bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 1 from Effects of Oral Contraceptives or a Gonadotropin-Releasing Hormone Agonist on Ovarian Carcinogenesis in Genetically Engineered Mice
Authors: Romero Iris L. , Gordon Ilyssa O. , Jagadeeswaran Sujatha , Mui Keeley L. , Lee Woo Seok , Dinulescu Daniela M. , Krausz Thomas N. , Kim Helen H. , Gilliam Melissa L. , Lengyel Ernst
Published: April 2023

Supplementary Figure 1 from Effects of Oral Contraceptives or a Gonadotropin-Releasing Hormone Agonist on Ovarian Carcinogenesis in Genetically Engineered Mice
Supplementary Materials from Endocytosis of Resveratrol via Lipid Rafts and Activation of Downstream Signaling Pathways in Cancer Cells
Authors: Colin Didier , Limagne Emeric , Jeanningros Sylvie , Jacquel Arnaud , Lizard Gérard , Athias Anne , Gambert Philippe , Hichami Aziz , Latruffe Norbert , Solary Eric , Delmas Dominique
Published: April 2023

Supplementary Materials from Endocytosis of Resveratrol via Lipid Rafts and Activation of Downstream Signaling Pathways in Cancer Cells
Supplementary Fig S2 from Cucurbitacin B Alters the Expression of Tumor-Related Genes by Epigenetic Modifications in NSCLC and Inhibits NNK-Induced Lung Tumorigenesis
Authors: Shukla Samriddhi , Khan Sajid , Kumar Sudhir , Sinha Sonam , Farhan Mohd. , Bora Himangsu K. , Maurya Rakesh , Meeran Syed Musthapa
Published: April 2023

Supplementary Fig S2. CuB alters the global as well as gene-specific pattern of methylation in H1299 cells
Supplementary Tables 1 - 4 from Chronic Social Isolation Is Associated with Metabolic Gene Expression Changes Specific to Mammary Adipose Tissue
Authors: Volden Paul A. , Wonder Erin L. , Skor Maxwell N. , Carmean Christopher M. , Patel Feenalie N. , Ye Honggang , Kocherginsky Masha , McClintock Martha K. , Brady Matthew J. , Conzen Suzanne D.
Published: April 2023

PDF file - 83K, Supplemental tables 1-4. Supp. Table 1: TAg gene expression analysis summary. Supp. Table 2: Metabolic cage measurements of isolated vs. grouped TAg and CD1 mice. Supp. Table 3:WT and CD1 gene expression analysis summary. Supp. Table 4:Measurements of circulating metabolic parameters, food consumption, and weights in grouped vs. isolated CD1 female mice.
Supplementary material 4 from Salivary microRNAs Show Potential as a Noninvasive Biomarker for Detecting Resectable Pancreatic Cancer
Authors: Xie Zijun , Yin Xiaoyu , Gong Bo , Nie Wenjing , Wu Bin , Zhang Xuchao , Huang Jian , Zhang Pingyou , Zhou Zhiwei , Li Zijun
Published: April 2023

Supplementary material 4. Normalised microarray data in the discovery phase.
Supplementary material 3 from Salivary microRNAs Show Potential as a Noninvasive Biomarker for Detecting Resectable Pancreatic Cancer
Authors: Xie Zijun , Yin Xiaoyu , Gong Bo , Nie Wenjing , Wu Bin , Zhang Xuchao , Huang Jian , Zhang Pingyou , Zhou Zhiwei , Li Zijun
Published: April 2023

Supplementary material 3. Detailed demographic, clinical and experimental information of the enrolled participants including patients with resectable pancreatic cancer and benign pancreatic tumor, and healthy controls.
Supplementary Data 4 from A New Biomarker That Predicts Colonic Neoplasia Outcome in Patients with Hyperplastic Colonic Polyps
Authors: Do Catherine , Bertrand Claudine , Palasse Julien , Delisle Marie-Bernadette , Shulkes Arthur , Cohen-Jonathan-Moyal Elizabeth , Ferrand Audrey , Seva Catherine
Published: April 2023

PDF file - 203K
Supplementary material 2 from Salivary microRNAs Show Potential as a Noninvasive Biomarker for Detecting Resectable Pancreatic Cancer
Authors: Xie Zijun , Yin Xiaoyu , Gong Bo , Nie Wenjing , Wu Bin , Zhang Xuchao , Huang Jian , Zhang Pingyou , Zhou Zhiwei , Li Zijun
Published: April 2023

Supplementary material 2. Pancreatic cancer staging based on The American Joint Committee on Cancer: 7th Edition on Cancer Staging.
Supplementary Figure S1 from Benzyl Isothiocyanate Inhibits Epithelial-Mesenchymal Transition in Cultured and Xenografted Human Breast Cancer Cells
Authors: Sehrawat Anuradha , Singh Shivendra V.
Published: April 2023

Supplementary Figure S1 from Benzyl Isothiocyanate Inhibits Epithelial-Mesenchymal Transition in Cultured and Xenografted Human Breast Cancer Cells
Supplementary Table 1 from Mapping of Three Genetic Determinants of Susceptibility to Estrogen-Induced Mammary Cancer within the Emca8 Locus on Rat Chromosome 5
Authors: Schaffer Beverly S. , Leland-Wavrin Kristin M. , Kurz Scott G. , Colletti John A. , Seiler Nicole L. , Warren Christopher L. , Shull James D.
Published: April 2023

XLS file - 12K, Markers Used in Generating ACI.BN-RNO5 Congenic Rat Strains
Supplementary Table 3 from Dynamic Tumor Growth Patterns in a Novel Murine Model of Colorectal Cancer
Authors: Paul Olson Terrah J. , Hadac Jamie N. , Sievers Chelsie K. , Leystra Alyssa A. , Deming Dustin A. , Zahm Christopher D. , Albrecht Dawn M. , Nomura Alice , Nettekoven Laura A. , Plesh Lauren K. , Clipson Linda , Sullivan Ruth , Newton Michael A. , Schelman William R. , Halberg Richard B.
Published: April 2023

PDF file - 28K, Differentially Expressed Gene Functional Categories between Adenomas and Intramucosal Carcinomas
Supplementary Table 1 from Stem Cell Antigen-1 Deficiency Enhances the Chemopreventive Effect of Peroxisome Proliferator–Activated Receptorγ Activation
Authors: Yuan Hongyan , Upadhyay Geeta , Yin Yuzhi , Kopelovich Levy , Glazer Robert I.
Published: April 2023

XLS file - 31K
Supplemental Figure 3 from The Human Gut Microbiome as a Screening Tool for Colorectal Cancer
Authors: Zackular Joseph P. , Rogers Mary A.M. , Ruffin Mack T. , Schloss Patrick D.
Published: April 2023

LeFSe analysis for healthy vs. colonic lesion clinical groups. Adenoma and carcinoma clinical groups were combined into one clinical group (colonic lesion clinical group). LDA values are represented for OTUs enriched in healthy and combined colonic lesions clinical groups.
Supplementary Table 1 from Dietary Soy Effects on Mammary Gland Development during the Pubertal Transition in Nonhuman Primates
Authors: Dewi Fitriya N. , Wood Charles E. , Lees Cynthia J. , Willson Cynthia J. , Register Thomas C. , Tooze Janet A. , Franke Adrian A. , Cline J. Mark
Published: April 2023

PDF file - 65K, Composition of diets used to assess the effect of high-soy diet on the breast of female cynomolgus macaque across pubertal transition.
Supplementary Figure 1 from Dietary Soy Effects on Mammary Gland Development during the Pubertal Transition in Nonhuman Primates
Authors: Dewi Fitriya N. , Wood Charles E. , Lees Cynthia J. , Willson Cynthia J. , Register Thomas C. , Tooze Janet A. , Franke Adrian A. , Cline J. Mark
Published: April 2023

PDF file - 115K, Bone mineral content (BMC) and bone mineral density (BMD) in the female cynomolgus macaque fed a soy or casein lactalbumin (CL) diet during pubertal development as measured by DEXA.
Perspective on this Article from Effects of Cigarette Smoke on the Human Oral Mucosal Transcriptome
Authors: Boyle Jay O. , Gümüş Zeynep H. , Kacker Ashutosh , Choksi Vishal L. , Bocker Jennifer M. , Zhou Xi Kathy , Yantiss Rhonda K. , Hughes Duncan B. , Du Baoheng , Judson Benjamin L. , Subbaramaiah Kotha , Dannenberg Andrew J.
Published: April 2023

Perspective on this Article from Effects of Cigarette Smoke on the Human Oral Mucosal Transcriptome
Supplementary Figure 5 from Beta-Endorphin Cell Therapy for Cancer Prevention
Authors: Zhang Changqing , Murugan Sengottuvelan , Boyadjieva Nadka , Jabbar Shaima , Shrivastava Pallavi , Sarkar Dipak K.
Published: April 2023

SFigure 5: Effect of nanosphere-delivered dbcAMP (N-cAMP) injection on tyrosine hydroxylase (TH) and corticotropin-releasing hormone (CRH) levels in the hypothalamus.
Supplementary Figure 1 from Beta-Endorphin Cell Therapy for Cancer Prevention
Authors: Zhang Changqing , Murugan Sengottuvelan , Boyadjieva Nadka , Jabbar Shaima , Shrivastava Pallavi , Sarkar Dipak K.
Published: April 2023

SFigure 1: Histopathology of livers from control neurons- or BEP neurons-transplanted groups.
Sup Materials from Activation of the Mitochondrial Apoptotic Pathway Produces Reactive Oxygen Species and Oxidative Damage in Hepatocytes That Contribute to Liver Tumorigenesis
Authors: Hikita Hayato , Kodama Takahiro , Tanaka Satoshi , Saito Yoshinobu , Nozaki Yasutoshi , Nakabori Tasuku , Shimizu Satoshi , Hayashi Yoshito , Li Wei , Shigekawa Minoru , Sakamori Ryotaro , Miyagi Takuya , Hiramatsu Naoki , Tatsumi Tomohide , Takehara Tetsuo
Published: April 2023

Supplemental Figure legend and Material and Methods
Table S1 from Evaluation of Biodistribution of Sulforaphane after Administration of Oral Broccoli Sprout Extract in Melanoma Patients with Multiple Atypical Nevi
Authors: Tahata Shawn , Singh Shivendra V. , Lin Yan , Hahm Eun-Ryeong , Beumer Jan H. , Christner Susan M. , Rao Uma N. , Sander Cindy , Tarhini Ahmad A. , Tawbi Hussein , Ferris Laura K. , Wilson Melissa , Rose Amy , Dietz Catherine M. , Hughes Ellen , Fahey Jed W. , Leachman Sancy A. , Cassidy Pamela B. , Butterfield Lisa H. , Zarour Hassane M. , Kirkwood John M.
Published: April 2023

Plasma sulforaphane concentrations by day, dose, and pre- or post-BSE-SFN administration
Supplemental Figure S1 from Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population
Authors: Wu Si , Zhang Yang , Zhang Lian , Ma Jun-Ling , Zhou Tong , Li Zhe-Xuan , Liu Wei-Dong , Li Wen-Qing , You Wei-Cheng , Pan Kai-Feng
Published: April 2023

Figure S1. Representative pictures of immunohistochemical staining for PCDH10 and PCDH17 (20X) PCDH10 and PCDH17 were expressed in the membrane and cytoplasm of epithelial and some stromal cell. (a, b) Representative pictures of immunohistochemical staining for PCDH10 negative and positive expression. (c, d) Representative pictures of immunohistochemical staining for PCDH17 negative and positive expression.
Supplementary Tables S1 to S9 from Gene Methylation and Cytological Atypia in Random Fine-Needle Aspirates for Assessment of Breast Cancer Risk
Authors: Stearns Vered , Fackler Mary Jo , Hafeez Sidra , Bujanda Zoila Lopez , Chatterton Robert T. , Jacobs Lisa K. , Khouri Nagi F. , Ivancic David , Kenney Kara , Shehata Christina , Jeter Stacie C. , Wolfman Judith A. , Zalles Carola M. , Huang Peng , Khan Seema A. , Sukumar Saraswati
Published: April 2023

Table S1: DNA methylation in rFNA samples Table S2: Association between methylation and menopause as measured by LH and FSH- Univariate analysis Table S3: Association between Methylation and Menstrual Cycle as Measured by Estradiol and Progesterone - Univariate Analysis Table S4: Association between DNA methylation and lifetime Gail risk score - multivariate analysis Table S5: Association between DNA Methylation and percent breast density Table S6: Association between DNA Methylation and Masood cytology score Table S7: Gene methylation versus standard cytology Table S8: Spearman correlation: relationship between biomarkers within the panel Table S9: Agreement between baseline and 6 month methylation levels in rFNA among individuals (n=15).
Supplementary Data from Randomized Controlled Trial of the Gastrin/CCK2 Receptor Antagonist Netazepide in Patients with Barrett's Esophagus
Authors: Abrams Julian A. , Del Portillo Armando , Hills Caitlin , Compres Griselda , Friedman Richard A. , Cheng Bin , Poneros John , Lightdale Charles J. , De La Rue Rachel , di Pietro Massimiliano , Fitzgerald Rebecca C. , Sepulveda Antonia , Wang Timothy C.
Published: April 2023

Supplementary Figure 1 and Supplementary Tables 1-3
Supplementary Figures from Prevalence of Aflatoxin-Associated TP53R249S Mutation in Hepatocellular Carcinoma in Hispanics in South Texas
Authors: Jiao Jingjing , Niu Weibo , Wang Ying , Baggerly Keith , Ye Yuanqing , Wu Xifeng , Davenport Dewitt , Almeda Jose Luis , Betancourt-Garcia Monica M. , Forse R. Armour , Stevenson Heather L. , Watt Gordon P. , McCormick Joseph B. , Fisher-Hoch Susan P. , Beretta Laura
Published: April 2023

Supplemental Figure S1. TP53R249S mutation detection in HCC tumors by RFLP. Supplemental Figure S2. TP53R249S mutation detection in cfDNA by RFLP. Supplementary Figure 3. Prognostic value of TP53R249S mutation in the cfDNA from HCC patients as shown by overall survival. Supplementary Figure S4. Clinical and demographic features associated with TP53R249S mutation in TCGA HCCs.
Supp data figure 1 from Effects of Black Raspberry Extract and Protocatechuic Acid on Carcinogen-DNA Adducts and Mutagenesis, and Oxidative Stress in Rat and Human Oral Cells
Authors: Guttenplan Joseph B. , Chen Kun-Ming , Sun Yuan-Wan , Kosinska Wieslawa , Zhou Ying , Kim Seungjin (Agatha) , Sung Youngjae , Gowda Krishne , Amin Shantu , Stoner Gary D. , El-Bayoumy Karam
Published: April 2023

HPLC of 5 ng DBPDE incubated in keratinocyte growth medium overnight at room temperature in the absence (lower trace) and presence of BRB extract (10 ug/ml, middle trace) or (50ug/ml, upper trace).
Supplementary Data 3 from Breast Cancer Chemoprevention: Use and Views of Australian Women and Their Clinicians
Authors: Macdonald Courtney , Saunders Christobel M. , Keogh Louise A. , Hunter Morgan , Mazza Danielle , McLachlan Sue-Anne , Jones Sandra C. , Nesci Stephanie , Friedlander Michael L. , Hopper John L. , Emery Jon D. , Hickey Martha , Milne Roger L. , Phillips Kelly-Anne
Published: April 2023

Strongest barriers to and facilitators of risk reducing medication use for kConFab women
Supplementary material 3 from Evaluation of the Associations Between Cervical Microbiota and HPV Infection, Clearance, and Persistence in Cytologically Normal Women
Authors: Ritu Wu , Enqi Wu , Zheng Siriguleng , Wang Jiandong , Ling Yaqin , Wang Yan
Published: April 2023

The proportion of each community state types (CST) in different group of HPV status
Supplementary Figure 1 from ProDiet: A Phase II Randomized Placebo-controlled Trial of Green Tea Catechins and Lycopene in Men at Increased Risk of Prostate Cancer
Authors: Lane J. Athene , Er Vanessa , Avery Kerry N.L. , Horwood Jeremy , Cantwell Marie , Caro Gema P. , Crozier Alan , Smith George Davey , Donovan Jenny L. , Down Liz , Hamdy Freddie C. , Gillatt David , Holly Jeff , Macefield Rhiannon , Moody Hilary , Neal David E. , Walsh Eleanor , Martin Richard M. , Metcalfe Chris
Published: April 2023

Figure of changes in lycopene and green tea intake over 6 months
Supplementary Tables S1-S2 from Lipidomic Profiles of Plasma Exosomes Identify Candidate Biomarkers for Early Detection of Hepatocellular Carcinoma in Patients with Cirrhosis
Authors: Sanchez Jessica I. , Jiao Jingjing , Kwan Suet-Ying , Veillon Lucas , Warmoes Marc O. , Tan Lin , Odewole Mobolaji , Rich Nicole E. , Wei Peng , Lorenzi Philip L. , Singal Amit G. , Beretta Laura
Published: April 2023

Supplementary Table S1. Demographic and clinical parameters in 72 participants with cirrhosis (31 with HCC and 41 without HCC). Supplementary Table S2. Relative abundance (%) of the lipid classes detected in non-HCC exosomes, HCC exosomes, non-HCC plasma and HCC plasma.
Supplemental Table S2. List of significantly enriched pathways (P<0.01). from Uninterrupted Sedentary Behavior Downregulates BRCA1 Gene Expression
Authors: Pettapiece-Phillips Rachael , Kotlyar Max , Chehade Rania , Salmena Leonardo , Narod Steven A. , Akbari Mohammad , Jurisica Igor , Kotsopoulos Joanne
Published: April 2023

Supplemental Table S2. List of significantly enriched pathways (P<0.01).
Supplementary Information from Myeloid Differentiation Factor 88 Signaling in Bone Marrow–Derived Cells Promotes Gastric Tumorigenesis by Generation of Inflammatory Microenvironment
Authors: Maeda Yusuke , Echizen Kanae , Oshima Hiroko , Yu Liang , Sakulsak Natthiya , Hirose Osamu , Yamada Yoichi , Taniguchi Tadatsugu , Jenkins Brendan J. , Saya Hideyuki , Oshima Masanobu
Published: April 2023

Supplementary Materials and Methods.
Supplementary Information from Aspirin Suppresses PGE2 and Activates AMP Kinase to Inhibit Melanoma Cell Motility, Pigmentation, and Selective Tumor Growth In Vivo
Authors: Kumar Dileep , Rahman Hafeez , Tyagi Ethika , Liu Tong , Li Chelsea , Lu Ran , Lum David , Holmen Sheri L. , Maschek J. Alan , Cox James E. , VanBrocklin Matthew W. , Grossman Douglas
Published: April 2023

S1. Effect of ASA on cell viability. S2. Effect of Celecoxib on cell viability and migration. S3. Mice are tolerant of chronic dailly gavage. S4. ASA delays tumor growth of cell implants. S5. ASA does not delay tumor growth of some cell implants. S6. Effect of chronic ASA exposure on cytokines.
Supplementary Tables and Figures from The Impact of One-week Dietary Supplementation with Kava on Biomarkers of Tobacco Use and Nitrosamine-based Carcinogenesis Risk among Active Smokers
Authors: Wang Yi , Narayanapillai Sreekanth C. , Tessier Katelyn M. , Strayer Lori G. , Upadhyaya Pramod , Hu Qi , Kingston Rick , Salloum Ramzi G. , Lu Junxuan , Hecht Stephen S. , Hatsukami Dorothy K. , Fujioka Naomi , Xing Chengguo
Published: April 2023

Supplemental Tables 1-7 and Supplemental Figures 1-5
Table S3 from Association of IgG Glycosylation and Esophageal Precancerosis Beyond Inflammation
Authors: Wu Zhiyuan , Pan Huiying , Liu Di , Zhou Di , Tao Lixin , Zhang Jie , Wang Xiaonan , Wang Youxin , Wang Wei , Guo Xiuhua
Published: April 2023

The dietary characteristics between esophageal precancerosis group and the control.
Table S1 from Association of IgG Glycosylation and Esophageal Precancerosis Beyond Inflammation
Authors: Wu Zhiyuan , Pan Huiying , Liu Di , Zhou Di , Tao Lixin , Zhang Jie , Wang Xiaonan , Wang Youxin , Wang Wei , Guo Xiuhua
Published: April 2023

The detailed information of questionnaire in this study.
Supplementary Table 4 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy
Authors: Mullooly Maeve , Puvanesarajah Samantha , Fan Shaoqi , Pfeiffer Ruth M. , Olsson Linnea T. , Hada Manila , Kirk Erin L. , Vacek Pamela M. , Weaver Donald L. , Shepherd John , Mahmoudzadeh Amir , Wang Jeff , Malkov Serghei , Johnson Jason M. , Hewitt Stephen M. , Herschorn Sally D. , Sherman Mark E. , Troester Melissa A. , Gierach Gretchen L.
Published: April 2023

Supplementary Table 4
Supplementary Table 3 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy
Authors: Mullooly Maeve , Puvanesarajah Samantha , Fan Shaoqi , Pfeiffer Ruth M. , Olsson Linnea T. , Hada Manila , Kirk Erin L. , Vacek Pamela M. , Weaver Donald L. , Shepherd John , Mahmoudzadeh Amir , Wang Jeff , Malkov Serghei , Johnson Jason M. , Hewitt Stephen M. , Herschorn Sally D. , Sherman Mark E. , Troester Melissa A. , Gierach Gretchen L.
Published: April 2023

Supplementary Table 3
Supplementary Table 2A from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy
Authors: Mullooly Maeve , Puvanesarajah Samantha , Fan Shaoqi , Pfeiffer Ruth M. , Olsson Linnea T. , Hada Manila , Kirk Erin L. , Vacek Pamela M. , Weaver Donald L. , Shepherd John , Mahmoudzadeh Amir , Wang Jeff , Malkov Serghei , Johnson Jason M. , Hewitt Stephen M. , Herschorn Sally D. , Sherman Mark E. , Troester Melissa A. , Gierach Gretchen L.
Published: April 2023

Supplementary Table 2A
Supplementary Data from Unmetabolized Folic Acid, Tetrahydrofolate, and Colorectal Adenoma Risk
Authors: Rees Judy R. , Morris Carolyn B. , Peacock Janet L. , Ueland Per M. , Barry Elizabeth L. , McKeown-Eyssen Gail E. , Figueiredo Jane C. , Snover Dale C. , Baron John A.
Published: April 2023

Additional analyses of folate and adenoma outcomes.
Supplementary Data - Tables S1 - S3 from Circulating Receptor Activator of Nuclear Factor-κB (RANK), RANK ligand (RANKL), and Mammographic Density in Premenopausal Women
Authors: Toriola Adetunji T. , Appleton Catherine M. , Zong Xiaoyu , Luo Jingqin , Weilbaecher Katherine , Tamimi Rulla M. , Colditz Graham A.
Published: April 2023

Table S1. Differences in Volumetric Percent Density by Tertiles of Circulating RANK and sRANKL. Table S2. Least Square Means of Non-Dense Volume by Tertiles of Circulating RANK and sRANKL. Table S3. Least Square Means of Volumetric Percent Density, Dense Volume, and Non Dense Volume by Tertiles of Circulating RANK, Excluding Women whose Circulating RANK Values were reported as<2 pg/mL.T
Supplemental Table S3 from Effect of Green Tea Supplements on Liver Enzyme Elevation: Results from a Randomized Intervention Study in the United States
Authors: Yu Zheming , Samavat Hamed , Dostal Allison M. , Wang Renwei , Torkelson Carolyn J. , Yang Chung S. , Butler Lesley M. , Kensler Thomas W. , Wu Anna H. , Kurzer Mindy S. , Yuan Jian-Min
Published: April 2023

Supplemental Table S3 describes the characteristics at baseline among study participants in the green tea extract group with and without ALT greater than 75 U/L.
Supplemental Table S1 from Dietary Methyl Donor Depletion Suppresses Intestinal Adenoma Development
Authors: Hanley Matthew P. , Kadaveru Krishna , Perret Christine , Giardina Charles , Rosenberg Daniel W.
Published: April 2023

Supplemental Table S1. Nutritional composition of the methyl donor sufficient (MDS; TD.99366, Harlan Laboratories, Madison WI) and methyl donor deficient (MDD; TD.00605, Harlan Laboratories, Madison WI).
Supplementary Table from Withaferin A Inhibits Fatty Acid Synthesis in Rat Mammary Tumors
Authors: Singh Krishna B. , Hahm Eun-Ryeong , Kim Su-Hyeong , Singh Shivendra V.
Published: April 2023

Supplementary Table from Withaferin A Inhibits Fatty Acid Synthesis in Rat Mammary Tumors
Supplementary Figure 2 from Gene Signatures Associated with Mouse Postnatal Hindbrain Neural Stem Cells and Medulloblastoma Cancer Stem Cells Identify Novel Molecular Mediators and Predict Human Medulloblastoma Molecular Classification
Authors: Corno Daniela , Pala Mauro , Cominelli Manuela , Cipelletti Barbara , Leto Ketty , Croci Laura , Barili Valeria , Brandalise Federico , Melzi Raffaella , Di Gregorio Alessandra , Sergi Lucia Sergi , Politi Letterio Salvatore , Piemonti Lorenzo , Bulfone Alessandro , Rossi Paola , Rossi Ferdinando , Consalez Gian Giacomo , Poliani Pietro Luigi , Galli Rossella
Published: April 2023

PDF file - 183K, Long term-cultured hindbrain- and forebrain-derived NSCs are Sonic Hedgehog (Shh) pathway-independent, as cyclopamine treatment negatively affects the survival/proliferation of short-term cultured but not of long term-cultured NSCs
Supplementary Figure S6 from Relief of Feedback Inhibition of HER3 Transcription by RAF and MEK Inhibitors Attenuates Their Antitumor Effects in BRAF-Mutant Thyroid Carcinomas
Authors: Montero-Conde Cristina , Ruiz-Llorente Sergio , Dominguez Jose M. , Knauf Jeffrey A. , Viale Agnes , Sherman Eric J. , Ryder Mabel , Ghossein Ronald A. , Rosen Neal , Fagin James A.
Published: April 2023

Supplementary Figure S6 PDF file - 107K, Genetic knock-down or pharmacological inhibition of HER3 synergizes with PLX4032 and AZD6244, respectively, to inhibit growth of BRAF mutant thyroid cancer cells. A, SW1736 cells were treated with PLX4032 (0-2000 nM) with or without 1 �gM lapatinib or after stable expression of a shRNA to HER3. Indicated concentrations of PLX4032 and lapatinib were added at day 0 and day 3 and growth was measured 6 days after the first treatment. Points represent percent change (mean +/- SD) in cell count of triplicate wells compared to untreated cells. B, SW1736 cells were treated with 2 �gM PLX4032 or 100 nM AZD6244 and lysates collected at 1 and 72 h. Immunoblotting shows induction of pHER3 by both inhibitors. C, SW1736 and 8505C cells were treated with increasing concentrations of AZD6244 alone (open bars) or in combination with 1 �gM lapatinib (black). Cells were collected and counted after 4 days of treatment. Bars represent percent change (mean +/- SD) in cell counts of triplicate wells compared to untreated cells
Supplementary Table S4 from Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State
Authors: Patricelli Matthew P. , Janes Matthew R. , Li Lian-Sheng , Hansen Rasmus , Peters Ulf , Kessler Linda V. , Chen Yuching , Kucharski Jeff M. , Feng Jun , Ely Tess , Chen Jeffrey H. , Firdaus Sarah J. , Babbar Anjali , Ren Pingda , Liu Yi
Published: April 2023

Supplementary Table 4. Excel table of all peptides identified and quantified in proteomic selectivity screen.
Supplementary Methods from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer
Authors: Zhang Haikuo , Qi Jun , Reyes Jaime M. , Li Lewyn , Rao Prakash K. , Li Fugen , Lin Charles Y. , Perry Jennifer A. , Lawlor Matthew A. , Federation Alexander , De Raedt Thomas , Li Yvonne Y. , Liu Yan , Duarte Melissa A. , Zhang Yanxi , Herter-Sprie Grit S. , Kikuchi Eiki , Carretero Julian , Perou Charles M. , Reibel Jacob B. , Paulk Joshiawa , Bronson Roderick T. , Watanabe Hideo , Brainson Christine Fillmore , Kim Carla F. , Hammerman Peter S. , Brown Myles , Cichowski Karen , Long Henry , Bradner James E. , Wong Kwok-Kin
Published: April 2023

Supplementary Methods
Supplementary Figures S1 - S5, Tables S1 - S2 from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer
Authors: Zhang Haikuo , Qi Jun , Reyes Jaime M. , Li Lewyn , Rao Prakash K. , Li Fugen , Lin Charles Y. , Perry Jennifer A. , Lawlor Matthew A. , Federation Alexander , De Raedt Thomas , Li Yvonne Y. , Liu Yan , Duarte Melissa A. , Zhang Yanxi , Herter-Sprie Grit S. , Kikuchi Eiki , Carretero Julian , Perou Charles M. , Reibel Jacob B. , Paulk Joshiawa , Bronson Roderick T. , Watanabe Hideo , Brainson Christine Fillmore , Kim Carla F. , Hammerman Peter S. , Brown Myles , Cichowski Karen , Long Henry , Bradner James E. , Wong Kwok-Kin
Published: April 2023

Supplementary Figure S1. Generation of LSL-EZH2 conditional transgenic mice. Supplementary Figure S2. H3K27ac super enhancer analysis in EZH2 mouse lung tumors. Supplementary Figure S3. Human NSCLC cells with low levels of EZH2 are not sensitive to disruption of EZH2. Supplementary Figure S4. Development and characterization of JQEZ5. Supplementary Figure S5. Cellular and in vivo characterization of JQEZ5. Supplementary Table S1. Summary of LSL-EZH2 mouse models. Supplementary Table S2. Summary of lung adenocarcinoma in LSL-EZH2 mouse models.
Supplementary Data from Repotrectinib (TPX-0005) Is a Next-Generation ROS1/TRK/ALK Inhibitor That Potently Inhibits ROS1/TRK/ALK Solvent- Front Mutations
Authors: Drilon Alexander , Ou Sai-Hong Ignatius , Cho Byoung Chul , Kim Dong-Wan , Lee Jeeyun , Lin Jessica J. , Zhu Viola W. , Ahn Myung-Ju , Camidge D. Ross , Nguyen Judy , Zhai Dayong , Deng Wei , Huang Zhongdong , Rogers Evan , Liu Juliet , Whitten Jeff , Lim John K. , Stopatschinskaja Shanna , Hyman David M. , Doebele Robert C. , Cui J. Jean , Shaw Alice T.
Published: April 2023

all supplementary files
Supp. Movie 1 from Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids
Authors: Jenkins Russell W. , Aref Amir R. , Lizotte Patrick H. , Ivanova Elena , Stinson Susanna , Zhou Chensheng W. , Bowden Michaela , Deng Jiehui , Liu Hongye , Miao Diana , He Meng Xiao , Walker William , Zhang Gao , Tian Tian , Cheng Chaoran , Wei Zhi , Palakurthi Sangeetha , Bittinger Mark , Vitzthum Hans , Kim Jong Wook , Merlino Ashley , Quinn Max , Venkataramani Chandrasekar , Kaplan Joshua A. , Portell Andrew , Gokhale Prafulla C. , Phillips Bart , Smart Alicia , Rotem Asaf , Jones Robert E. , Keogh Lauren , Anguiano Maria , Stapleton Lance , Jia Zhiheng , Barzily-Rokni Michal , Cañadas Israel , Thai Tran C. , Hammond Marc R. , Vlahos Raven , Wang Eric S. , Zhang Hua , Li Shuai , Hanna Glenn J. , Huang Wei , Hoang Mai P. , Piris Adriano , Eliane Jean-Pierre , Stemmer-Rachamimov Anat O. , Cameron Lisa , Su Mei-Ju , Shah Parin , Izar Benjamin , Thakuria Manisha , LeBoeuf Nicole R. , Rabinowits Guilherme , Gunda Viswanath , Parangi Sareh , Cleary James M. , Miller Brian C. , Kitajima Shunsuke , Thummalapalli Rohit , Miao Benchun , Barbie Thanh U. , Sivathanu Vivek , Wong Joshua , Richards William G. , Bueno Raphael , Yoon Charles H. , Miret Juan , Herlyn Meenhard , Garraway Levi A. , Van Allen Eliezer M. , Freeman Gordon J. , Kirschmeier Paul T. , Lorch Jochen H. , Ott Patrick A. , Hodi F. Stephen , Flaherty Keith T. , Kamm Roger D. , Boland Genevieve M. , Wong Kwok-Kin , Dornan David , Paweletz Cloud Peter , Barbie David A.
Published: April 2023

PDOTS Movie
Supplementary Figure S1 from Loss of RasGAP Tumor Suppressors Underlies the Aggressive Nature of Luminal B Breast Cancers
Authors: Olsen Sarah Naomi , Wronski Ania , Castaño Zafira , Dake Benjamin , Malone Clare , De Raedt Thomas , Enos Miriam , DeRose Yoko S. , Zhou Wenhui , Guerra Stephanie , Loda Massimo , Welm Alana , Partridge Ann H. , McAllister Sandra S. , Kuperwasser Charlotte , Cichowski Karen
Published: April 2023

DAB2IP Expression and Promoter Methylation Analysis in Breast Cancer Cell Lines.
Tables S1, S2, S3, S4, S5 from An RNA-Based Digital Circulating Tumor Cell Signature Is Predictive of Drug Response and Early Dissemination in Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Kalinich Mark , LiCausi Joseph A. , Zheng Yu , Chen Tianqi , Milner John D. , Emmons Erin , Ho Uyen , Broderick Katherine , Silva Erin , Javaid Sarah , Kwan Tanya Todorova , Hong Xin , Dahl Douglas M. , McGovern Francis J. , Efstathiou Jason A. , Smith Matthew R. , Sequist Lecia V. , Kapur Ravi , Wu Chin-Lee , Stott Shannon L. , Ting David T. , Giobbie-Hurder Anita , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Supplementary Table S1. Genes tested for Prostate CTC digital PCR Assay; Supplementary Table S2. Clinical information for prostate cancer patients and healthy donor subjects; Supplementary Table S3. Clinical information for patients enrolled on prospective trial of first-line abiraterone for mCRPC; Supplementary Table S4. Clinical information for patients with localized prostate cancer in radical prostatectomy study; Supplementary Table S5. Droplet digital PCR primers used in this study.
Supplementary Material and Methods from Discovery and Optimization of HKT288, a Cadherin-6–Targeting ADC for the Treatment of Ovarian and Renal Cancers
Authors: Bialucha Carl U. , Collins Scott D. , Li Xiao , Saxena Parmita , Zhang Xiamei , Dürr Clemens , Lafont Bruno , Prieur Pierric , Shim Yeonju , Mosher Rebecca , Lee David , Ostrom Lance , Hu Tiancen , Bilic Sanela , Rajlic Ivana Liric , Capka Vladimir , Jiang Wei , Wagner Joel P. , Elliott GiNell , Veloso Artur , Piel Jessica C. , Flaherty Meghan M. , Mansfield Keith G. , Meseck Emily K. , Rubic-Schneider Tina , London Anne Serdakowski , Tschantz William R. , Kurz Markus , Nguyen Duc , Bourret Aaron , Meyer Matthew J. , Faris Jason E. , Janatpour Mary J. , Chan Vivien W. , Yoder Nicholas C. , Catcott Kalli C. , McShea Molly A. , Sun Xiuxia , Gao Hui , Williams Juliet , Hofmann Francesco , Engelman Jeffrey A. , Ettenberg Seth A. , Sellers William R. , Lees Emma
Published: April 2023

This file describes supplementary material and methods used.
Figures S1, S2, S3, S4, S5, S6 from An RNA-Based Digital Circulating Tumor Cell Signature Is Predictive of Drug Response and Early Dissemination in Prostate Cancer
Authors: Miyamoto David T. , Lee Richard J. , Kalinich Mark , LiCausi Joseph A. , Zheng Yu , Chen Tianqi , Milner John D. , Emmons Erin , Ho Uyen , Broderick Katherine , Silva Erin , Javaid Sarah , Kwan Tanya Todorova , Hong Xin , Dahl Douglas M. , McGovern Francis J. , Efstathiou Jason A. , Smith Matthew R. , Sequist Lecia V. , Kapur Ravi , Wu Chin-Lee , Stott Shannon L. , Ting David T. , Giobbie-Hurder Anita , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Supplementary Figure S1. (A) Schematic of d-CTC assay. Whole blood is processed using the CTC-iChip, resulting in a bulk product highly enriched for intact CTCs (labeled green) but also contains WBCs (labeled red) and RBCs (unlabeled); Supplementary Figure S2. Graphs showing droplet digital PCR signal for each gene in 12 metastatic prostate cancer patients compared to 34 healthy male control subjects; Supplementary Figure S3. (A, B) Graphs of relationships between Prostate CTCM Score and serum PSA, and CTC droplet digital PCR KLK3 signal and serum PSA at the pre-treatment time point; Supplementary Figure S4. (A) Kaplan-Meier curves for radiographic progression-free survival (R-PFS) by CTC HOXB13 status at pretreatment; Supplementary Figure S5. (A) Heatmap of droplet digital PCR CTC signal after whole transcriptome amplification for blood samples from healthy donor controls arranged by sex and age, and from patients with clinically localized prostate cancer, arranged by D'Amico Risk Group; Supplementary Figure S6. (A) Box plots showing pre-operative leave-one-out cross validated (LOOCV) CTCL Score in clinically localized prostate cancer patients according to microscopic SVI or pelvic LN involvement identified at the time of radical prostatectomy
Supplementary Tables 1 - 8 from AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations
Authors: Yen Katharine , Travins Jeremy , Wang Fang , David Muriel D. , Artin Erin , Straley Kimberly , Padyana Anil , Gross Stefan , DeLaBarre Byron , Tobin Erica , Chen Yue , Nagaraja Raj , Choe Sung , Jin Lei , Konteatis Zenon , Cianchetta Giovanni , Saunders Jeffrey O. , Salituro Francesco G. , Quivoron Cyril , Opolon Paule , Bawa Olivia , Saada Véronique , Paci Angelo , Broutin Sophie , Bernard Olivier A. , de Botton Stéphane , Marteyn Benoît S. , Pilichowska Monika , Xu YingXia , Fang Cheng , Jiang Fan , Wei Wentao , Jin Shengfang , Silverman Lee , Liu Wei , Yang Hua , Dang Lenny , Dorsch Marion , Penard-Lacronique Virginie , Biller Scott A. , Su Shin-San Michael
Published: April 2023

Supplementary Table 1. Drug metabolism and pharmacokinetic attributes of AG-221. Supplementary Table 2. Selectivity of AG-221 confirmed by testing against a panel of kinases. Supplementary Table 3. Clinical characteristics of patients with IDH2R140Q-mutated AML. Supplementary Table 4. Treated NSG mice (AML-1, AML-2, AML-3) engrafted with human IDH2R140Q mononuclear cells display stable levels of AG-221 in serum. Supplementary Table 5. AG-221 inhibits 2HG production in models AML-1, AML-2, and AML-3. Supplementary Table 6. Summary of pharmacokinetics/pharmacodynamics in primary human acute myeloid leukemia xenograft model (AML-4). Supplementary Table 7. Summary of data collection and refinement statistics. Supplementary Table 8. Percentage of human chimerism in peripheral blood in models AML-1 and AML-2.
Figure S1-S7 from SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models
Authors: Fedele Carmine , Ran Hao , Diskin Brian , Wei Wei , Jen Jayu , Geer Mitchell J. , Araki Kiyomi , Ozerdem Ugur , Simeone Diane M. , Miller George , Neel Benjamin G. , Tang Kwan Ho
Published: April 2023

Supplementary Figure S1: Combined SHP2/MEK inhibition prevents adaptive resistance in PDAC and NSCLC lines Supplementary Figure S2: SHP2 inhibition abrogates MEK-I-evoked reactivation of the ERK MAPK pathway Supplementary Figure S3: Distinct mechanisms of resistance to MEK-I/SHP099 combination in PDAC lines Supplementary Figure S4: Development of tolerable SHP099/trametinib regimen Supplementary Figure S5: Combination decreases tumor cell proliferation and promotes programmed cell death (PDAC and NSCLC) Supplementary Figure S6: Combination decreases tumor cell proliferation and promotes programmed cell death (PDAC, TNBC and HGSC) Supplementary Figure S7: RTKs/RTK ligand expression and Annexin V/cell cycle analysis of TNBC and HGSC lines
Tables S1-S16 from VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma
Authors: Yao Xiaosai , Tan Jing , Lim Kevin Junliang , Koh Joanna , Ooi Wen Fong , Li Zhimei , Huang Dachuan , Xing Manjie , Chan Yang Sun , Qu James Zhengzhong , Tay Su Ting , Wijaya Giovani , Lam Yue Ning , Hong Jing Han , Lee-Lim Ai Ping , Guan Peiyong , Ng Michelle Shu Wen , He Cassandra Zhengxuan , Lin Joyce Suling , Nandi Tannistha , Qamra Aditi , Xu Chang , Myint Swe Swe , Davies James O. J. , Goh Jian Yuan , Loh Gary , Tan Bryan C. , Rozen Steven G. , Yu Qiang , Tan Iain Bee Huat , Cheng Christopher Wai Sam , Li Shang , Chang Kenneth Tou En , Tan Puay Hoon , Silver David Lawrence , Lezhava Alexander , Steger Gertrud , Hughes Jim R. , Teh Bin Tean , Tan Patrick
Published: April 2023

Supplementary tables
Supplementary Methods, Figure Legends, Tables S1 - S4 from An Acquired HER2 T798I Gatekeeper Mutation Induces Resistance to Neratinib in a Patient with HER2 Mutant–Driven Breast Cancer
Authors: Hanker Ariella B. , Brewer Monica Red , Sheehan Jonathan H. , Koch James P. , Sliwoski Gregory R. , Nagy Rebecca , Lanman Richard , Berger Michael F. , Hyman David M. , Solit David B. , He Jie , Miller Vincent , Cutler Richard E. , Lalani Alshad S. , Cross Darren , Lovly Christine M. , Meiler Jens , Arteaga Carlos L.
Published: April 2023

Supplementary Table S1. Summary of mutations identified by FoundationOne profiling of the original, pre-neratinib skin metastasis. Supplementary Table S2. Frequency of HER2L869R and HER2T798I mutations. Supplementary Table S3. Sequencing of plasma DNA. Supplementary Table S4. ERBB2 targeted capture.
Supplementary Figures S1 - S2 from An Acquired HER2 T798I Gatekeeper Mutation Induces Resistance to Neratinib in a Patient with HER2 Mutant–Driven Breast Cancer
Authors: Hanker Ariella B. , Brewer Monica Red , Sheehan Jonathan H. , Koch James P. , Sliwoski Gregory R. , Nagy Rebecca , Lanman Richard , Berger Michael F. , Hyman David M. , Solit David B. , He Jie , Miller Vincent , Cutler Richard E. , Lalani Alshad S. , Cross Darren , Lovly Christine M. , Meiler Jens , Arteaga Carlos L.
Published: April 2023

Supplementary Figure S1. HER2L869R and HER3E928G cooperate to drive ERBB signaling output. Supplementary Figure S2. MG132 treatment restores expression of HER2T798I.
Supplementary Methods and Supplementary Figure and Table Legends from Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
Authors: Jusakul Apinya , Cutcutache Ioana , Yong Chern Han , Lim Jing Quan , Huang Mi Ni , Padmanabhan Nisha , Nellore Vishwa , Kongpetch Sarinya , Ng Alvin Wei Tian , Ng Ley Moy , Choo Su Pin , Myint Swe Swe , Thanan Raynoo , Nagarajan Sanjanaa , Lim Weng Khong , Ng Cedric Chuan Young , Boot Arnoud , Liu Mo , Ong Choon Kiat , Rajasegaran Vikneswari , Lie Stefanus , Lim Alvin Soon Tiong , Lim Tse Hui , Tan Jing , Loh Jia Liang , McPherson John R. , Khuntikeo Narong , Bhudhisawasdi Vajaraphongsa , Yongvanit Puangrat , Wongkham Sopit , Totoki Yasushi , Nakamura Hiromi , Arai Yasuhito , Yamasaki Satoshi , Chow Pierce Kah-Hoe , Chung Alexander Yaw Fui , Ooi London Lucien Peng Jin , Lim Kiat Hon , Dima Simona , Duda Dan G. , Popescu Irinel , Broet Philippe , Hsieh Sen-Yung , Yu Ming-Chin , Scarpa Aldo , Lai Jiaming , Luo Di-Xian , Carvalho André Lopes , Vettore André Luiz , Rhee Hyungjin , Park Young Nyun , Alexandrov Ludmil B. , Gordân Raluca , Rozen Steven G. , Shibata Tatsuhiro , Pairojkul Chawalit , Teh Bin Tean , Tan Patrick
Published: April 2023

Further details of methods, in addition to the supplementary figure and table legends.
Supplemental Figure 5 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 5: C7R does not significantly increase intracranial EphA2-CAR T-cell expansion against U373 tumors
Supplemental Figure 1 from Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells
Authors: Shum Thomas , Omer Bilal , Tashiro Haruko , Kruse Robert L. , Wagner Dimitrios L. , Parikh Kathan , Yi Zhongzhen , Sauer Tim , Liu Daofeng , Parihar Robin , Castillo Paul , Liu Hao , Brenner Malcolm K. , Metelitsa Leonid S. , Gottschalk Stephen , Rooney Cliona M.
Published: April 2023

Supplementary Figure 1: CD34-IL7R* (C7R) is stably expressed in T-cells and enhances constitutive STAT5 activation relative to IL7R*.
Supplementary Table S10 from BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells
Authors: Valls Ester , Lobry Camille , Geng Huimin , Wang Ling , Cardenas Mariano , Rivas Martín , Cerchietti Leandro , Oh Philmo , Yang Shao Ning , Oswald Erin , Graham Camille W. , Jiang Yanwen , Hatzi Katerina , Agirre Xabier , Perkey Eric , Li Zhuoning , Tam Wayne , Bhatt Kamala , Leonard John P. , Zweidler-McKay Patrick A. , Maillard Ivan , Elemento Olivier , Ci Weimin , Aifantis Iannis , Melnick Ari
Published: April 2023

Supplementary Table S10. p value of NOTCH2 target genes and members of its transcriptional complex that are inversely correlated to BCL6 in primary GC B-cells.
Supplementary Table 2 from Prediction of DNA Repair Inhibitor Response in Short-Term Patient-Derived Ovarian Cancer Organoids
Authors: Hill Sarah J. , Decker Brennan , Roberts Emma A. , Horowitz Neil S. , Muto Michael G. , Worley Michael J. , Feltmate Colleen M. , Nucci Marisa R. , Swisher Elizabeth M. , Nguyen Huy , Yang Chunyu , Morizane Ryuji , Kochupurakkal Bose S. , Do Khanh T. , Konstantinopoulos Panagiotis A. , Liu Joyce F. , Bonventre Joseph V. , Matulonis Ursula A. , Shapiro Geoffrey I. , Berkowitz Ross S. , Crum Christopher P. , D'Andrea Alan D.
Published: April 2023

Supplementary Table 2
SuppTable4 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer
Authors: Liu Hui , Murphy Charles J. , Karreth Florian A. , Emdal Kristina B. , White Forest M. , Elemento Olivier , Toker Alex , Wulf Gerburg M. , Cantley Lewis C.
Published: April 2023

Supplementary Table 4 lists all fusions
Supplementary Figure S1-13 and Supplementary Table S1,3 from Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes
Authors: Hayashi Yoshihiro , Zhang Yue , Yokota Asumi , Yan Xiaomei , Liu Jinqin , Choi Kwangmin , Li Bing , Sashida Goro , Peng Yanyan , Xu Zefeng , Huang Rui , Zhang Lulu , Freudiger George M. , Wang Jingya , Dong Yunzhu , Zhou Yile , Wang Jieyu , Wu Lingyun , Bu Jiachen , Chen Aili , Zhao Xinghui , Sun Xiujuan , Chetal Kashish , Olsson Andre , Watanabe Miki , Romick-Rosendale Lindsey E. , Harada Hironori , Shih Lee-Yung , Tse William , Bridges James P. , Caligiuri Michael A. , Huang Taosheng , Zheng Yi , Witte David P. , Wang Qian-fei , Qu Cheng-Kui , Salomonis Nathan , Grimes H. Leighton , Nimer Stephen D. , Xiao Zhijian , Huang Gang
Published: April 2023

Figure S1-13 and Table S1,3
supplementary table S1-S8 from FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor
Authors: Ran Leili , Chen Yuedan , Sher Jessica , Wong Elissa W.P. , Murphy Devan , Zhang Jenny Q. , Li Dan , Deniz Kemal , Sirota Inna , Cao Zhen , Wang Shangqian , Guan Youxin , Shukla Shipra , Li Katie Yang , Chramiec Alan , Xie Yuanyuan , Zheng Deyou , Koche Richard P. , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

S1. De novo motifs in GIST-Specific ETV1 enhancers; S2. De novo motifs in Prostate Specific ETV1 enhancers; S3. De novo motifs in Shared ETV1 enhancers; S4. De novo motifs in Shared ETV1 promoters; S5: Expression of Forkhead Transcription Factors in GIST and non-GIST tumors from GENT dataset; S6: Custom Gene Sets Used for GSEA; S7: GSEA results of gene sets enriched among downregulated genes in GIST48 transfected with siFOXF1 compared with siScrambled; S8: GSEA results of gene sets enriched among downregulated genes in GIST48 treated with siETV1
Figure S1-S8 from FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor
Authors: Ran Leili , Chen Yuedan , Sher Jessica , Wong Elissa W.P. , Murphy Devan , Zhang Jenny Q. , Li Dan , Deniz Kemal , Sirota Inna , Cao Zhen , Wang Shangqian , Guan Youxin , Shukla Shipra , Li Katie Yang , Chramiec Alan , Xie Yuanyuan , Zheng Deyou , Koche Richard P. , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

Figure S1. Expression of forkhead family transcription factors in GIST; S2. Motif analysis of the FOXF1 cistrome and validation of FOXF1 binding sites in GIST 48 cells; S3. FOXF1 regulates ETV1, KIT, and ETV1- and KIT-dependent transcriptome as well as cell cycle regulated genes; S4. Representative ChIP-seq and ATAC-seq profiles with siRNAmediated downregulation of ETV1 and FOXF1 in GIST48 cells; S5. FOXF1 regulates KIT expression and signaling; S6. FOXF1 regulates cell cycle progression and is required for growth and proliferation of GIST cells in vitro; S7. Generation of the Foxf1f-HA-Foxf1 allele; S8. Foxf1 expression in mouse GI tract and Foxf1 ablation reduces mutant Kit-mediated hyperplasia of mouse large intestine.
Dataset 1 from Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer
Authors: Zou Min , Toivanen Roxanne , Mitrofanova Antonina , Floch Nicolas , Hayati Sheida , Sun Yanping , Le Magnen Clémentine , Chester Daniel , Mostaghel Elahe A. , Califano Andrea , Rubin Mark A. , Shen Michael M. , Abate-Shen Cory
Published: April 2023

Differentially expressed genes for mouse CRPC tumors
Supplementary Figures S1 through S6 from Identification of a DNA Damage–Induced Alternative Splicing Pathway That Regulates p53 and Cellular Senescence Markers
Authors: Chen Jing , Crutchley John , Zhang Dadong , Owzar Kouros , Kastan Michael B.
Published: April 2023

Figure S1: Detection of p53beta mRNA. Figure S2: Regulation of p53beta splicing by CP466722 (CP) and other protein factors. Figure S3: Regulation of p53beta expression by RPL26. Figure S4: Regulation of p53beta expression by SRSF7. Figure S5: Characterization of stable cell lines overexpressing p53beta and p53beta CRISPR knockout cells. Figure S6: Modulators of DNA damage induced cellular senescence.
Supplementary Table S7 from Chemotherapy-Resistant Human Acute Myeloid Leukemia Cells Are Not Enriched for Leukemic Stem Cells but Require Oxidative Metabolism
Authors: Farge Thomas , Saland Estelle , de Toni Fabienne , Aroua Nesrine , Hosseini Mohsen , Perry Robin , Bosc Claudie , Sugita Mayumi , Stuani Lucille , Fraisse Marine , Scotland Sarah , Larrue Clément , Boutzen Héléna , Féliu Virginie , Nicolau-Travers Marie-Laure , Cassant-Sourdy Stéphanie , Broin Nicolas , David Marion , Serhan Nizar , Sarry Audrey , Tavitian Suzanne , Kaoma Tony , Vallar Laurent , Iacovoni Jason , Linares Laetitia K. , Montersino Camille , Castellano Rémy , Griessinger Emmanuel , Collette Yves , Duchamp Olivier , Barreira Yara , Hirsch Pierre , Palama Tony , Gales Lara , Delhommeau François , Garmy-Susini Barbara H. , Portais Jean-Charles , Vergez François , Selak Mary , Danet-Desnoyers Gwenn , Carroll Martin , Récher Christian , Sarry Jean-Emmanuel
Published: April 2023

Summary of all GSEA data identified in AraC- versus PBS-treated AML cells in PDX and LOW versus HIGH Responder to AraC in PDX.
Supplementary Table S5 from Chemotherapy-Resistant Human Acute Myeloid Leukemia Cells Are Not Enriched for Leukemic Stem Cells but Require Oxidative Metabolism
Authors: Farge Thomas , Saland Estelle , de Toni Fabienne , Aroua Nesrine , Hosseini Mohsen , Perry Robin , Bosc Claudie , Sugita Mayumi , Stuani Lucille , Fraisse Marine , Scotland Sarah , Larrue Clément , Boutzen Héléna , Féliu Virginie , Nicolau-Travers Marie-Laure , Cassant-Sourdy Stéphanie , Broin Nicolas , David Marion , Serhan Nizar , Sarry Audrey , Tavitian Suzanne , Kaoma Tony , Vallar Laurent , Iacovoni Jason , Linares Laetitia K. , Montersino Camille , Castellano Rémy , Griessinger Emmanuel , Collette Yves , Duchamp Olivier , Barreira Yara , Hirsch Pierre , Palama Tony , Gales Lara , Delhommeau François , Garmy-Susini Barbara H. , Portais Jean-Charles , Vergez François , Selak Mary , Danet-Desnoyers Gwenn , Carroll Martin , Récher Christian , Sarry Jean-Emmanuel
Published: April 2023

Up- and down-regulated genes in AML patients that have the lower response (LowR) to AraC in vivo in NSG mice compared to high responder (HighR) to AraC in vivo using PDX assay.