bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure and Table Legends from Metastatic Tumor-in-a-Dish, a Novel Multicellular Organoid to Study Lung Colonization and Predict Therapeutic Response
Authors: Ramamoorthy Prabhu , Thomas Sufi Mary , Kaushik Gaurav , Subramaniam Dharmalingam , Chastain Katherine M. , Dhar Animesh , Tawfik Ossama , Kasi Anup , Sun Weijing , Ramalingam Satish , Gunewardena Sumedha , Umar Shahid , Mammen Joshua M. , Padhye Subhash B. , Weir Scott J. , Jensen Roy A. , Sittampalam G. Sitta , Anant Shrikant
Published: March 2023

This file has the legends for all the supplementary figures and tables
Supplementary Fig S5 Table S3 from Metastatic Tumor-in-a-Dish, a Novel Multicellular Organoid to Study Lung Colonization and Predict Therapeutic Response
Authors: Ramamoorthy Prabhu , Thomas Sufi Mary , Kaushik Gaurav , Subramaniam Dharmalingam , Chastain Katherine M. , Dhar Animesh , Tawfik Ossama , Kasi Anup , Sun Weijing , Ramalingam Satish , Gunewardena Sumedha , Umar Shahid , Mammen Joshua M. , Padhye Subhash B. , Weir Scott J. , Jensen Roy A. , Sittampalam G. Sitta , Anant Shrikant
Published: March 2023

Characterization of primary cancer cells
Table S1 from ERRα Expression in Bone Metastases Leads to an Exacerbated Antitumor Immune Response
Authors: Bouchet Mathilde , Lainé Alexandra , Boyault Cyril , Proponnet-Guerault Mathilde , Meugnier Emmanuelle , Bouazza Lamia , Kan Casina W.S. , Geraci Sandra , El-Moghrabi Soumaya , Hernandez-Vargas Hector , Benetollo Claire , Yoshiko Yuji , Duterque-Coquillaud Martine , Clézardin Philippe , Marie Julien C. , Bonnelye Edith
Published: March 2023

Human and mouse primer sequences and PCR cycling and ChIP conditions used.
Video S1 from lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays
Authors: Zheng Yueyuan , Xu Qingxian , Liu Mengni , Hu Huanjing , Xie Yubin , Zuo Zhixiang , Ren Jian
Published: March 2023

This file is the video showing the web interface and usage of lnCAR.
Supplementary Table S8 from lnCAR: A Comprehensive Resource for lncRNAs from Cancer Arrays
Authors: Zheng Yueyuan , Xu Qingxian , Liu Mengni , Hu Huanjing , Xie Yubin , Zuo Zhixiang , Ren Jian
Published: March 2023

Table S8 Comparison of lnCAR with other lncRNA resources
Figure S6 from EZH2 Inhibitor GSK126 Suppresses Antitumor Immunity by Driving Production of Myeloid-Derived Suppressor Cells
Authors: Huang Shuo , Wang Zhongyu , Zhou Jie , Huang Jiani , Zhou Li , Luo Jing , Wan Yisong Y. , Long Haixia , Zhu Bo
Published: March 2023

Effect of GSK126 plus gemcitabine/5Fu treatment on anti-tumor immunity
Figure S5 from EZH2 Inhibitor GSK126 Suppresses Antitumor Immunity by Driving Production of Myeloid-Derived Suppressor Cells
Authors: Huang Shuo , Wang Zhongyu , Zhou Jie , Huang Jiani , Zhou Li , Luo Jing , Wan Yisong Y. , Long Haixia , Zhu Bo
Published: March 2023

Effect of GSK126 plus Gr-1 antibody treatment on the tumor
Figure S4 from EZH2 Inhibitor GSK126 Suppresses Antitumor Immunity by Driving Production of Myeloid-Derived Suppressor Cells
Authors: Huang Shuo , Wang Zhongyu , Zhou Jie , Huang Jiani , Zhou Li , Luo Jing , Wan Yisong Y. , Long Haixia , Zhu Bo
Published: March 2023

GSK126 results in accumulation of MDSCs in the TME
Supplementary Figure 1 from ICOS Is an Indicator of T-cell–Mediated Response to Cancer Immunotherapy
Authors: Xiao Zunyu , Mayer Aaron T. , Nobashi Tomomi W. , Gambhir Sanjiv S.
Published: March 2023

Figure S1: Stability of 89Zr-DFO-ICOS mAb in PBS and serum
Supplementary Data from p53-Suppressed Oncogene TET1 Prevents Cellular Aging in Lung Cancer
Authors: Filipczak Piotr T. , Leng Shuguang , Tellez Carmen S. , Do Kieu C. , Grimes Marcie J. , Thomas Cynthia L. , Walton-Filipczak Stephanie R. , Picchi Maria A. , Belinsky Steven A.
Published: March 2023

Fig. S2. Growth of WT p53 cells after TET1 KD.
Supplementary Data from p53-Suppressed Oncogene TET1 Prevents Cellular Aging in Lung Cancer
Authors: Filipczak Piotr T. , Leng Shuguang , Tellez Carmen S. , Do Kieu C. , Grimes Marcie J. , Thomas Cynthia L. , Walton-Filipczak Stephanie R. , Picchi Maria A. , Belinsky Steven A.
Published: March 2023

Fig. S5. Effect of TET1 depletion in H1299 cells on histone methyltransferases and lysine methylation.
Supplementary Data from p53-Suppressed Oncogene TET1 Prevents Cellular Aging in Lung Cancer
Authors: Filipczak Piotr T. , Leng Shuguang , Tellez Carmen S. , Do Kieu C. , Grimes Marcie J. , Thomas Cynthia L. , Walton-Filipczak Stephanie R. , Picchi Maria A. , Belinsky Steven A.
Published: March 2023

Supplementary methods, figure legends and tables
Supplementary Table 1 from Shaping Chromatin States in Prostate Cancer by Pioneer Transcription Factors
Authors: Hankey William , Chen Zhong , Wang Qianben
Published: March 2023

Supplementary Table 1
Supplementary Table 1 from Nod1 Imprints Inflammatory and Carcinogenic Responses toward the Gastric Pathogen Helicobacter pylori
Authors: Suarez Giovanni , Romero-Gallo Judith , Piazuelo Maria B. , Sierra Johanna C. , Delgado Alberto G. , Washington M. Kay , Shah Shailja C. , Wilson Keith T. , Peek Richard M.
Published: March 2023

Number and gender of mice used in this study.
Supplementary Figures from Golgi-Localized PAQR4 Mediates Antiapoptotic Ceramidase Activity in Breast Cancer
Authors: Pedersen Line , Panahandeh Pouda , Siraji Muntequa I. , Knappskog Stian , Lønning Per Eystein , Gordillo Ruth , Scherer Philipp E. , Molven Anders , Teigen Knut , Halberg Nils
Published: March 2023

Supplementary Figures and legends
Supplemental Video from Golgi-Localized PAQR4 Mediates Antiapoptotic Ceramidase Activity in Breast Cancer
Authors: Pedersen Line , Panahandeh Pouda , Siraji Muntequa I. , Knappskog Stian , Lønning Per Eystein , Gordillo Ruth , Scherer Philipp E. , Molven Anders , Teigen Knut , Halberg Nils
Published: March 2023

Supplemental Video
Supplementary Table 2 from MDH1 and MPP7 Regulate Autophagy in Pancreatic Ductal Adenocarcinoma
Authors: New Maria , Van Acker Tim , Sakamaki Jun-Ichi , Jiang Ming , Saunders Rebecca E. , Long Jaclyn , Wang Victoria M.-Y. , Behrens Axel , Cerveira Joana , Sudhakar Padhmanand , Korcsmaros Tamas , Jefferies Harold B.J. , Ryan Kevin M. , Howell Michael , Tooze Sharon A.
Published: March 2023

Deconvolution data and network analysis for top 200 hits
Supplementary Table 1 from MDH1 and MPP7 Regulate Autophagy in Pancreatic Ductal Adenocarcinoma
Authors: New Maria , Van Acker Tim , Sakamaki Jun-Ichi , Jiang Ming , Saunders Rebecca E. , Long Jaclyn , Wang Victoria M.-Y. , Behrens Axel , Cerveira Joana , Sudhakar Padhmanand , Korcsmaros Tamas , Jefferies Harold B.J. , Ryan Kevin M. , Howell Michael , Tooze Sharon A.
Published: March 2023

LC3 parameters for top 200 decreasers
Supplementary figure 3 from RIPK3-Induced Inflammation by I-MDSCs Promotes Intestinal Tumors
Authors: Jayakumar Asha , Bothwell Alfred L.M.
Published: March 2023

Surface marker analysis of Apc min/+ and MC38 tumor myeloid cells
Supplementary Table 1 from Oncogene-Induced Senescence Limits the Progression of Pancreatic Neoplasia through Production of Activin A
Authors: Zhao Yajie , Wu Zhichong , Chanal Marie , Guillaumond Fabienne , Goehrig Delphine , Bachy Sophie , Principe Moitza , Ziverec Audrey , Flaman Jean-Michel , Collin Guillaume , Tomasini Richard , Pasternack Arja , Ritvos Olli , Vasseur Sophie , Bernard David , Hennino Ana , Bertolino Philippe
Published: March 2023

Supplemental Table 1. List of used Primary antibodies.
Supplementary Table S2 from LncSpA: LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues
Authors: Lv Dezhong , Xu Kang , Jin Xiyun , Li Junyi , Shi Yuchen , Zhang Mengying , Jin Xiaoyan , Li Yongsheng , Xu Juan , Li Xia
Published: March 2023

The annotation entry statistics for TE lncRNAs.
Supplementary Figures S1-S7 from MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors
Authors: Howard Thomas P. , Arnoff Taylor E. , Song Melinda R. , Giacomelli Andrew O. , Wang Xiaofeng , Hong Andrew L. , Dharia Neekesh V. , Wang Su , Vazquez Francisca , Pham Minh-Tam , Morgan Ann M. , Wachter Franziska , Bird Gregory H. , Kugener Guillaume , Oberlick Elaine M. , Rees Matthew G. , Tiv Hong L. , Hwang Justin H. , Walsh Katherine H. , Cook April , Krill-Burger John M. , Tsherniak Aviad , Gokhale Prafulla C. , Park Peter J. , Stegmaier Kimberly , Walensky Loren D. , Hahn William C. , Roberts Charles W.M.
Published: March 2023

S1: RNAi data and CRISPR-Cas9 data divided by p53 status. S2: Expression of MDM2 and MDM4 in MRT and control cell lines. S3: CRISPR-Cas9 mediated inactivation of TP53 in MRT cell lines. S4: Immunoblots for p53 pathway activation upon MDM2 and MDM2/4 inhibition in MRT and control cell lines. S5: Cell counts, flow cytometry, and senescence assays in MRT cells following MDM2 and MDM2/4 inhibition. S6: Characterization of MRT cells expressing SMARCB1 or p16. S7: MRT xenograft growth characteristics and pharmacodynamic responses.
Supplementary Figure 3 from Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue
Authors: Ostmeyer Jared , Christley Scott , Toby Inimary T. , Cowell Lindsay G.
Published: March 2023

model weights for breast cancer model
Supplementary cfDNA Mutation Dataset from Drug Sensitivity and Allele Specificity of First-Line Osimertinib Resistance EGFR Mutations
Authors: Starrett Jacqueline H. , Guernet Alexis A. , Cuomo Maria Emanuela , Poels Kamrine E. , van Alderwerelt van Rosenburgh Iris K. , Nagelberg Amy , Farnsworth Dylan , Price Kristin S. , Khan Hina , Ashtekar Kumar Dilip , Gaefele Mmaserame , Ayeni Deborah , Stewart Tyler F. , Kuhlmann Alexandra , Kaech Susan M. , Unni Arun M. , Homer Robert , Lockwood William W. , Michor Franziska , Goldberg Sarah B. , Lemmon Mark A. , Smith Paul D. , Cross Darren A.E. , Politi Katerina
Published: March 2023

Cell-free DNA Mutation Dataset
Supplementary Table S1 from A Feed-Forward Mechanosignaling Loop Confers Resistance to Therapies Targeting the MAPK Pathway in BRAF-Mutant Melanoma
Authors: Girard Christophe A. , Lecacheur Margaux , Ben Jouira Rania , Berestjuk Ilona , Diazzi Serena , Prod'homme Virginie , Mallavialle Aude , Larbret Frédéric , Gesson Maéva , Schaub Sébastien , Pisano Sabrina , Audebert Stéphane , Mari Bernard , Gaggioli Cédric , Leucci Eleonora , Marine Jean-Christophe , Deckert Marcel , Tartare-Deckert Sophie
Published: March 2023

The table displays MS analysis of the matrisome between parental and BRAFi resistant melanoma cells
Figures S2 and S3 from A Feed-Forward Mechanosignaling Loop Confers Resistance to Therapies Targeting the MAPK Pathway in BRAF-Mutant Melanoma
Authors: Girard Christophe A. , Lecacheur Margaux , Ben Jouira Rania , Berestjuk Ilona , Diazzi Serena , Prod'homme Virginie , Mallavialle Aude , Larbret Frédéric , Gesson Maéva , Schaub Sébastien , Pisano Sabrina , Audebert Stéphane , Mari Bernard , Gaggioli Cédric , Leucci Eleonora , Marine Jean-Christophe , Deckert Marcel , Tartare-Deckert Sophie
Published: March 2023

Morphology and focal adhesions complexes of parental and BRAFi-resistant cells on hydrogels of various stiffness
Figure S7 from A Feed-Forward Mechanosignaling Loop Confers Resistance to Therapies Targeting the MAPK Pathway in BRAF-Mutant Melanoma
Authors: Girard Christophe A. , Lecacheur Margaux , Ben Jouira Rania , Berestjuk Ilona , Diazzi Serena , Prod'homme Virginie , Mallavialle Aude , Larbret Frédéric , Gesson Maéva , Schaub Sébastien , Pisano Sabrina , Audebert Stéphane , Mari Bernard , Gaggioli Cédric , Leucci Eleonora , Marine Jean-Christophe , Deckert Marcel , Tartare-Deckert Sophie
Published: March 2023

Drug-protective effect of M229R melanoma cells-derived ECM
Supplementary Figures from Truncated ASPP2 Drives Initiation and Progression of Invasive Lobular Carcinoma via Distinct Mechanisms
Authors: Schipper Koen , Drenth Anne Paulien , van der Burg Eline , Cornelissen Samuel , Klarenbeek Sjoerd , Nethe Micha , Jonkers Jos
Published: March 2023

Supplementary Figures 1-7
Supplementary Video 8 from Pattern of Invasion in Human Pancreatic Cancer Organoids Is Associated with Loss of SMAD4 and Clinical Outcome
Authors: Huang Wenjie , Navarro-Serer Bernat , Jeong Yea Ji , Chianchiano Peter , Xia Limin , Luchini Claudio , Veronese Nicola , Dowiak Cameron , Ng Tammy , Trujillo Maria A. , Huang Bo , Pflüger Michael J. , Macgregor-Das Anne M. , Lionheart Gemma , Jones Danielle , Fujikura Kohei , Nguyen-Ngoc Kim-Vy , Neumann Neil M. , Groot Vincent P. , Hasanain Alina , van Oosten A. Floortje , Fischer Sandra E. , Gallinger Steven , Singhi Aatur D. , Zureikat Amer H. , Brand Randall E. , Gaida Matthias M. , Heinrich Stefan , Burkhart Richard A. , He Jin , Wolfgang Christopher L. , Goggins Michael G. , Thompson Elizabeth D. , Roberts Nicholas J. , Ewald Andrew J. , Wood Laura D.
Published: March 2023

Supplementary Video 8. Time-lapse analysis of SMAD4-mutant PDAC organoids: Dox+TGFβ+.
Supplementary Video 7 from Pattern of Invasion in Human Pancreatic Cancer Organoids Is Associated with Loss of SMAD4 and Clinical Outcome
Authors: Huang Wenjie , Navarro-Serer Bernat , Jeong Yea Ji , Chianchiano Peter , Xia Limin , Luchini Claudio , Veronese Nicola , Dowiak Cameron , Ng Tammy , Trujillo Maria A. , Huang Bo , Pflüger Michael J. , Macgregor-Das Anne M. , Lionheart Gemma , Jones Danielle , Fujikura Kohei , Nguyen-Ngoc Kim-Vy , Neumann Neil M. , Groot Vincent P. , Hasanain Alina , van Oosten A. Floortje , Fischer Sandra E. , Gallinger Steven , Singhi Aatur D. , Zureikat Amer H. , Brand Randall E. , Gaida Matthias M. , Heinrich Stefan , Burkhart Richard A. , He Jin , Wolfgang Christopher L. , Goggins Michael G. , Thompson Elizabeth D. , Roberts Nicholas J. , Ewald Andrew J. , Wood Laura D.
Published: March 2023

Supplementary Video 7. Time-lapse analysis of SMAD4-mutant PDAC organoids: Dox-TGFβ+.
Supplemental Figures from MEF2c-Dependent Downregulation of Myocilin Mediates Cancer-Induced Muscle Wasting and Associates with Cachexia in Patients with Cancer
Authors: Judge Sarah M. , Deyhle Michael R. , Neyroud Daria , Nosacka Rachel L. , D'Lugos Andrew C. , Cameron Miles E. , Vohra Ravneet S. , Smuder Ashley J. , Roberts Brandon M. , Callaway Chandler S. , Underwood Patrick W. , Chrzanowski Stephen M. , Batra Abhinandan , Murphy Meghan E. , Heaven Jonathan D. , Walter Glenn A. , Trevino Jose G. , Judge Andrew R.
Published: March 2023

Figures S1-S9
Supplementary Video 4 from Pattern of Invasion in Human Pancreatic Cancer Organoids Is Associated with Loss of SMAD4 and Clinical Outcome
Authors: Huang Wenjie , Navarro-Serer Bernat , Jeong Yea Ji , Chianchiano Peter , Xia Limin , Luchini Claudio , Veronese Nicola , Dowiak Cameron , Ng Tammy , Trujillo Maria A. , Huang Bo , Pflüger Michael J. , Macgregor-Das Anne M. , Lionheart Gemma , Jones Danielle , Fujikura Kohei , Nguyen-Ngoc Kim-Vy , Neumann Neil M. , Groot Vincent P. , Hasanain Alina , van Oosten A. Floortje , Fischer Sandra E. , Gallinger Steven , Singhi Aatur D. , Zureikat Amer H. , Brand Randall E. , Gaida Matthias M. , Heinrich Stefan , Burkhart Richard A. , He Jin , Wolfgang Christopher L. , Goggins Michael G. , Thompson Elizabeth D. , Roberts Nicholas J. , Ewald Andrew J. , Wood Laura D.
Published: March 2023

Supplementary Video 4. Collective invasion in PDAC organoid cultured in collagen I.
Supplementary Table 1 from Fibroblasts from Distinct Pancreatic Pathologies Exhibit Disease-Specific Properties
Authors: Barrera Lawrence N. , Evans Anthony , Lane Brian , Brumskill Sarah , Oldfield Frances E. , Campbell Fiona , Andrews Timothy , Lu Zipeng , Perez-Mancera Pedro A. , Liloglou Triantafillos , Ashworth Milton , Jalali Mehdi , Dawson Rebecca , Nunes Quentin , Phillips Phoebe A. , Timms John F. , Halloran Christopher , Greenhalf William , Neoptolemos John P. , Costello Eithne
Published: March 2023

Patient characteristics of samples used for discovery and independent validation.
Supplementary Data 3 from An LTR Retrotransposon-Derived Long Noncoding RNA lncMER52A Promotes Hepatocellular Carcinoma Progression by Binding p120-Catenin
Authors: Wu Yangjun , Zhao Yiming , Huan Lin , Zhao Jingjing , Zhou Yuqiang , Xu Linguo , Hu Zhixiang , Liu Yizhe , Chen Zhiao , Wang Lu , Huang Shenglin , He Xianghuo , Liang Linhui
Published: March 2023

Differentiated expressed genes after lncMER52A knockdown.
Supplementary Table 1 from CoA Synthase (COASY) Mediates Radiation Resistance via PI3K Signaling in Rectal Cancer
Authors: Ferrandon Sylvain , DeVecchio Jennifer , Duraes Leonardo , Chouhan Hanumant , Karagkounis Georgios , Davenport Jacqueline , Orloff Matthew , Liska David , Kalady Matthew F.
Published: March 2023

List of 660 differentially expressed genes identified comparing COASYhigh and COASYlow pretreatment rectal adenocarcinoma patient samples.
Table S3 from Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology
Authors: Failmezger Henrik , Muralidhar Sathya , Rullan Antonio , de Andrea Carlos E. , Sahai Erik , Yuan Yinyin
Published: March 2023

Genes identified by CNx to underpin stromal clustering
Supplementary Fig S2 from Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology
Authors: Failmezger Henrik , Muralidhar Sathya , Rullan Antonio , de Andrea Carlos E. , Sahai Erik , Yuan Yinyin
Published: March 2023

Figure S2
Supplementary Data Fig. S7 from Lymphoma Angiogenesis Is Orchestrated by Noncanonical Signaling Pathways
Authors: Gloger Marleen , Menzel Lutz , Grau Michael , Vion Anne-Clemence , Anagnostopoulos Ioannis , Zapukhlyak Myroslav , Gerlach Kerstin , Kammertöns Thomas , Hehlgans Thomas , Zschummel Maria , Lenz Georg , Gerhardt Holger , Höpken Uta E. , Rehm Armin
Published: March 2023

Solid tumors respond to VEGFR-2 inhibition
Supplementary Table S4 from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance
Authors: Chandra Ankush , Jahangiri Arman , Chen William , Nguyen Alan T. , Yagnik Garima , Pereira Matheus P. , Jain Saket , Garcia Joseph H. , Shah Sumedh S. , Wadhwa Harsh , Joshi Rushikesh S. , Weiss Jacob , Wolf Kayla J. , Lin Jung-Ming G. , Müller Sören , Rick Jonathan W. , Diaz Aaron A. , Gilbert Luke A. , Kumar Sanjay , Aghi Manish K.
Published: March 2023

Supplementary Table S4 has primer sequences used to assess connexin expression
Supplementary Table S3 from Clonal ZEB1-Driven Mesenchymal Transition Promotes Targetable Oncologic Antiangiogenic Therapy Resistance
Authors: Chandra Ankush , Jahangiri Arman , Chen William , Nguyen Alan T. , Yagnik Garima , Pereira Matheus P. , Jain Saket , Garcia Joseph H. , Shah Sumedh S. , Wadhwa Harsh , Joshi Rushikesh S. , Weiss Jacob , Wolf Kayla J. , Lin Jung-Ming G. , Müller Sören , Rick Jonathan W. , Diaz Aaron A. , Gilbert Luke A. , Kumar Sanjay , Aghi Manish K.
Published: March 2023

Supplementary Table S3 has primer sequences used to validate GBM subtype genes
Materials and Methods from A Sox2:miR-486-5p Axis Regulates Survival of GBM Cells by Inhibiting Tumor Suppressor Networks
Authors: Lopez-Bertoni Hernando , Kotchetkov Ivan S. , Mihelson Nicole , Lal Bachchu , Rui Yuan , Ames Heather , Lugo-Fagundo Maria , Guerrero-Cazares Hugo , Quiñones-Hinojosa Alfredo , Green Jordan J. , Laterra John
Published: March 2023

File containing methods used for polymer synthesis, Luciferase Reporter Assay, qRT-PCR and miRNA expression, Chromatin Immunoprecipitation, Lentivirus Generation, Cell Transduction, Immunoblotting
Supplementary Data from Risk SNP-Mediated Enhancer–Promoter Interaction Drives Colorectal Cancer through Both FADS2 and AP002754.2
Authors: Tian Jianbo , Lou Jiao , Cai Yimin , Rao Meilin , Lu Zequn , Zhu Ying , Zou Danyi , Peng Xiating , Wang Haoxue , Zhang Ming , Niu Siyuan , Li Yue , Zhong Rong , Chang Jiang , Miao Xiaoping
Published: March 2023

Including supplementary methods, 8 figures and 5 tables
Supplementary Table 4 from A Proof of Concept for Biomarker-Guided Targeted Therapy against Ovarian Cancer Based on Patient-Derived Tumor Xenografts
Authors: Palmer Adam C. , Plana Deborah , Gao Hui , Korn Joshua M. , Yang Guizhi , Green John , Zhang Xiamei , Velazquez Roberto , McLaughlin Margaret E. , Ruddy David A. , Kowal Colleen , Muszynski Julie , Bullock Caroline , Rivera Stacy , Rakiec Daniel P. , Elliott GiNell , Fordjour Paul , Meyer Ronald , Loo Alice , Kurth Esther , Engelman Jeffrey A. , Bitter Hans , Sellers William R. , Williams Juliet A. , Sorger Peter K.
Published: March 2023

Mean tumor volume change difference between best monotherapy and each of 9 combinations. Hazard ratio for combination versus independent action simulation PFS.
Supplementary Table 1 from Molecular Profiles of Matched Primary and Metastatic Tumor Samples Support a Linear Evolutionary Model of Breast Cancer
Authors: Chen Runpu , Goodison Steve , Sun Yijun
Published: March 2023

Table S1: Patient clinical information
Table S4 from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer
Authors: Dai Chen , Charlestin Verodia , Wang Man , Walker Zachary T. , Miranda-Vergara Maria Cristina , Facchine Beth A. , Wu Junmin , Kaliney William J. , Dovichi Norman J. , Li Jun , Littlepage Laurie E.
Published: March 2023

Raw data and heat maps for metabolomics of cell lines and tumors.
Table S3 from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer
Authors: Dai Chen , Charlestin Verodia , Wang Man , Walker Zachary T. , Miranda-Vergara Maria Cristina , Facchine Beth A. , Wu Junmin , Kaliney William J. , Dovichi Norman J. , Li Jun , Littlepage Laurie E.
Published: March 2023

Genes highly correlated with AQP7 gene expression in human breast cancer patient tumor tissue.
Supplementary Figure S6 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Role of metabolic pathways imparting gemcitabine resistance in pancreatic cancer
Supplementary Figure S4 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Effects of NRF2 activation on metabolomics
Figure S2 from Aquaporin-7 Regulates the Response to Cellular Stress in Breast Cancer
Authors: Dai Chen , Charlestin Verodia , Wang Man , Walker Zachary T. , Miranda-Vergara Maria Cristina , Facchine Beth A. , Wu Junmin , Kaliney William J. , Dovichi Norman J. , Li Jun , Littlepage Laurie E.
Published: March 2023

Aquaporin-7 dependent analysis of metabolomics and complex lipid profiling in cell lines and tumors.
Supplementary Figure S3 from Undermining Glutaminolysis Bolsters Chemotherapy While NRF2 Promotes Chemoresistance in KRAS-Driven Pancreatic Cancers
Authors: Mukhopadhyay Suman , Goswami Debanjan , Adiseshaiah Pavan P. , Burgan William , Yi Ming , Guerin Theresa M. , Kozlov Serguei V. , Nissley Dwight V. , McCormick Frank
Published: March 2023

Knockdown and over-expression of NRF2 in PDAC cells
Supplementary Data from Wnt-Induced Stabilization of KDM4C Is Required for Wnt/β-Catenin Target Gene Expression and Glioblastoma Tumorigenesis
Authors: Chen Yaohui , Fang Runping , Yue Chen , Chang Guoqiang , Li Peng , Guo Qing , Wang Jing , Zhou Aidong , Zhang Sicong , Fuller Gregory N. , Shi Xiaobing , Huang Suyun
Published: March 2023

The Supplementary Data file contains 8 supplementary figures, 4 supplementary tables and supplementary methods.
Supplemental Data from Loss of Estrogen-Regulated MIR135A1 at 3p21.1 Promotes Tamoxifen Resistance in Breast Cancer
Authors: Zhang Weijie , Wu Mingming , Chong Qing-Yun , Zhang Min , Zhang Xiao , Hu Lan , Zhong Yanghao , Qian Pengxu , Kong Xiangjun , Tan Sheng , Li Gaopeng , Ding Keshuo , Lobie Peter E. , Zhu Tao
Published: March 2023

Supplementary table S1 lists all the sequence of miR-135a mimic, siRNAs, shRNAs, and primers for plasmid construction, ChIP assay, and qRT-PCR used in this study. Supplementary table S2 shows the information of antibodies used in this study. Supplementary table S3 and S4 show the correlation of MIR135A1 deletion and low miR-135a-1 with the clinicopathologic features of breast cancer in the TCGA breast tumors, respectively. Supplementary table S5 lists genes including EMT markers, ERα cofactors and interacting proteins, and predicted miR-135a targets which expression levels negatively correlate with miR-135a in breast tumors. Supplementary figure S1 shows that the copy number of MIR135A1 gene and the expression levels of pri-miR-135a-1 are decreased in breast cancer. Supplementary figure S2 shows that miR-135a is a tumor suppressor gene in T47D and MDA-MB-231 cells and inhibits EMT of breast cancer cells. Supplementary figure S3 shows that miR-135a impairs the in vivo tumor growth. Supplementary figure S4 shows that the transcription of MIR135A1 positively correlates with E2-ERα axis. Supplementary figure S5 shows that miR-135a modulates the estrogen independent growth and the response to tamoxifen in ERα+ breast cancer cells. Supplementary figure S6 shows the validation of miR-135a targets in breast cancer cells. Supplementary figure S7 shows that miR-135a modulates ERα-ERK-AKT crosstalk.
Table S4 from Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma
Authors: Mitra Sanhita , Muralidharan Somsundar Veppil , Di Marco Mirco , Juvvuna Prasanna Kumar , Kosalai Subazini Thankaswamy , Reischl Silke , Jachimowicz Daniel , Subhash Santhilal , Raimondi Ivan , Kurian Leo , Huarte Maite , Kogner Per , Fischer Matthias , Johnsen John Inge , Mondal Tanmoy , Kanduri Chandrasekhar
Published: March 2023

Details of NB tumors with NBAT1 expression, p53 localization.
Supplementary Figures 1-6, Supplementary Materials and Methods from Downregulation of miR-223 Expression Is an Early Event during Mammary Transformation and Confers Resistance to CDK4/6 Inhibitors in Luminal Breast Cancer
Authors: Citron Francesca , Segatto Ilenia , Vinciguerra Gian Luca Rampioni , Musco Lorena , Russo Francesca , Mungo Giorgia , D'Andrea Sara , Mattevi Maria Chiara , Perin Tiziana , Schiappacassi Monica , Massarut Samuele , Marchini Cristina , Amici Augusto , Vecchione Andrea , Baldassarre Gustavo , Belletti Barbara
Published: March 2023

Supplementary Information, Methods and Figures. Supplementary Figure 1. Loss of miR-223 does not alter the murine mammary gland architecture; Supplementary Figure 2. miR-223 KO mice do not display any proliferative advantage during â^†16HER2-driven mammary tumorigenesis; Supplementary Figure 3. miR-223 WT and KO â^†16HER2 tumor-derived mammary epithelial cells (mMECs) display comparable tumorigenic potential; Supplementary Figure 4. miR-223 partially counteracts HER2-driven BC cell proliferation and 3D-organization; Supplementary Figure 5. miR-223 is rapidly down-modulated during cell transformation; Supplementary Figure 6. miR-223 is upregulated in response to anti-proliferative stimuli
Table S3 from Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma
Authors: Mitra Sanhita , Muralidharan Somsundar Veppil , Di Marco Mirco , Juvvuna Prasanna Kumar , Kosalai Subazini Thankaswamy , Reischl Silke , Jachimowicz Daniel , Subhash Santhilal , Raimondi Ivan , Kurian Leo , Huarte Maite , Kogner Per , Fischer Matthias , Johnsen John Inge , Mondal Tanmoy , Kanduri Chandrasekhar
Published: March 2023

GSEA enriched pathways and list of enriched p53 pathway genes in nutlin-3a treated control and NBAT1 depleted SH-SY5Y cells detected by RNA-seq.
Supplementary Data from Mathematical Modeling Provides Evidence for Niche Competition in Human AML and Serves as a Tool to Improve Risk Stratification
Authors: Stiehl Thomas , Wang Wenwen , Lutz Christoph , Marciniak-Czochra Anna
Published: March 2023

Supplementary Methods, Supplementary Figures 1-7 and Supplementary Tables 1-3.
Supplementary Materials and Methods from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Supplementary materials and methods
Table S1 from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

Clinical and pathologic features of the chRCC cohort
Supplementary file captions from Decreased Mitochondrial DNA Content Drives OXPHOS Dysregulation in Chromophobe Renal Cell Carcinoma
Authors: Xiao Yi , Clima Rosanna , Busch Jonas , Rabien Anja , Kilic Ergin , Villegas Sonia L. , Timmermann Bernd , Attimonelli Marcella , Jung Klaus , Meierhofer David
Published: March 2023

Supplementary file captions
Supplemental Movie 6 from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Movie of A375 control cells in the tail over the course of 12 hours following injection.
Supplemental table 4 from IL2RA Promotes Aggressiveness and Stem Cell–Related Properties of Acute Myeloid Leukemia
Authors: Nguyen Chi Huu , Schlerka Angela , Grandits Alexander M. , Koller Elisabeth , van der Kouwe Emiel , Vassiliou George S. , Staber Philipp B. , Heller Gerwin , Wieser Rotraud
Published: March 2023

Supplemental Table 4 shows the effect of hIL2RA antibody on the relative abundance of different progenitor populations among healthy human BM cells.
Supplemental table 2 from IL2RA Promotes Aggressiveness and Stem Cell–Related Properties of Acute Myeloid Leukemia
Authors: Nguyen Chi Huu , Schlerka Angela , Grandits Alexander M. , Koller Elisabeth , van der Kouwe Emiel , Vassiliou George S. , Staber Philipp B. , Heller Gerwin , Wieser Rotraud
Published: March 2023

Supplemental Table 2 shows genes whose expression correlated (Rho >0.4 or <-0.4) with that of IL2RA in 177 AML, and pathways enriched among genes whose expression correlated with that of IL2RA in the TCGA_LAML data set (Metacore).
Supplemental information from IL2RA Promotes Aggressiveness and Stem Cell–Related Properties of Acute Myeloid Leukemia
Authors: Nguyen Chi Huu , Schlerka Angela , Grandits Alexander M. , Koller Elisabeth , van der Kouwe Emiel , Vassiliou George S. , Staber Philipp B. , Heller Gerwin , Wieser Rotraud
Published: March 2023

Supplemental information shows Supplemental methods, Supplemental Table 1, 3, Supplemental Figure Legends, and Supplemental Figures 1 to 8.
Supplementary Data from A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers
Authors: Powers Jacquelyn , Pinto Emilia M. , Barnoud Thibaut , Leung Jessica C. , Martynyuk Tetyana , Kossenkov Andrew V. , Philips Aaron H. , Desai Heena , Hausler Ryan , Kelly Gregory , Le Anh N. , Li Marilyn M. , MacFarland Suzanne P. , Pyle Louise C. , Zelley Kristin , Nathanson Katherine L. , Domchek Susan M. , Slavin Thomas P. , Weitzel Jeffrey N. , Stopfer Jill E. , Garber Judy E. , Joseph Vijai , Offit Kenneth , Dolinsky Jill S. , Gutierrez Stephanie , McGoldrick Kelly , Couch Fergus J. , Levin Brooke , Edelman Morris C. , Levy Carolyn Fein , Spunt Sheri L. , Kriwacki Richard W. , Zambetti Gerard P. , Ribeiro Raul C. , Murphy Maureen E. , Maxwell Kara N.
Published: March 2023

Supplementary Figures 1-4. Supplementary Figure S1: Full Pedigrees from TP53 c.1000G>C;p.G334R clinically ascertained families. Fam ID allows reference to Table 1; Supplementary Figure S2: Constructs encoding p53 wild-type (TP53-WT), p53-R175H (TP53-R175H), and p53-G334R (c.1000G>A and c.1000G>C) were transiently transfected into p53 deficient Saos-2 cells; Supplementary Figure S3: p53 levels after treatment with 10uM cisplatin (CDDP); Supplementary Figure S4: Heatmap showing fold activation of a canonical p53 signature at 24 hours post nutlin with wildtype versus mutant lymphoblastoid cell lines.
Supplementary Data from A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Cancers
Authors: Powers Jacquelyn , Pinto Emilia M. , Barnoud Thibaut , Leung Jessica C. , Martynyuk Tetyana , Kossenkov Andrew V. , Philips Aaron H. , Desai Heena , Hausler Ryan , Kelly Gregory , Le Anh N. , Li Marilyn M. , MacFarland Suzanne P. , Pyle Louise C. , Zelley Kristin , Nathanson Katherine L. , Domchek Susan M. , Slavin Thomas P. , Weitzel Jeffrey N. , Stopfer Jill E. , Garber Judy E. , Joseph Vijai , Offit Kenneth , Dolinsky Jill S. , Gutierrez Stephanie , McGoldrick Kelly , Couch Fergus J. , Levin Brooke , Edelman Morris C. , Levy Carolyn Fein , Spunt Sheri L. , Kriwacki Richard W. , Zambetti Gerard P. , Ribeiro Raul C. , Murphy Maureen E. , Maxwell Kara N.
Published: March 2023

Supplementary Tables S1-S6
Figure S2. from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

Wild-type YAP does not enhance metastasis in zebrafish embryos.
Figure S1 from YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation
Authors: Benjamin David C. , Kang Joon Ho , Hamza Bashar , King Emily M. , Lamar John M. , Manalis Scott R. , Hynes Richard O.
Published: March 2023

YAP-AA enhances metastasis using multiple quantification methods.
Supplementary Table S5 from Integrated Genomic Characterization of the Human Immunome in Cancer
Authors: Li Yongsheng , Burgman Brandon , McGrail Daniel J. , Sun Ming , Qi Dan , Shukla Sachet A. , Wu Erxi , Capasso Anna , Lin Shiaw-Yih , Wu Catherine J. , Eckhardt S. Gail , Mills Gordon B. , Li Bo , Sahni Nidhi , Yi S. Stephen
Published: March 2023

Table S5. Small molecules that alter immunological gene expression signatures.
Supplementary Table S2 from Integrated Genomic Characterization of the Human Immunome in Cancer
Authors: Li Yongsheng , Burgman Brandon , McGrail Daniel J. , Sun Ming , Qi Dan , Shukla Sachet A. , Wu Erxi , Capasso Anna , Lin Shiaw-Yih , Wu Catherine J. , Eckhardt S. Gail , Mills Gordon B. , Li Bo , Sahni Nidhi , Yi S. Stephen
Published: March 2023

Table S2. Immunological gene signatures enriched in multiple cancer types.
Supplementary Figures from Integrated Genomic Characterization of the Human Immunome in Cancer
Authors: Li Yongsheng , Burgman Brandon , McGrail Daniel J. , Sun Ming , Qi Dan , Shukla Sachet A. , Wu Erxi , Capasso Anna , Lin Shiaw-Yih , Wu Catherine J. , Eckhardt S. Gail , Mills Gordon B. , Li Bo , Sahni Nidhi , Yi S. Stephen
Published: March 2023

Supplementary Figures 1-10. Figure-S1. Immune score prediction of response to PD-1 immune checkpoint blockade; Figure-S2. Immune mutation burden in cancer; Figure-S3. Transcriptome alteration of immunome in cancer; Figure-S4. Enrichment of differentially expressed genes (DEGs) in immunological gene signatures; Figure-S5. Immune infiltration score in cancer; Figure-S6. Candidate immune responder genes in cancer; Figure-S7. The ROC curves for different signatures in two datasets; Figure-S8. Barplots showing the AUCs of different signatures across 17 datasets; Figure-S9. CNV alteration and QTL of immune-related genes; Figure-S10. QTLs of immune-related genes across cancer types.
Figure S5 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Supplementary Figure S5
Figure S4 from YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice
Authors: Park Jaeoh , Eisenbarth David , Choi Wonyoung , Kim Hail , Choi Chan , Lee Dahye , Lim Dae-Sik
Published: March 2023

Figure S4
Figure S4 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Figure S4. Loss of Erbin does not significantly alter the expression of genes associated with intestinal stem cells and differentiation in normal intestinal organoids. (A) Representative phase contrast images of intestinal organoids derived WT and Erbin-/- (KO) mice grown in 3D Matrigel for 5 days. Scale bar, 200μm. (B) Intestinal organoids from WT, Erbin+/- (Het) and Erbin-/- (KO) mice were grown in 3D Matrigel and collected after 5 days. Total RNA were prepared and used for qRT-PCR analysis for the expression of genes associated with intestinal stem and progenitor cells (Lgr5, Axin2 and Cd44), cell proliferation (Ccnd1 and Ki67) and intestinal cell differentiation (Alpi, Chga, Muc2 and Cdh1). (C) MEF cells generated from WT and Erbin KO mice were stimulated with EGF (10ng/mL) for the indicated times and analyzed for the activation of Akt and RAS/RAF signaling by western blot.
Figure S3 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Figure S3. Knockout of Erbin has no significant effect on the proliferation and differentiation of normal intestinal epithelial cells. Swiss rolls of intestinal tissues from WT, Erbin+/- (Het) and Erbin-/- (KO) mice were analyzed for the appearance of normal crypt-villus structure using H&E staining. Alcian blue and PAS staining were used to identify goblet cells and Paneth cells; whereas Ki67 and chromogranin A IHC staining detects proliferating cells and enteroendocrine cells, respectively. Scale bar, 200μm.
Figure S2 from Erbin Suppresses KSR1-Mediated RAS/RAF Signaling and Tumorigenesis in Colorectal Cancer
Authors: Stevens Payton D. , Wen Yang-An , Xiong Xiaopeng , Zaytseva Yekaterina Y. , Li Austin T. , Wang Chi , Stevens Ashley T. , Farmer Trevor N. , Gan Tong , Weiss Heidi L. , Inagaki Masaki , Marchetto Sylvie , Borg Jean-Paul , Gao Tianyan
Published: March 2023

Figure S2. Knockdown of Erbin increases Akt and RAS/RAF signaling and cell motility. (A) EGF-induced activation of RAS/RAF signaling in sh-Control and sh-Erbin (A2) LIM2405 cells. Cells were stimulated with EGF (10 ng/mL) for the indicated times and activation of signaling molecules were analyzed by western blot. (B) Stable sh-Control and sh-Erbin HT29 cells were analyzed for the activation of Akt and ERK by western blot. (C) Stable sh-Control and sh-Erbin HT29 cells were subjected to Transwell migration assays using collagen and EGF (10 ng/mL) as chemoattractants. The number of migrated cells per field of view were counted. Data represents mean {plus minus} SEM (n=12, * p<0.05). (D) Stable sh-Control and sh-Erbin SW480 cells (generating using both A1 and A2 targeting lentivirus) were subjected Transwell migration assays. The number of migrated cells per field of view were counted. Data represents mean {plus minus} SEM (n = 16, * p<0.05 and # p<0.0001).
Supplementary Table 5 from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency
Authors: Gupta Manav , Concepcion Carla P. , Fahey Caroline G. , Keshishian Hasmik , Bhutkar Arjun , Brainson Christine F. , Sanchez-Rivera Francisco J. , Pessina Patrizia , Kim Jonathan Y. , Simoneau Antoine , Paschini Margherita , Beytagh Mary C. , Stanclift Caroline R. , Schenone Monica , Mani D.R. , Li Chendi , Oh Audris , Li Fei , Hu Hai , Karatza Angeliki , Bronson Roderick T. , Shaw Alice T. , Hata Aaron N. , Wong Kwok-Kin , Zou Lee , Carr Steven A. , Jacks Tyler , Kim Carla F.
Published: March 2023

Cancer dependency analysis in pan cancer datasets - DRIVE and ACHILLES.
Supplementary Table 2 from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency
Authors: Gupta Manav , Concepcion Carla P. , Fahey Caroline G. , Keshishian Hasmik , Bhutkar Arjun , Brainson Christine F. , Sanchez-Rivera Francisco J. , Pessina Patrizia , Kim Jonathan Y. , Simoneau Antoine , Paschini Margherita , Beytagh Mary C. , Stanclift Caroline R. , Schenone Monica , Mani D.R. , Li Chendi , Oh Audris , Li Fei , Hu Hai , Karatza Angeliki , Bronson Roderick T. , Shaw Alice T. , Hata Aaron N. , Wong Kwok-Kin , Zou Lee , Carr Steven A. , Jacks Tyler , Kim Carla F.
Published: March 2023

Differential RNA-seq analysis and list of all gene ontology and cancer reactome pathways found for top differentially upregulated genes in isogenic murine Brg1 knockout lung cancer cells compared to Brg1 wildtype cells.
Table S3 from The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity
Authors: Carles Annaïck , Trigo-Gonzalez Genny , Cao Qi , Cheng S.-W. Grace , Moksa Michelle , Bilenky Misha , Huntsman David G. , Morin Gregg B. , Hirst Martin
Published: March 2023

Known transcription factor motifs enriched in shared and FOXL2 mutant-specific peaks predicted by Homer motif analysis.
Supplemental Table S3. from Ablation of the Brca1–Palb2 Interaction Phenocopies Fanconi Anemia in Mice
Authors: Park Dongju , Bergin Stephen M. , Jones Dan , Ru Peng , Koivisto Christopher S. , Jeon Young-Jun , Sizemore Gina M. , Kladney Raleigh D. , Hadjis Ashley , Shakya Reena , Ludwig Thomas
Published: March 2023

Notch1 mutations detected by exome sequencing from Brca1L1363P/ L1363P; p53-/- thymic tumor
Supplementary Figure from Accumulation of Molecular Aberrations Distinctive to Hepatocellular Carcinoma Progression
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tatsuno Kenji , Renard-Guillet Claire , Tsuji Shingo , Hayashi Akimasa , Ueda Hiroki , Fukuda Shiro , Fujita Takanori , Katoh Hiroto , Ishikawa Shumpei , Covington Kyle R. , Creighton Chad J. , Sugitani Masahiko , Wheeler David A. , Shibata Tatsuhiro , Nagae Genta , Takayama Tadatoshi , Aburatani Hiroyuki
Published: March 2023

Figure S1 shows Histological findings of stepwise hepatocarcinogenesis and somatic substitution patterns. Figure S2 shows Activation of WNT targets. Figure S3 shows Homozygous deletion in 4q and 16q. Figure S4 shows Circos plot and transcription of the 5' portion of fusion genes that included TERT sequences. Figure S5 shows Upregulation mechanisms of TERT gene. Figure S6 shows Classification of HCC samples based on the methylation data.
Supplementary Methods from Chromothripsis in Human Breast Cancer
Authors: Bolkestein Michiel , Wong John K.L. , Thewes Verena , Körber Verena , Hlevnjak Mario , Elgaafary Shaymaa , Schulze Markus , Kommoss Felix K.F. , Sinn Hans-Peter , Anzeneder Tobias , Hirsch Steffen , Devens Frauke , Schröter Petra , Höfer Thomas , Schneeweiss Andreas , Lichter Peter , Zapatka Marc , Ernst Aurélie
Published: March 2023

Supplementary Methods
Figure S3 from HDAC6 Inhibition Synergizes with Anti-PD-L1 Therapy in ARID1A-Inactivated Ovarian Cancer
Authors: Fukumoto Takeshi , Fatkhutdinov Nail , Zundell Joseph A. , Tcyganov Evgenii N. , Nacarelli Timothy , Karakashev Sergey , Wu Shuai , Liu Qin , Gabrilovich Dmitry I. , Zhang Rugang
Published: March 2023

Figure S3 shows that the effects of HDAC6 inhibitor ACY1215 alone or in combination with anti-PD-L1 on tumor immune microenvironment and that the combination of HDAC6 inhibitor ACY1215 and anti-PD-L1 does not affect the body weight of the treated mice.
Supplementary Data from E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer
Authors: Suzuki Masami , Saito-Adachi Mihoko , Arai Yasuhito , Fujiwara Yuko , Takai Erina , Shibata Shinsuke , Seki Masahide , Rokutan Hirofumi , Maeda Daichi , Horie Masafumi , Suzuki Yutaka , Shibata Tatsuhiro , Kiyono Tohru , Yachida Shinichi
Published: March 2023

Supplemental experimental procedures, Figure S1-S16, Table S5
Supplementary Fig 4 from FGFR1 Is Critical for RBL2 Loss–Driven Tumor Development and Requires PLCG1 Activation for Continued Growth of Small Cell Lung Cancer
Authors: Kim Kee-Beom , Kim Youngchul , Rivard Christopher J. , Kim Dong-Wook , Park Kwon-Sik
Published: March 2023

RT-qPCR for Fgfr1 mRNA normalized to Gapdh (n=3 replicates per group). Fgfr1 transcript levels are higher in subcutaneous tumors generated from preSCs with mutant Rbl2, Crebbp, or Ep300 than control or Col22a1 mutant preSCs.
Supplementary Data from ALPPL2 Is a Highly Specific and Targetable Tumor Cell Surface Antigen
Authors: Su Yang , Zhang Xin , Bidlingmaier Scott , Behrens Christopher R. , Lee Nam-Kyung , Liu Bin
Published: March 2023

Supplementary Tables and Figures
Supplementary Data from ATF3 Coordinates Antitumor Synergy between Epigenetic Drugs and Protein Disulfide Isomerase Inhibitors
Authors: Duncan Ravyn M. , Reyes Leticia , Moats Katelyn , Robinson Reeder M. , Murphy Sara A. , Kaur Balveen , Stessman Holly A.F. , Dolloff Nathan G.
Published: March 2023

The supplementary tables provide a list of antibodies, plasmids, and primer sets that were used throughout the study. They also include gene transcripts from RNA-Seq analysis that show the genomic pathways altered by the combination of PDI and HDAC inhibitors, as well as ATF3-dependent gene transcripts.
Supplementary Figure S4 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: March 2023

Supplementary Figure S4 shows additional images of immunofluorescent staining in GBM intracranial xenografts.
Supplementary Data from Spatial Density and Distribution of Tumor-Associated Macrophages Predict Survival in Non–Small Cell Lung Carcinoma
Authors: Zheng Xiang , Weigert Andreas , Reu Simone , Guenther Stefan , Mansouri Siavash , Bassaly Birgit , Gattenlöhner Stefan , Grimminger Friedrich , Savai Pullamsetti Soni , Seeger Werner , Winter Hauke , Savai Rajkumar
Published: March 2023

Supplementary Data with figures
Supplemental tables 1, 2 and 3 from Replication Stress Drives Constitutive Activation of the DNA Damage Response and Radioresistance in Glioblastoma Stem-like Cells
Authors: Carruthers Ross D. , Ahmed Shafiq U. , Ramachandran Shaliny , Strathdee Karen , Kurian Kathreena M. , Hedley Ann , Gomez-Roman Natividad , Kalna Gabriela , Neilson Mathew , Gilmour Lesley , Stevenson Katrina H. , Hammond Ester M. , Chalmers Anthony J.
Published: March 2023

Supplemental Table 1 Summary table of in vivo growth characteristics of E2, G7, R10, R15, R24, R9 and S2 GSC primary GBM cultures after intracranial injection in CD1 nude mice. Supplemental Table 2 List of primary antibodies utilised Supplemental Table 3 List of secondary antibodies utilised
Supplementary Figure Legend from Oncogenic ERG Represses PI3K Signaling through Downregulation of IRS2
Authors: Mao Ninghui , Gao Dong , Hu Wenhuo , Gadal Sunyana , Hieronymus Haley , Wang Shangqian , Lee Young Sun , Sullivan Patrick , Zhang Zeda , Choi Danielle , Rosen Neal , Sawyers Charles L. , Gopalan Anuradha , Chen Yu , Carver Brett S.
Published: March 2023

Figure Legend for supplementary figures
Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation
Authors: Zhang Fan , Lou Lihong , Peng Bo , Song Xiaotian , Reizes Ofer , Almasan Alexandru , Gong Zihua
Published: March 2023

Supplementary Data from Nudix Hydrolase NUDT16 Regulates 53BP1 Protein by Reversing 53BP1 ADP-Ribosylation