bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods from Hybrid Epithelial–Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors
Authors: Selvaggio Gianluca , Canato Sara , Pawar Archana , Monteiro Pedro T. , Guerreiro Patrícia S. , Brás M. Manuela , Janody Florence , Chaouiya Claudine
Published: April 2023

Supplementary Methods
Figure S2 from CXCR4 in Tumor Epithelial Cells Mediates Desmoplastic Reaction in Pancreatic Ductal Adenocarcinoma
Authors: Morita Toshihiro , Kodama Yuzo , Shiokawa Masahiro , Kuriyama Katsutoshi , Marui Saiko , Kuwada Takeshi , Sogabe Yuko , Matsumori Tomoaki , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Nishikawa Yoshihiro , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Nagasawa Takashi , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Cxcr4 KO does not affect Cxcr4 expression in immune cells of the spleen.
Table S3 from Epigenetic CRISPR Screens Identify Npm1 as a Therapeutic Vulnerability in Non–Small Cell Lung Cancer
Authors: Li Fei , Ng Wai-Lung , Luster Troy A. , Hu Hai , Sviderskiy Vladislav O. , Dowling Catríona M. , Hollinshead Kate E.R. , Zouitine Paula , Zhang Hua , Huang Qingyuan , Ranieri Michela , Wang Wei , Fang Zhaoyuan , Chen Ting , Deng Jiehui , Zhao Kai , So Hon-Cheong , Khodadadi-Jamayran Alireza , Xu Mousheng , Karatza Angeliki , Pyon Val , Li Shuai , Pan Yuanwang , Labbe Kristen , Almonte Christina , Poirier John T. , Miller George , Possemato Richard , Qi Jun , Wong Kwok-Kin
Published: April 2023

Enriched gene sets in KP cells with or without Npm1 knockdown
Table S1 from Epigenetic CRISPR Screens Identify Npm1 as a Therapeutic Vulnerability in Non–Small Cell Lung Cancer
Authors: Li Fei , Ng Wai-Lung , Luster Troy A. , Hu Hai , Sviderskiy Vladislav O. , Dowling Catríona M. , Hollinshead Kate E.R. , Zouitine Paula , Zhang Hua , Huang Qingyuan , Ranieri Michela , Wang Wei , Fang Zhaoyuan , Chen Ting , Deng Jiehui , Zhao Kai , So Hon-Cheong , Khodadadi-Jamayran Alireza , Xu Mousheng , Karatza Angeliki , Pyon Val , Li Shuai , Pan Yuanwang , Labbe Kristen , Almonte Christina , Poirier John T. , Miller George , Possemato Richard , Qi Jun , Wong Kwok-Kin
Published: April 2023

Reads count for CRISPR screens
Supplementary Figure S1 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

The expression amounts of BACH1 in pancreatic cancer cell lines and the effect of BACH1 silencing on cellular proliferation in wild type KRAS cells. Details are described in methods and legends file (Supplementary_methods_and_legends).
Figure S7 from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Related to Figure 5: Human SCLC cells are sensitive to inhibition of the mevalonate pathway
Figure S2 from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Related to Figure 2: MEK5 and ERK5 knock-down induces cell death in SCLC cells
Supplemental Materials and Methods and Figure Legends from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Supplemental Materials and Methods. Supplemental Figure Legends 1-4
Figure S4 from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Fig. S4 YY1 and AR jointly regulate the expression of eEF2K and in turn affect proliferation and apoptosis of ESCC cells under acute ND.
Supplementary Figure S4 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S4 shows results from the co-culture of cancer cells, monocytes, and endothelial cells within a single hydrogel layer.
Figure S3 from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Fig. S3 The m6A modification of LINC00278 and corresponding regulators.
Figure S2 from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Fig. S2 Transcription and translation of LINC00278.
Supplementary Figure S1 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figures S1 shows the fabrication diagram of the tumor-on-chip device.
Supplementary Figure Captions from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure captions for the Supplementary Figures.
Supplementary figures from Transcriptionally Active Androgen Receptor Splice Variants Promote Hepatocellular Carcinoma Progression
Authors: Dauki Anees M. , Blachly James S. , Kautto Esko A. , Ezzat Sameera , Abdel-Rahman Mohamed H. , Coss Christopher C.
Published: April 2023

This file contains supplementary figures 1-8.
Supplementary Data from Sustained Coevolution in a Stochastic Model of Cancer–Immune Interaction
Authors: George Jason T. , Levine Herbert
Published: April 2023

Main SI file: This file contains all supplementary information, including detailed mathematical derivations and supplemental figures: SF1: Probability densities for the inter-temporal clone arrival times SF2: Escape and elimination probabilities as a function of cycle number assuming clearance probabilities that decline as a function of cycle number. SF3: Escape probabilities as a function of cycle number assuming constant clearance probability as well as clearance probabilities that decline as a function of current clone size. SF4: Simulated population trajectories as a function of time for both the deterministic and adaptive immune recognition assumptions SF5: Simulated population trajectories as a function of time conditioned on ultimate escape. SF6: Empirical cancer incidence as a function of age. SF7: Changes in early cancer incidence as a function of per-cell mutation rate SF8: General features of the co-evolutionary framework, including initiation, branching, recognition, ultimate elimination, and ultimate escape. SF9: Example simulated trajectories as a function of time for various clearance probabilities and branching parameters. SF10: Detection size and mean dispersion assuming adaptive recognition as a function of the adaptive immune detection parameter and per-cell growth rate SF11: Mean recognition cycles and escape probabilities as a function of clearance probability and branching parameter. SF12: Cycle number and escape probability as a function of clearance probability and branching parameter, assuming mean cycle numbers +/- 1 standard deviation of estimated cycle number. ST1: TRACERx empirical mutational burden partitioned by lung cancer subtype.
Supplementary Data from Increased Tumor Penetration of Single-Domain Antibody–Drug Conjugates Improves In Vivo Efficacy in Prostate Cancer Models
Authors: Nessler Ian , Khera Eshita , Vance Steven , Kopp Anna , Qiu Qifeng , Keating Thomas A. , Abu-Yousif Adnan O. , Sandal Thomas , Legg James , Thompson Lorraine , Goodwin Normann , Thurber Greg M.
Published: April 2023

This file contains information on the methods used during drug formulation, reaction, and purification as well as an in-depth description of in vitro assays, experimental/computational spheroid work, and tumor growth measurements. The figures and tables provide characterization of therapeutic constructs, rationale for efficacy study dosing, and Krogh Cylinder simulation parameters.
Supplementary Figure 3 from miR-149 Suppresses Breast Cancer Metastasis by Blocking Paracrine Interactions with Macrophages
Authors: Sánchez-González Ismael , Bobien Anja , Molnar Christian , Schmid Simone , Strotbek Michaela , Boerries Melanie , Busch Hauke , Olayioye Monilola A.
Published: April 2023

Characterization of MDA-MB-231 cells stably expressing miR-149
Supplementary Figure 2 from miR-149 Suppresses Breast Cancer Metastasis by Blocking Paracrine Interactions with Macrophages
Authors: Sánchez-González Ismael , Bobien Anja , Molnar Christian , Schmid Simone , Strotbek Michaela , Boerries Melanie , Busch Hauke , Olayioye Monilola A.
Published: April 2023

miR-149 regulation of cell motility by paracrine signaling
Supplementary Figure 1 from miR-149 Suppresses Breast Cancer Metastasis by Blocking Paracrine Interactions with Macrophages
Authors: Sánchez-González Ismael , Bobien Anja , Molnar Christian , Schmid Simone , Strotbek Michaela , Boerries Melanie , Busch Hauke , Olayioye Monilola A.
Published: April 2023

Predicted miR-149 target genes in TNBC.
Supplementary Tables from A Feedback Circuitry between Polycomb Signaling and Fructose-1, 6-Bisphosphatase Enables Hepatic and Renal Tumorigenesis
Authors: Liao Kun , Deng Shuye , Xu Liyan , Pan Wenfeng , Yang Shiyu , Zheng Fufu , Wu Xingui , Hu Hongrong , Liu Zhijun , Luo Junhang , Zhang Rui , Kuang Dong-Ming , Dong Jiajun , Wu Yi , Zhang Hui , Zhou Penghui , Bei Jin-Xin , Xu Yang , Ji Yin , Wang Peng , Ju Huai-Qiang , Xu Rui-Hua , Li Bo
Published: April 2023

Supplementary tables S1-S4 show analytic details of the ENCODE ChIP-Seq data and TCGA RNA-Seq data, together with primer sequences used in this study.
Supplementary Figures and Materials and Methods from A Feedback Circuitry between Polycomb Signaling and Fructose-1, 6-Bisphosphatase Enables Hepatic and Renal Tumorigenesis
Authors: Liao Kun , Deng Shuye , Xu Liyan , Pan Wenfeng , Yang Shiyu , Zheng Fufu , Wu Xingui , Hu Hongrong , Liu Zhijun , Luo Junhang , Zhang Rui , Kuang Dong-Ming , Dong Jiajun , Wu Yi , Zhang Hui , Zhou Penghui , Bei Jin-Xin , Xu Yang , Ji Yin , Wang Peng , Ju Huai-Qiang , Xu Rui-Hua , Li Bo
Published: April 2023

Supplementary Figures S1-S6 describe additional data to support the EZH2-FBP1 feedback circuitry in hepatic and renal cells upon genotoxin-induced tumorigenesis. Supplementary Materials and Methods provide experimental details on standard assays using commercial reagents and kits.
Supplementary Material from MiR-30e-3p Influences Tumor Phenotype through MDM2/TP53 Axis and Predicts Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Gramantieri Laura , Pollutri Daniela , Gagliardi Martina , Giovannini Catia , Quarta Santina , Ferracin Manuela , Casadei-Gardini Andrea , Callegari Elisa , De Carolis Sabrina , Marinelli Sara , Benevento Francesca , Vasuri Francesco , Ravaioli Matteo , Cescon Matteo , Piscaglia Fabio , Negrini Massimo , Bolondi Luigi , Fornari Francesca
Published: April 2023

Microarray analysis, cell transfection and infection, cell proliferation assay, clonogenic and sphere formation assays, TP53 hypothetical binding sites.
Table S2 from Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer Is Associated with Indigenous American Ancestry in Latin American Women
Authors: Marker Katie M. , Zavala Valentina A. , Vidaurre Tatiana , Lott Paul C. , Vásquez Jeannie Navarro , Casavilca-Zambrano Sandro , Calderón Mónica , Abugattas Julio E. , Gómez Henry L. , Fuentes Hugo A. , Picoaga Ruddy Liendo , Cotrina Jose M. , Neciosup Silvia P. , Castañeda Carlos A. , Morante Zaida , Valencia Fernando , Torres Javier , Echeverry Magdalena , Bohórquez Mabel E. , Polanco-Echeverry Guadalupe , Estrada-Florez Ana P. , Serrano-Gómez Silvia J. , Carmona-Valencia Jenny A. , Alvarado-Cabrero Isabel , Sanabria-Salas María Carolina , Velez Alejandro , Donado Jorge , Song Sikai , Cherry Daniel , Tamayo Lizeth I. , Huntsman Scott , Hu Donglei , Ruiz-Cordero Roberto , Balassanian Ronald , Ziv Elad , Zabaleta Jovanny , Carvajal-Carmona Luis , Fejerman Laura
Published: April 2023

Association between ER/PR/HER2 defined groups and Indigenous American genetic ancestry including stage and region of residence as covariates
Supplementary Figure 6 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

Pevonedistat increases p21 and p27 expression and apoptosis in Rb/p53-deficient MFS and UPS xenografts with negligible toxicity.
Supplementary Figure 4 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

Skp2 knockdown causes cell cycle arrest and reduces Akt activation
Supplementary Video 3 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of invasive ductal carcinoma with adipose tissue
Supplementary Video 2 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of benign stroma
Supplementary Video 1 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of adipose tissue
Supplementary Data from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

ST1, ST2, Note on Prevalence, SF1, SF2, SF3, Note on Elastography
Table S7 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Association between a genetic predisposition to breast cancer (using family history of breast cancer and estrogen-receptor specific polygenic risk scores) among women withour breast cancer
Table S5 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Association between a genetic predisposition to breast cancer and % mammographic density
Table S2 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Univariate ACE estimates after re-randomisation of siblings
Table S1 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Model fitting from univariate analyses after re-randomisation of siblings
Supplementary Table 1 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Table lists primers used for RQ-PCR.
Supplementary Figure Legends from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Legends for supplementary figures 1-8
Supplementary Figure 4 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure reports additional RPPA data.
Supplementary Figure 8 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S8 shows that a cisplatin and NAMPT inhibitor FK866 combination reduces ALDH activity in vivo.
Supplementary Figure 5 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S5 shows that NMN supplementation during cisplatin-induced senescence of ovarian cancer cells promotes cancer stem-like cells.
Supplementary Figure 3 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S3 shows that small molecule NAMPT inhibitors suppress ovarian cancer stem-like cells and promote apoptosis.
Supplementary Tables 2-13 from Acquired Resistance to HER2-Targeted Therapies Creates Vulnerability to ATP Synthase Inhibition
Authors: Gale Molly , Li Yao , Cao Jian , Liu Zongzhi Z. , Holmbeck Marissa A. , Zhang Meiling , Lang Sabine M. , Wu Lizhen , Do Carmo Mariana , Gupta Swati , Aoshima Keisuke , DiGiovanna Michael P. , Stern David F. , Rimm David L. , Shadel Gerald S. , Chen Xiang , Yan Qin
Published: April 2023

Supplementary Table 2: BT-TR1 versus BT474 RNA sequencing normalized gene expression Supplementary Table 3: BT-TR2 versus BT474 RNA sequencing normalized gene expression Supplementary Table 4: BT-TPR1 versus BT474 RNA sequencing normalized gene expression Supplementary Table 5: BT-TPR2 versus BT474 RNA sequencing normalized gene expression Supplementary Table 6: BT-TR1 versus BT474 positively enriched hallmark pathways. Supplementary Table 7: BT-TR2 versus BT474 positively enriched hallmark pathways. Supplementary Table 8: BT-TPR1 versus BT474 positively enriched hallmark pathways. Supplementary Table 9: BT-TPR2 versus BT474 positively enriched hallmark pathways. Supplementary Table 10: BT-TR1 versus BT474 negatively enriched hallmark pathways. Supplementary Table 11: BT-TR2 versus BT474 negatively enriched hallmark pathways. Supplementary Table 12: BT-TPR1 versus BT474 negatively enriched hallmark pathways. Supplementary Table 13: BT-TPR2 versus BT474 negatively enriched hallmark pathways.
Supplementary Table S4 from Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma
Authors: Tamura Naoka , Shaikh Nadeem , Muliaditan Daniel , Soliman Tanya N. , McGuinness Jennifer R. , Maniati Eleni , Moralli Daniela , Durin Mary-Anne , Green Catherine M. , Balkwill Frances R. , Wang Jun , Curtius Kit , McClelland Sarah E.
Published: April 2023

RNA seq pathway analysis
Supplementary Table S3 from Specific Mechanisms of Chromosomal Instability Indicate Therapeutic Sensitivities in High-Grade Serous Ovarian Carcinoma
Authors: Tamura Naoka , Shaikh Nadeem , Muliaditan Daniel , Soliman Tanya N. , McGuinness Jennifer R. , Maniati Eleni , Moralli Daniela , Durin Mary-Anne , Green Catherine M. , Balkwill Frances R. , Wang Jun , Curtius Kit , McClelland Sarah E.
Published: April 2023

RNA sequencing of HGSC cell lines
Supplementary Figure 4 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

LPAR and S1PR expression in human TSC2-deficient cells
Supplementary Figure 1 from Therapeutic Targeting of the Secreted Lysophospholipase D Autotaxin Suppresses Tuberous Sclerosis Complex-Associated Tumorigenesis
Authors: Feng You , Mischler William J. , Gurung Ashish C. , Kavanagh Taylor R. , Androsov Grigoriy , Sadow Peter M. , Herbert Zachary T. , Priolo Carmen
Published: April 2023

mTOR signaling in human TSC2-deficient cells versus TSC2 add-back cells
Supplementary Table S1 from The Fire Within: NF-κB Involvement in Non–Small Cell Lung Cancer
Authors: Dimitrakopoulos Foteinos-Ioannis D. , Kottorou Anastasia E. , Kalofonou Melpomeni , Kalofonos Haralabos P.
Published: April 2023

Supplementary Table S1. Published studies and key findings on the translational value of NF-κB family members in NSCLC patients.
Supplementary Data from USP22 Functions as an Oncogenic Driver in Prostate Cancer by Regulating Cell Proliferation and DNA Repair
Authors: McCann Jennifer J. , Vasilevskaya Irina A. , Poudel Neupane Neermala , Shafi Ayesha A. , McNair Christopher , Dylgjeri Emanuela , Mandigo Amy C. , Schiewer Matthew J. , Schrecengost Randy S. , Gallagher Peter , Stanek Timothy J. , McMahon Steven B. , Berman-Booty Lisa D. , Ostrander William F. , Knudsen Karen E.
Published: April 2023

SF1: Analysis of USP22 expression with known drivers of disease progression; SF2: USP22 modulates DNA repair factors expression and survival after DNA damage; SF3: Genetically engineered mouse model of tumor-associated USP22 expression; SF4: The USP22-sensitive ubiquitylome reveals altered modification of DNA repair proteins; SF5: USP22 deubiquitylates the NER protein XPC, modulating foci formation.
Figure S1 from Remission of Spontaneous Canine Tumors after Systemic Cellular Viroimmunotherapy
Authors: Cejalvo Teresa , Perisé-Barrios Ana Judith , del Portillo Isabel , Laborda Eduardo , Rodriguez-Milla Miguel A. , Cubillo Isabel , Vázquez Fernando , Sardón David , Ramirez Manuel , Alemany Ramon , del Castillo Noemí , García-Castro Javier
Published: April 2023

. Characterization of canine mesenchymal stem cells and their susceptibility to canine adenoviral infection and replication
Supplementary Table S1 from Intake of Dietary Fruit, Vegetables, and Fiber and Risk of Colorectal Cancer According to Molecular Subtypes: A Pooled Analysis of 9 Studies
Authors: Hidaka Akihisa , Harrison Tabitha A. , Cao Yin , Sakoda Lori C. , Barfield Richard , Giannakis Marios , Song Mingyang , Phipps Amanda I. , Figueiredo Jane C. , Zaidi Syed H. , Toland Amanda E. , Amitay Efrat L. , Berndt Sonja I. , Borozan Ivan , Chan Andrew T. , Gallinger Steven , Gunter Marc J. , Guinter Mark A. , Harlid Sophia , Hampel Heather , Jenkins Mark A. , Lin Yi , Moreno Victor , Newcomb Polly A. , Nishihara Reiko , Ogino Shuji , Obón-Santacana Mireia , Parfrey Patrick S. , Potter John D. , Slattery Martha L. , Steinfelder Robert S. , Um Caroline Y. , Wang Xiaoliang , Woods Michael O. , Van Guelpen Bethany , Thibodeau Stephen N. , Hoffmeister Michael , Sun Wei , Hsu Li , Buchanan Daniel D. , Campbell Peter T. , Peters Ulrike
Published: April 2023

Supplementary Table S1
Supplementary Data from Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer
Authors: Hanrahan Aphrothiti J. , Sylvester Brooke E. , Chang Matthew T. , Elzein Arijh , Gao Jianjiong , Han Weiwei , Liu Ye , Xu Dong , Gao Sizhi P. , Gorelick Alexander N. , Jones Alexis M. , Kiliti Amber J. , Nissan Moriah H. , Nimura Clare A. , Poteshman Abigail N. , Yao Zhan , Gao Yijun , Hu Wenhuo , Wise Hannah C. , Gavrila Elena I. , Shoushtari Alexander N. , Tiwari Shakuntala , Viale Agnes , Abdel-Wahab Omar , Merghoub Taha , Berger Michael F. , Rosen Neal , Taylor Barry S. , Solit David B.
Published: April 2023

This supplementary data file contains 5 figures pertaining to the tumor distribution of MEK1 hotspot mutations, functional characterization of further MEK1/2 mutants with and without MEK or ERK inhibitor treatment, and the sequence paralogy alignment of MEK1 and MEK2. This file also contains 4 tables detailing hotspot analysis q values for MEK1/2 mutants, tumor incidence of MEK1 in-frame deletions, and a summary of MEK1/2 paralogous residues and their concordant activation status.
Supplementary Tables 1-6 from High-Throughput Screening of Combinatorial Immunotherapies with Patient-Specific In Silico Models of Metastatic Colorectal Cancer
Authors: Kather Jakob Nikolas , Charoentong Pornpimol , Suarez-Carmona Meggy , Herpel Esther , Klupp Fee , Ulrich Alexis , Schneider Martin , Zoernig Inka , Luedde Tom , Jaeger Dirk , Poleszczuk Jan , Halama Niels
Published: April 2023

Detailed description of the parameters used in the model. Also, these tables show detailed clinical data for the patient cohorts that were used in this study.
Supplementary Figure S1-S10, Table 1-3 and supplementary word-1. from CircNT5E Acts as a Sponge of miR-422a to Promote Glioblastoma Tumorigenesis
Authors: Wang Renjie , Zhang Sai , Chen Xuyi , Li Nan , Li Jianwei , Jia Ruichao , Pan Yuanqing , Liang Haiqian
Published: April 2023

The supplementary file contains the Supplementary Figure S1-S10, Table 1-3 and supplementary word-1. Figure S1 indicated the identification of three cases with low expression of miR-422a. Figure S2 suggested validation of microarray results by qRT-PCR analysis of six randomly selected lncRNAs and six randomly selected circRNAs in three cases. Figure S3 was identification of differentially expressed lncRNAs in GBM tumour and adjacent normal tissues. Figure S4 was Identification of differentially expressed circRNAs in GBM tumour and adjacent normal tissues. Figure S5 was the screen of possible interaction between lncRNA/circRNAs and miR-422a in glioblastoma. Figure S6 indicated circNT5E affects the cell apoptosis of glioblastoma. Figure S7 was CRISPR/Cas9 system targeting Alusq and Alusg. Figure S8 indicated ADARB2 directly interacts with the Alusq region of NT5E pre-mRNA. Figure S9 demonstrated circNT5E regulates cell apoptosis by miR-422a in glioblastoma. Figure S10 suggested circNT5E functions as an efficient miRNA sponge in glioblastoma. Supplementary Table 1 was the detailed clinical patients information. Supplementary Table 2 was the summary of primers and RNA sequences used in this study. Supplementary Table 3 was the summary of GBM-related tumor suppressor miRNAs extracted from the literature. Supplementary Word-1 indicated the sequences of Alu elements of circNT5E analysis.
Supplementary Figures 1-4 from High-Throughput Screening of Combinatorial Immunotherapies with Patient-Specific In Silico Models of Metastatic Colorectal Cancer
Authors: Kather Jakob Nikolas , Charoentong Pornpimol , Suarez-Carmona Meggy , Herpel Esther , Klupp Fee , Ulrich Alexis , Schneider Martin , Zoernig Inka , Luedde Tom , Jaeger Dirk , Poleszczuk Jan , Halama Niels
Published: April 2023

Detailed information on the procedure of fitting the mathematical model to clinical data as well as details on treatment simulation.
Supplementary Video S6 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Supplementary Video S3 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Figure S5 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Expression of chemokines in WT and CCR2-/- T-ALL mice.
Supplementary Video S1 from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

movie file
Supplementary Data from Nonlinear Optics with Near-Infrared Excitation Enable Real-Time Quantitative Diagnosis of Human Cervical Cancers
Authors: Matsui Takahiro , Tamoto Ryo , Iwasa Akio , Mimura Masafumi , Taniguchi Seiji , Hasegawa Tetsuo , Sudo Takao , Mizuno Hiroki , Kikuta Junichi , Onoyama Ichiro , Okugawa Kaoru , Shiomi Mayu , Matsuzaki Shinya , Morii Eiichi , Kimura Tadashi , Kato Kiyoko , Kiyota Yasujiro , Ishii Masaru
Published: April 2023

Supplementary Figures and Legends
Figure S3 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

RNA-seq analysis of SP normal macrophage and LAM subsets.
Figure S1 from Monocyte-Derived Leukemia-Associated Macrophages Facilitate Extramedullary Distribution of T-cell Acute Lymphoblastic Leukemia Cells
Authors: Yang Feifei , Feng Wenli , Wang Hao , Wang Lina , Liu Xiaoli , Wang Rong , Chen Chong , Yang Xiao , Zhang Dongyue , Ren Qian , Zheng Guoguang
Published: April 2023

Gating strategy for macrophages in the liver and SP as well as monocytes/ macrophages in the transplantation experiments at the steady state.
Supplemental Figure S4 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Figure S4. NR4A1 antagonist inhibit 4T1-luc cell growth and invasion, and induce apoptosis. 4T1-Luc cells were treated with different concentrations of CDIM8 or Cl-OCH3 and effects on cell proliferation (A), invasion (B) and induction of Annexin V staining (C) were determined as outlined in the Materials and Methods. Results are expressed as means {plus minus} SD for at least 3 replicate determinations per treatment group and significant (p<0.05) effects caused by the NR4A1 antagonists are indicated (*). The control (solvent) results are set at 1.0.
Supplementary Table 4 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Primary COAD tumor samples from TCGA RPPA data
Supplemental Figure S3 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Figure S3. Role of Sp1, Sp3, Sp4 and p300 in PD-L1 expression. MDA-MB-231 and 4T1 cells were transfected with oligonucleotides targeting Sp1 (iSp1) (A), Sp3 (iSp3), Sp4 (iSp4) and p300 (ip300) (B) and whole cell lysates were analyzed by western blots. The Sp3 bands represent the high and low molecular weight bands in descending order.
Supplementary Table 3. from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Primary COAD tumor samples selected from TCGA RNA expression data
Supplemental Figure S2 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Figure S2. Quantitation of results in Figure 1F and 1G. and mRNA results A. Breast cancer cells were treated with Cl-OCH3 (Fig. 1F) and effects on PD-L1, NR4A1 and Sp1 were determined by western blots and quantitation of the results are summarized. B. MDA-MB-231 and 4T1 cells were treated with NR4A1 antagonists, MG132 and their combinations, whole cell lysates were analyzed by western blots (Fig. 1G) and quantitation of the results are summarized. Results of both studies (A, B) are means {plus minus} SD for at least 3 replicate determinations for each treatment groups and changes in expression were determined relative to the control group (set ratio) significantly (p<0.05) decreased effects are indicated (*) and inhibition (reversal of degradation) by MG132 is also indicated (**). C. Basal PD-L1 and NR4A1 mRNA levels in cancer cell lines were determined as described in the Methods.
Supplemental Figure S1 from A Bis-Indole–Derived NR4A1 Antagonist Induces PD-L1 Degradation and Enhances Antitumor Immunity
Authors: Karki Keshav , Wright Gus A. , Mohankumar Kumaravel , Jin Un-Ho , Zhang Xing-Han , Safe Stephen
Published: April 2023

Supplemental Figure S1. Quantitation of results in Figures 1C, 1D and 1E cells were treated with CDIM8 or Cl-OCH3 and effects on PD-L1, NR4A1 and Sp1 expression was determined by western blots; quantitation of the effects of CDIM8 (A), Cl-OCH3 (B) and CDIM8 (C) on protein expression (normalized to β-actin) in A549, SW480 and 786-0 cells (Fig. 1C and 1D) and HS578T, SUM159, MDA-MB-231 and 4T1 cells (Fig. 1E) are summarized. Significant (p<0.05) effects compared to control (untreated cells set at 1.0) are indicated (*) and results are expressed at means {plus minus} SD for 3 replicate determinations for each treatment group.
Spplementary Table 2 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Correlation between SMAD4 and CTNNB1, NFκB and Rb protein expression in human colorectal adenocarcinoma
Spplementary Table 1 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Correlation of WNT signature genes with SMAD4 in human colorectal adenocarcinoma.
Figure S5 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

nuclear b-catenin
Supplementary Figures from Nitrogen Trapping as a Therapeutic Strategy in Tumors with Mitochondrial Dysfunction
Authors: Madala Hanumantha Rao , Helenius Iiro Taneli , Zhou Wen , Mills Evanna , Zhang Yiyun , Liu Yan , Metelo Ana M. , Kelley Michelle L. , Punganuru Surendra , Kim Kyung Bo , Olenchock Benjamin , Rhee Eugene , Intlekofer Andrew M. , Iliopoulos Othon , Chouchani Edward , Yeh Jing-Ruey Joanna
Published: April 2023

Figure S1-S18
Figure S2 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Phenotype of b-catenin gain of function mutants
Figure S1 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium
Authors: Perekatt Ansu O. , Shah Pooja P. , Cheung Shannon , Jariwala Nidhi , Wu Alex , Gandhi Vishal , Kumar Namit , Feng Qiang , Patel Neeket , Chen Lei , Joshi Shilpy , Zhou Anbo , Taketo M. Mark , Xing Jinchuan , White Eileen , Gao Nan , Gatza Michael L. , Verzi Michael P.
Published: April 2023

Loss of Smad4 in the intestinal epithelium
Supplementary Data from Glutamate Is a Noninvasive Metabolic Biomarker of IDH1-Mutant Glioma Response to Temozolomide Treatment
Authors: Subramani Elavarasan , Radoul Marina , Najac Chloe , Batsios Georgios , Molloy Abigail R. , Hong Donghyun , Gillespie Anne Marie , Santos Romelyn Delos , Viswanath Pavithra , Costello Joseph F. , Pieper Russell O. , Ronen Sabrina M.
Published: April 2023

Supplementary Figures S1-S9 and tables S1-S6
Supplementary Data from Fulvestrant-Mediated Attenuation of the Innate Immune Response Decreases ER+ Breast Cancer Growth In Vivo More Effectively than Tamoxifen
Authors: Abrahamsson Annelie , Rodriguez Gabriela Vazquez , Dabrosin Charlotta
Published: April 2023

Table S1.
Supplementary Data from PEG10 Promoter–Driven Expression of Reporter Genes Enables Molecular Imaging of Lethal Prostate Cancer
Authors: Shapovalova Mariya , Lee John K. , Li Yingming , Vander Griend Donald J. , Coleman Ilsa M. , Nelson Peter S. , Dehm Scott M. , LeBeau Aaron M.
Published: April 2023

Fig. S1. Plasmid map of A.TSTAPEG101KB in pGL3- Basic Fig. S2. PEG10 staining in positive control and healthy tissue Fig. S3. TSTA Schematic Fig. S4. Luciferase expression in empty pGL3 vector Fig. S5. PEG10 expression by IHC in HT-29 xenografts Fig. S6. HSV-TK and PEG10 expression in CWR-R1 tumors Table S1. Primers for PEG10 promoter cloning.
Supplementary table S3 from UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Authors: Qiao Xi , Liu Ying , Prada Maria Llamazares , Mohan Aravind K. , Gupta Abhishekh , Jaiswal Alok , Sharma Mukund , Merisaari Joni , Haikala Heidi M. , Talvinen Kati , Yetukuri Laxman , Pylvänäinen Joanna W. , Klefström Juha , Kronqvist Pauliina , Meinander Annika , Aittokallio Tero , Hietakangas Ville , Eilers Martin , Westermarck Jukka
Published: April 2023

Genes co-regulated by MYC and UBR5A1
Supplementary table S2 from UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Authors: Qiao Xi , Liu Ying , Prada Maria Llamazares , Mohan Aravind K. , Gupta Abhishekh , Jaiswal Alok , Sharma Mukund , Merisaari Joni , Haikala Heidi M. , Talvinen Kati , Yetukuri Laxman , Pylvänäinen Joanna W. , Klefström Juha , Kronqvist Pauliina , Meinander Annika , Aittokallio Tero , Hietakangas Ville , Eilers Martin , Westermarck Jukka
Published: April 2023

Top hits from Ubiqiuitin ligase siRNA screen with T58AMYC IF phenotype
Supplementary table S1 from UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Authors: Qiao Xi , Liu Ying , Prada Maria Llamazares , Mohan Aravind K. , Gupta Abhishekh , Jaiswal Alok , Sharma Mukund , Merisaari Joni , Haikala Heidi M. , Talvinen Kati , Yetukuri Laxman , Pylvänäinen Joanna W. , Klefström Juha , Kronqvist Pauliina , Meinander Annika , Aittokallio Tero , Hietakangas Ville , Eilers Martin , Westermarck Jukka
Published: April 2023

siRNA and primer sequences
Supplementary materials and methods from UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Authors: Qiao Xi , Liu Ying , Prada Maria Llamazares , Mohan Aravind K. , Gupta Abhishekh , Jaiswal Alok , Sharma Mukund , Merisaari Joni , Haikala Heidi M. , Talvinen Kati , Yetukuri Laxman , Pylvänäinen Joanna W. , Klefström Juha , Kronqvist Pauliina , Meinander Annika , Aittokallio Tero , Hietakangas Ville , Eilers Martin , Westermarck Jukka
Published: April 2023

Includes description of materials and methods related to Western Blot, Quantitative RT-PCR, siRNA library and high-content screening, Analysis of mutual exclusivity of MYC and UBR5 on single cell level, Mouse experiments, RNA sequencing.
Supplementary Data from FTO Inhibition Enhances the Antitumor Effect of Temozolomide by Targeting MYC-miR-155/23a Cluster-MXI1 Feedback Circuit in Glioma
Authors: Xiao Li , Li Xiaodi , Mu Zekun , Zhou Jianwen , Zhou Peng , Xie Chen , Jiang Songshan
Published: April 2023

Supplementary Figure S1-S10 and Table S1-S6
Supplementary Material from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplemental Figure Legends
Supplementary Data from Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System
Authors: Tubeuf Hélène , Caputo Sandrine M. , Sullivan Teresa , Rondeaux Julie , Krieger Sophie , Caux-Moncoutier Virginie , Hauchard Julie , Castelain Gaia , Fiévet Alice , Meulemans Laëtitia , Révillion Françoise , Léoné Mélanie , Boutry-Kryza Nadia , Delnatte Capucine , Guillaud-Bataille Marine , Cleveland Linda , Reid Susan , Southon Eileen , Soukarieh Omar , Drouet Aurélie , Di Giacomo Daniela , Vezain Myriam , Bonnet-Dorion Françoise , Bourdon Violaine , Larbre Hélène , Muller Danièle , Pujol Pascal , Vaz Fátima , Audebert-Bellanger Séverine , Colas Chrystelle , Venat-Bouvet Laurence , Solano Angela R. , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Gaildrat Pascaline , Sharan Shyam K. , Martins Alexandra
Published: April 2023

Word doc, UNmarked changes. Supp Table of contents, Supp Materials and Methods, Supp Figures S1-S17 (including description of BRCA2 mRNA and protein domains, selection of BRCA2 variants, minigene structure, RNA splicing data versus bioinformatics predictions, minigene results versus patients' RNA and mESC's data, and results from mESC complementation assays), Supp Note and Supp Reference
Figure S6 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 6
Supplementary Data from Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System
Authors: Tubeuf Hélène , Caputo Sandrine M. , Sullivan Teresa , Rondeaux Julie , Krieger Sophie , Caux-Moncoutier Virginie , Hauchard Julie , Castelain Gaia , Fiévet Alice , Meulemans Laëtitia , Révillion Françoise , Léoné Mélanie , Boutry-Kryza Nadia , Delnatte Capucine , Guillaud-Bataille Marine , Cleveland Linda , Reid Susan , Southon Eileen , Soukarieh Omar , Drouet Aurélie , Di Giacomo Daniela , Vezain Myriam , Bonnet-Dorion Françoise , Bourdon Violaine , Larbre Hélène , Muller Danièle , Pujol Pascal , Vaz Fátima , Audebert-Bellanger Séverine , Colas Chrystelle , Venat-Bouvet Laurence , Solano Angela R. , Stoppa-Lyonnet Dominique , Houdayer Claude , Frebourg Thierry , Gaildrat Pascaline , Sharan Shyam K. , Martins Alexandra
Published: April 2023

Supp Table of contents, Supp Materials and Methods, Supp Figures S1-S17 (including description of BRCA2 mRNA and protein domains, selection of BRCA2 variants, minigene structure, RNA splicing data versus bioinformatics predictions, minigene results versus patients' RNA and mESC's data, and results from mESC complementation assays), Supp Note and Supp Reference
Figure S4 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 4
Figure S3 from SLC43A3 Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Batten Kimberly , Peyton Michael , Vemula Aishwarya , Cornelius Crystal , Girard Luc , Gao Boning , Minna John D. , Shay Jerry W.
Published: April 2023

Supplementary Data 3