sarah , Gydush Greg , Rotem Denisse , Davison Jon , Imamura Yu , Adalsteinsson Viktor , Lee Jeeyun , Bass Adam J. , Catenacci Daniel V.
Published: April 2023

Supplementary Table 1. Tumor and sequencing information for Cohort 1, paired primary and metastatic gastric adenocarcinoma samples; Supplementary Table 2. 243-gene targeted panel used for sequencing of Cohort 2 samples; Supplementary Table 3: Wild type and mutant read counts for paired primary and metastatic samples in cohort 1; Supplementary Table 4. Clinical and pathologic characteristics of Cohort 2; Supplementary Table 5. Complete sequencing results of Cohort 2; Supplementary Table 6. Clinical characteristics of Cohort 3; Supplementary Table 7. Treatment assignment algorithm of PANGEA clinical trial; Supplementary Table 8. Clinical Characteristics and Response Data of evaluable patients in the PANGEA cohort (N = 21)
Supplementary Figures 1-4 from Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma
Authors: Pectasides Eirini , Stachler Matthew D. , Derks Sarah , Liu Yang , Maron Steven , Islam Mirazul , Alpert Lindsay , Kwak Heewon , Kindler Hedy , Polite Blase , Sharma Manish R. , Allen Kenisha , O'Day Emily , Lomnicki Samantha , Maranto Melissa , Kanteti Rajani , Fitzpatrick Carrie , Weber Christopher , Setia Namrata , Xiao Shu-Yuan , Hart John , Nagy Rebecca J. , Kim Kyoung-Mee , Choi Min-Gew , Min Byung-Hoon , Nason Katie S. , O'Keefe Lea , Watanabe Masayuki , Baba Hideo , Lanman Rick , Agoston Agoston T. , Oh David J. , Dunford Andrew , Thorner Aaron R. , Ducar Matthew D. , Wollison Bruce M. , Coleman Haley A. , Ji Yuan , Posner Mitchell C. , Roggin Kevin , Turaga Kiran , Chang Paul , Hogarth Kyle , Siddiqui Uzma , Gelrud Andres , Ha Gavin , Freeman Samuel S. , Rhoades Justin , Reed Sarah , Gydush Greg , Rotem Denisse , Davison Jon , Imamura Yu , Adalsteinsson Viktor , Lee Jeeyun , Bass Adam J. , Catenacci Daniel V.
Published: April 2023

Supplementary Fig. 1: Mutation rate and ploidy for each individual patient's primary and metastatic sample (cohort 1);Supplementary Fig. 2: Validation of genomic heterogeneity within primary tumor and between primary tumor and lymph node (LN) metastases detected by next generation sequencing (NGS) with fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC);Supplementary Fig. 3: PANGEA: Platform clinical trial of molecularly driven therapies in patients with previously untreated GEA;Supplementary Fig. 4: Biomarker profiling of PANGEA where the biomarker profiling of the metastatic tumor did not lead to treatment reassignment relative to treatments assigned based upon the primary tumor
Supplementary Methods from Multidimensional Analyses of Donor Memory-Like NK Cells Reveal New Associations with Response after Adoptive Immunotherapy for Leukemia
Authors: Berrien-Elliott Melissa M. , Cashen Amanda F. , Cubitt Celia C. , Neal Carly C. , Wong Pamela , Wagner Julia A. , Foster Mark , Schappe Timothy , Desai Sweta , McClain Ethan , Becker-Hapak Michelle , Foltz Jennifer A. , Cooper Matthew L. , Jaeger Natalia , Srivatsan Sridhar Nonavinkere , Gao Feng , Romee Rizwan , Abboud Camille N. , Uy Geoffrey L. , Westervelt Peter , Jacoby Meagan A. , Pusic Iskra , Stockerl-Goldstein Keith E. , Schroeder Mark A. , DiPersio John , Fehniger Todd A.
Published: April 2023

Supplementary patient data, supplementary materials and methods
Table S6 from H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone
Authors: Khazaei Sima , De Jay Nicolas , Deshmukh Shriya , Hendrikse Liam D. , Jawhar Wajih , Chen Carol C.L. , Mikael Leonie G. , Faury Damien , Marchione Dylan M. , Lanoix Joel , Bonneil Éric , Ishii Takeaki , Jain Siddhant U. , Rossokhata Kateryna , Sihota Tianna S. , Eveleigh Robert , Lisi Véronique , Harutyunyan Ashot S. , Jung Sungmi , Karamchandani Jason , Dickson Brendan C. , Turcotte Robert , Wunder Jay S. , Thibault Pierre , Lewis Peter W. , Garcia Benjamin A. , Mack Stephen C. , Taylor Michael D. , Garzia Livia , Kleinman Claudia L. , Jabado Nada
Published: April 2023

Interactions between Stromal and Myeloid compartments
Table S5 from H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone
Authors: Khazaei Sima , De Jay Nicolas , Deshmukh Shriya , Hendrikse Liam D. , Jawhar Wajih , Chen Carol C.L. , Mikael Leonie G. , Faury Damien , Marchione Dylan M. , Lanoix Joel , Bonneil Éric , Ishii Takeaki , Jain Siddhant U. , Rossokhata Kateryna , Sihota Tianna S. , Eveleigh Robert , Lisi Véronique , Harutyunyan Ashot S. , Jung Sungmi , Karamchandani Jason , Dickson Brendan C. , Turcotte Robert , Wunder Jay S. , Thibault Pierre , Lewis Peter W. , Garcia Benjamin A. , Mack Stephen C. , Taylor Michael D. , Garzia Livia , Kleinman Claudia L. , Jabado Nada
Published: April 2023

Golgi Secretome Analysis in Isogenic Lines
Table S2 from H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone
Authors: Khazaei Sima , De Jay Nicolas , Deshmukh Shriya , Hendrikse Liam D. , Jawhar Wajih , Chen Carol C.L. , Mikael Leonie G. , Faury Damien , Marchione Dylan M. , Lanoix Joel , Bonneil Éric , Ishii Takeaki , Jain Siddhant U. , Rossokhata Kateryna , Sihota Tianna S. , Eveleigh Robert , Lisi Véronique , Harutyunyan Ashot S. , Jung Sungmi , Karamchandani Jason , Dickson Brendan C. , Turcotte Robert , Wunder Jay S. , Thibault Pierre , Lewis Peter W. , Garcia Benjamin A. , Mack Stephen C. , Taylor Michael D. , Garzia Livia , Kleinman Claudia L. , Jabado Nada
Published: April 2023

Differential Expression in Isogenic Lines
Supplementary Data from H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone
Authors: Khazaei Sima , De Jay Nicolas , Deshmukh Shriya , Hendrikse Liam D. , Jawhar Wajih , Chen Carol C.L. , Mikael Leonie G. , Faury Damien , Marchione Dylan M. , Lanoix Joel , Bonneil Éric , Ishii Takeaki , Jain Siddhant U. , Rossokhata Kateryna , Sihota Tianna S. , Eveleigh Robert , Lisi Véronique , Harutyunyan Ashot S. , Jung Sungmi , Karamchandani Jason , Dickson Brendan C. , Turcotte Robert , Wunder Jay S. , Thibault Pierre , Lewis Peter W. , Garcia Benjamin A. , Mack Stephen C. , Taylor Michael D. , Garzia Livia , Kleinman Claudia L. , Jabado Nada
Published: April 2023

Supplementary Information
Supplementary Data from Somatic Tissue Engineering in Mouse Models Reveals an Actionable Role for WNT Pathway Alterations in Prostate Cancer Metastasis
Authors: Leibold Josef , Ruscetti Marcus , Cao Zhen , Ho Yu-Jui , Baslan Timour , Zou Min , Abida Wassim , Feucht Judith , Han Teng , Barriga Francisco M. , Tsanov Kaloyan M. , Zamechek Leah , Kulick Amanda , Amor Corina , Tian Sha , Rybczyk Katarzyna , Salgado Nelson R. , Sánchez-Rivera Francisco J. , Watson Philip A. , de Stanchina Elisa , Wilkinson John E. , Dow Lukas E. , Abate-Shen Cory , Sawyers Charles L. , Lowe Scott W.
Published: April 2023

Supplementary Figures and Legends
Table S3 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Enriched gene sets in ASF1A-low tumors and Asf1a KO cells
Figure S9 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Asf1a KO and anti-PD-1 combination therapy primes and activates T cells that can recognize specific tumor-associated antigen
Figure S8 from In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma
Authors: Li Fei , Huang Qingyuan , Luster Troy A. , Hu Hai , Zhang Hua , Ng Wai-Lung , Khodadadi-Jamayran Alireza , Wang Wei , Chen Ting , Deng Jiehui , Ranieri Michela , Fang Zhaoyuan , Pyon Val , Dowling Catríona M. , Bagdatlioglu Ece , Almonte Christina , Labbe Kristen , Silver Heather , Rabin Alexandra R. , Jani Kandarp , Tsirigos Aristotelis , Papagiannakopoulos Thales , Hammerman Peter S. , Velcheti Vamsidhar , Freeman Gordon J. , Qi Jun , Miller George , Wong Kwok-Kin
Published: April 2023

Alterations of T cell populations in an orthotopic KP lung tumor model with short-term treatment
Supplementary Data 1 from The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies
Authors: Prager Briana C. , Vasudevan Harish N. , Dixit Deobrat , Bernatchez Jean A. , Wu Qiulian , Wallace Lisa C. , Bhargava Shruti , Lee Derrick , King Bradley H. , Morton Andrew R. , Gimple Ryan C. , Pekmezci Melike , Zhu Zhe , Siqueira-Neto Jair L. , Wang Xiuxing , Xie Qi , Chen Clark , Barnett Gene H. , Vogelbaum Michael A. , Mack Stephen C. , Chavez Lukas , Perry Arie , Raleigh David R. , Rich Jeremy N.
Published: April 2023

Supplementary Data
Supplementary Table 8 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

SRSF Family Proteins Essentiality in Tumor Cell Lines
Supplementary Table 7 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Alternative Spliced Genes Between HR and NHR T-ALL Patients and Enrichment Analysis
Supplementary Table 6 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Motif Analysis of Skip Exon Events in T-ALL Compared to CD3 T Cells
Supplementary Table 5 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

KEGG Enrichment Analysis of Overlapped rMATS Transcripts in CD3 T Cells vs Thymus and CD4 T Cells vs Thymus
Supplementary Table 4 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

KEGG Enrichment Analysis of Differential Expressed Genes Between Thymus and T-ALL
Supplementary Table 3 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between CD4 T-Cells and T-ALL
Supplementary Table 2 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between Thymus and T-ALL
Supplementary Table 13 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Gene Ontology Analysis of Overlap Proteins from USP7-IP-MS and KGG-MS
Supplementary Table 10 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

Mutation Status of Selected Splicing Factors in T-ALL patients
Supplementary Table 1 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia
Authors: Zhou Yalu , Han Cuijuan , Wang Eric , Lorch Adam H. , Serafin Valentina , Cho Byoung-Kyu , Gutierrez Diaz Blanca T. , Calvo Julien , Fang Celestia , Khodadadi-Jamayran Alireza , Tabaglio Tommaso , Marier Christian , Kuchmiy Anna , Sun Limin , Yacu George , Filip Szymon K. , Jin Qi , Takahashi Yoh-Hei , Amici David R. , Rendleman Emily J. , Rawat Radhika , Bresolin Silvia , Paganin Maddalena , Zhang Cheng , Li Hu , Kandela Irawati , Politanska Yuliya , Abdala-Valencia Hiam , Mendillo Marc L. , Zhu Ping , Palhais Bruno , Van Vlierberghe Pieter , Taghon Tom , Aifantis Iannis , Goo Young Ah , Guccione Ernesto , Heguy Adriana , Tsirigos Aristotelis , Wee Keng Boon , Mishra Rama K. , Pflumio Francoise , Accordi Benedetta , Basso Giuseppe , Ntziachristos Panagiotis
Published: April 2023

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between CD3 T-Cells and T-ALL
Table S1 from ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
Authors: Huang Yun-Han , Hu Jing , Chen Fei , Lecomte Nicolas , Basnet Harihar , David Charles J. , Witkin Matthew D. , Allen Peter J. , Leach Steven D. , Hollmann Travis J. , Iacobuzio-Donahue Christine A. , Massagué Joan
Published: April 2023

Table S1
Supplementary methods from ID1 Mediates Escape from TGFβ Tumor Suppression in Pancreatic Cancer
Authors: Huang Yun-Han , Hu Jing , Chen Fei , Lecomte Nicolas , Basnet Harihar , David Charles J. , Witkin Matthew D. , Allen Peter J. , Leach Steven D. , Hollmann Travis J. , Iacobuzio-Donahue Christine A. , Massagué Joan
Published: April 2023

Supplementary methods
Supplementary Table S4 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

Chemicals and Drugs
Supplementary Table S3 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

Primers
Supplementary Table S2 from Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer
Authors: Zhang Haisheng , Schaefer Antje , Wang Yichen , Hodge Richard G. , Blake Devon R. , Diehl J. Nathaniel , Papageorge Alex G. , Stachler Matthew D. , Liao Jennifer , Zhou Jin , Wu Zhong , Akarca Fahire G. , de Klerk Leonie K. , Derks Sarah , Pierobon Mariaelena , Hoadley Katherine A. , Wang Timothy C. , Church George , Wong Kwok-Kin , Petricoin Emanuel F. , Cox Adrienne D. , Lowy Douglas R. , Der Channing J. , Bass Adam J.
Published: April 2023

RPPA data
Supplementary Tables from Type I Interferon Regulates a Coordinated Gene Network to Enhance Cytotoxic T Cell–Mediated Tumor Killing
Authors: Fan Jun-Bao , Miyauchi Sayuri , Xu Hui-Zhong , Liu Dan , Kim Leo J.Y. , Burkart Christoph , Cheng Hua , Arimoto Kei-ichiro , Yan Ming , Zhou Yu , Győrffy Balázs , Knobeloch Klaus-Peter , Rich Jeremy N. , Cang Hu , Fu Xiang-Dong , Zhang Dong-Er
Published: April 2023

Supplementary tables
Supplementary Data from PRMT5 Inhibition Modulates E2F1 Methylation and Gene-Regulatory Networks Leading to Therapeutic Efficacy in JAK2V617F-Mutant MPN
Authors: Pastore Friederike , Bhagwat Neha , Pastore Alessandro , Radzisheuskaya Aliaksandra , Karzai Abdul , Krishnan Aishwarya , Li Bing , Bowman Robert L. , Xiao Wenbin , Viny Aaron D. , Zouak Anouar , Park Young C. , Cordner Keith B. , Braunstein Stephanie , Maag Jesper L. , Grego Alexander , Mehta Jaanvi , Wang Min , Lin Hong , Durham Benjamin H. , Koche Richard P. , Rampal Raajit K. , Helin Kristian , Scherle Peggy , Vaddi Kris , Levine Ross L.
Published: April 2023

supplementary tables and material and methods
Supplementary Data from PRMT5 Inhibition Modulates E2F1 Methylation and Gene-Regulatory Networks Leading to Therapeutic Efficacy in JAK2V617F-Mutant MPN
Authors: Pastore Friederike , Bhagwat Neha , Pastore Alessandro , Radzisheuskaya Aliaksandra , Karzai Abdul , Krishnan Aishwarya , Li Bing , Bowman Robert L. , Xiao Wenbin , Viny Aaron D. , Zouak Anouar , Park Young C. , Cordner Keith B. , Braunstein Stephanie , Maag Jesper L. , Grego Alexander , Mehta Jaanvi , Wang Min , Lin Hong , Durham Benjamin H. , Koche Richard P. , Rampal Raajit K. , Helin Kristian , Scherle Peggy , Vaddi Kris , Levine Ross L.
Published: April 2023

Supplementary Figures
Supplementary Table S2 from Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer
Authors: Hou Pingping , Kapoor Avnish , Zhang Qiang , Li Jiexi , Wu Chang-Jiun , Li Jun , Lan Zhengdao , Tang Ming , Ma Xingdi , Ackroyd Jeffrey J. , Kalluri Raghu , Zhang Jianhua , Jiang Shan , Spring Denise J. , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

antibody information
Supplementary Table S1 from Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer
Authors: Hou Pingping , Kapoor Avnish , Zhang Qiang , Li Jiexi , Wu Chang-Jiun , Li Jun , Lan Zhengdao , Tang Ming , Ma Xingdi , Ackroyd Jeffrey J. , Kalluri Raghu , Zhang Jianhua , Jiang Shan , Spring Denise J. , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Epigenetic library information
Supplementary Table S1 from TBK1 Is a Synthetic Lethal Target in Cancer with VHL Loss
Authors: Hu Lianxin , Xie Haibiao , Liu Xijuan , Potjewyd Frances , James Lindsey I. , Wilkerson Emily M. , Herring Laura E. , Xie Ling , Chen Xian , Cabrera Johnny Castillo , Hong Kai , Liao Chengheng , Tan Xianming , Baldwin Albert S. , Gong Kan , Zhang Qing
Published: April 2023

Quantification of IHC staining
Supplementary table S1 from Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock
Authors: Dong Zhen , Zhang Guoxin , Qu Meng , Gimple Ryan C. , Wu Qiulian , Qiu Zhixin , Prager Briana C. , Wang Xiuxing , Kim Leo J.Y. , Morton Andrew R. , Dixit Deobrat , Zhou Wenchao , Huang Haidong , Li Bin , Zhu Zhe , Bao Shideng , Mack Stephen C. , Chavez Lukas , Kay Steve A. , Rich Jeremy N.
Published: April 2023

Table S1 showing the sequence of primers and sgRNAs
Supplementary methods from Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock
Authors: Dong Zhen , Zhang Guoxin , Qu Meng , Gimple Ryan C. , Wu Qiulian , Qiu Zhixin , Prager Briana C. , Wang Xiuxing , Kim Leo J.Y. , Morton Andrew R. , Dixit Deobrat , Zhou Wenchao , Huang Haidong , Li Bin , Zhu Zhe , Bao Shideng , Mack Stephen C. , Chavez Lukas , Kay Steve A. , Rich Jeremy N.
Published: April 2023

Supplementary methods
Supplementary figures and legends from Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock
Authors: Dong Zhen , Zhang Guoxin , Qu Meng , Gimple Ryan C. , Wu Qiulian , Qiu Zhixin , Prager Briana C. , Wang Xiuxing , Kim Leo J.Y. , Morton Andrew R. , Dixit Deobrat , Zhou Wenchao , Huang Haidong , Li Bin , Zhu Zhe , Bao Shideng , Mack Stephen C. , Chavez Lukas , Kay Steve A. , Rich Jeremy N.
Published: April 2023

Supplementary figures 1-8 and figures legends.
Supplementary Table 4: H4 from A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
Authors: Bennett Richard L. , Bele Aditya , Small Eliza C. , Will Christine M. , Nabet Behnam , Oyer Jon A. , Huang Xiaoxiao , Ghosh Rajarshi P. , Grzybowski Adrian T. , Yu Tao , Zhang Qiao , Riva Alberto , Lele Tanmay P. , Schatz George C. , Kelleher Neil L. , Ruthenburg Alexander J. , Liphardt Jan , Licht Jonathan D.
Published: April 2023

List of all H4 missense mutations in cBioPortal nad dbSNP analysis
Supplementary Table 1: H2A from A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
Authors: Bennett Richard L. , Bele Aditya , Small Eliza C. , Will Christine M. , Nabet Behnam , Oyer Jon A. , Huang Xiaoxiao , Ghosh Rajarshi P. , Grzybowski Adrian T. , Yu Tao , Zhang Qiao , Riva Alberto , Lele Tanmay P. , Schatz George C. , Kelleher Neil L. , Ruthenburg Alexander J. , Liphardt Jan , Licht Jonathan D.
Published: April 2023

List of all H2A missense mutations in cBioPortal and dbSNP analysis
Figure S7 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S7 shows PPARg as a therapeutic target for brain metastasis.
Figure S5 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S5 shows PPAR pathway is activated in MDA231-BrM and Yumm1.7-BrM cells and further enhanced by astrocyte co-culture.
Figure S4 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S4 shows gene set variation analyses (GSVA) of PPAR and EIF2 pathways in WM4265.2-BrMs.
Figure S3 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S3 shows WM4265.2 and two BrM cells response to staurosporine-induced cell death at similar level.
Figure S2 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S2 shows astrocytes facilitate the growth and survival of brain metastatic cancer cells.
Figure S1 from Polyunsaturated Fatty Acids from Astrocytes Activate PPARγ Signaling in Cancer Cells to Promote Brain Metastasis
Authors: Zou Yongkang , Watters Andrea , Cheng Nan , Perry Caroline E. , Xu Ke , Alicea Gretchen M. , Parris Joshua L.D. , Baraban Ezra , Ray Pulak , Nayak Anupma , Xu Xiaowei , Herlyn Meenhard , Murphy Maureen E. , Weeraratna Ashani T. , Schug Zachary T. , Chen Qing
Published: April 2023

Figure S1 shows the generation of brain metastasis models.
Table S4 from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Table S4: KEGG Metabolism Gene Sets. List of 70 gene sets selected from the MSigDB KEGG database used to metabolically profile MBMs, ECMs, and primary tumors.
Table S3 from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Table S3: Pathway Analysis of Intracranial and Subcutaneous Melanoma Xenografts. Results of EGSEA analyses of ICr (n=3) vs. SQ (n=3) tumors of 4 melanoma cell lines implanted into CD-1 nude mice. RNA-seq data were processed via Xenome to filter out contaminating mouse stromal signatures. "Gene Set" lists the database (MSigDB) and the specific collection of gene sets (Hallmark and c2: Curated) included in each analysis. Median rank was used to order the top 20 gene sets in each analysis. All gene sets listed have an adjusted p-value<0.001. Gene sets up-regulated in ICr tumors are shown in red. Gene sets down-regulated in ICr tumors are shown in blue. Of note, we identified no upregulation of nervous system gene sets in ICr xenografts and instead observed highly significant upregulation of numerous OXPHOS-related gene sets.
Table S2 from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Table S2: Differentially Expressed Genes in Patient-Matched Melanoma Brain and Extracranial Metastases. Comprehensive list of the 494 differentially expressed genes (adjusted p<0.05) between 35 MBMs and 42 patient-matched ECMs (from 29 patients). Results acquired via EdgeR-limma-voom R packages. Gene names are listed according to HGNC nomenclature. "Log2FC" is the estimate of the log2-fold-change of the gene in MBMs relative to patient-matched ECMs. "AveExr" is the average log2-expression for the gene across all samples. "t" is the moderated t-statistic. "P.Value" is the nominal p-value. "Adj.P.Val" is the p-value corrected for multiple testing via Benjamini-Hochberg procedure. "B" is the log-odds that the gene is differentially expressed.
Table S1 from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Table S1: Clinical Characteristics of Melanoma Brain Metastases, Extracranial Metastases, and Primary Tumors. Tab 1. Clinical data for the MBMs and ECMs from melanoma patients utilized in this manuscript. Tab 2. Clinical data for primary melanomas from melanoma patients utilized in this manuscript.
Supplementary Materials from Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases
Authors: Fischer Grant M. , Jalali Ali , Kircher David A. , Lee Won-Chul , McQuade Jennifer L. , Haydu Lauren E. , Joon Aron Y. , Reuben Alexandre , de Macedo Mariana P. , Carapeto Fernando C. L. , Yang Chendong , Srivastava Anuj , Ambati Chandrashekar R. , Sreekumar Arun , Hudgens Courtney W. , Knighton Barbara , Deng Wanleng , Ferguson Sherise D. , Tawbi Hussein A. , Glitza Isabella C. , Gershenwald Jeffrey E. , Vashisht Gopal Y. N. , Hwu Patrick , Huse Jason T. , Wargo Jennifer A. , Futreal P. Andrew , Putluri Nagireddy , Lazar Alexander J. , DeBerardinis Ralph J. , Marszalek Joseph R. , Zhang Jianjun , Holmen Sheri L. , Tetzlaff Michael T. , Davies Michael A.
Published: April 2023

Supplemental Methods; Supplemental References
Figure S7 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S7
Figure S6 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S6
Figure S5 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S5
Figure S4 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S4
Figure S2 from β-Catenin Activation Promotes Immune Escape and Resistance to Anti–PD-1 Therapy in Hepatocellular Carcinoma
Authors: Ruiz de Galarreta Marina , Bresnahan Erin , Molina-Sánchez Pedro , Lindblad Katherine E. , Maier Barbara , Sia Daniela , Puigvehi Marc , Miguela Verónica , Casanova-Acebes María , Dhainaut Maxime , Villacorta-Martin Carlos , Singhi Aatur D. , Moghe Akshata , von Felden Johann , Tal Grinspan Lauren , Wang Shuang , Kamphorst Alice O. , Monga Satdarshan P. , Brown Brian D. , Villanueva Augusto , Llovet Josep M. , Merad Miriam , Lujambio Amaia
Published: April 2023

Figure S2
Supplementary Data from Genetically Defined, Syngeneic Organoid Platform for Developing Combination Therapies for Ovarian Cancer
Authors: Zhang Shuang , Iyer Sonia , Ran Hao , Dolgalev Igor , Gu Shengqing , Wei Wei , Foster Connor J.R. , Loomis Cynthia A. , Olvera Narciso , Dao Fanny , Levine Douglas A. , Weinberg Robert A. , Neel Benjamin G.
Published: April 2023

Supplementary data includes suppl methods, FigS1-8ï¼Œ Table S1-3
Figure S3 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 3
Figure S2 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 2
Supplementary Video1 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 1 week after IGO transplantation
Supplementary Table S1-S4 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

Supplementary Table S1 Survival times of IGO and OGO mice Supplementary Table S2 Characteristics of patient-derived organoids, including KRAS, TP53, SMAD4, CDKN2A mutation status and patient stage Supplementary Table S3 Summary of Survival Data, including engraftment rate, mean survival, metastatic frequency Supplementary Table S4 Primers for quantitative PCR
Supplementary Method SM1 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

Method Used to Define the Thresholds for Fast- and Slow-Progressing IGO-Derived Tumors
Supplementary Figure S8 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

KRAS activation promotes a more basal-like phenotype in vivo.
Supplementary Figure S6 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

Comparison of invasive and intraductal regions of tumors derived from IGO transplants of Slow-progressor organoids
Supplementary Figure S4 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

PDAC molecular subtype is a plastic phenotype that can be influenced by stromal interactions.
Supplementary Figure S1 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

Comparison of IGO- and OGO-derived lesions