bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 3 from Improving the Performance of Somatic Mutation Identification by Recovering Circulating Tumor DNA Mutations
Authors: Fu Yu , Jovelet Cécile , Filleron Thomas , Pedrero Marion , Motté Nelly , Boursin Yannick , Luo Yufei , Massard Christophe , Campone Mario , Levy Christelle , Diéras Véronique , Bachelot Thomas , Garrabey Julie , Soria Jean-Charles , Lacroix Ludovic , André Fabrice , Lefebvre Celine
Published: April 2023

Number of ctDNA mutations according to previous chemotherapy treatment.
Supplementary Figure 1 from Improving the Performance of Somatic Mutation Identification by Recovering Circulating Tumor DNA Mutations
Authors: Fu Yu , Jovelet Cécile , Filleron Thomas , Pedrero Marion , Motté Nelly , Boursin Yannick , Luo Yufei , Massard Christophe , Campone Mario , Levy Christelle , Diéras Véronique , Bachelot Thomas , Garrabey Julie , Soria Jean-Charles , Lacroix Ludovic , André Fabrice , Lefebvre Celine
Published: April 2023

ctDNA mutations identified by somatic mutation callers and cmDetect in the simulated data set. Scatter plot of the allele frequency in blood (x-axis) and in tumor (y-axis) of the simulated ctDNA mutations. ctDNA mutations identified by Mutect (Varscan2) or cmDetect are shown in green; ctDNA mutations identified only by cmDetect are shown in blue; ctDNA mutations not identified are shown in gray.
Supplementary Materials and Methods and Supplementary Figure Legends from Preclinical Efficacy of the Auristatin-Based Antibody–Drug Conjugate BAY 1187982 for the Treatment of FGFR2-Positive Solid Tumors
Authors: Sommer Anette , Kopitz Charlotte , Schatz Christoph A. , Nising Carl F. , Mahlert Christoph , Lerchen Hans-Georg , Stelte-Ludwig Beatrix , Hammer Stefanie , Greven Simone , Schuhmacher Joachim , Braun Manuela , Zierz Ruprecht , Wittemer-Rump Sabine , Harrenga Axel , Dittmer Frank , Reetz Frank , Apeler Heiner , Jautelat Rolf , Huynh Hung , Ziegelbauer Karl , Kreft Bertolt
Published: April 2023

Supplementary Materials and Methods and Supplementary Figure Legends
Supplementary Table S1 from An Integrated Nanotechnology-Enabled Transbronchial Image-Guided Intervention Strategy for Peripheral Lung Cancer
Authors: Jin Cheng S. , Wada Hironobu , Anayama Takashi , McVeigh Patrick Z. , Hu Hsin Pei , Hirohashi Kentaro , Nakajima Takahiro , Kato Tatsuya , Keshavjee Shaf , Hwang David , Wilson Brian C. , Zheng Gang , Yasufuku Kazuhiro
Published: April 2023

Porphysome-enhanced photothermal therapy in rabbit VX2 lung tumor models.
Supplementary Movie S1 from An Integrated Nanotechnology-Enabled Transbronchial Image-Guided Intervention Strategy for Peripheral Lung Cancer
Authors: Jin Cheng S. , Wada Hironobu , Anayama Takashi , McVeigh Patrick Z. , Hu Hsin Pei , Hirohashi Kentaro , Nakajima Takahiro , Kato Tatsuya , Keshavjee Shaf , Hwang David , Wilson Brian C. , Zheng Gang , Yasufuku Kazuhiro
Published: April 2023

In vivo prototype fluorescence bronchoscope imaging of rabbit lung tumor at 48 h post-injection, and fluorescence signal of submucosal tumor is shown in green.
Supplementary Figures S1-S6 from An Integrated Nanotechnology-Enabled Transbronchial Image-Guided Intervention Strategy for Peripheral Lung Cancer
Authors: Jin Cheng S. , Wada Hironobu , Anayama Takashi , McVeigh Patrick Z. , Hu Hsin Pei , Hirohashi Kentaro , Nakajima Takahiro , Kato Tatsuya , Keshavjee Shaf , Hwang David , Wilson Brian C. , Zheng Gang , Yasufuku Kazuhiro
Published: April 2023

Porphysome accumulation in mouse orthotopic A549 cancer at 24h post injection (S1); Biodistribution of porphysomes in mice bearing each of the three subtypes of human lung cancer at 48 h post-IV injection (S2); Porphysome fluorescence images in phantoms at 0, 29 and 58 nM concentration, with and without dissociation using 1% Triton-100 (S3); Gross sections and high-resolution H&E stained tissues following transbronchial PTT at 250 mW in rabbit with IV-administration of 20 mg/kg porphysomes (S4); In vivo transpleural porphysome-enabled fluorescence localization and PTT in the rabbit model using a straight-cut fiber at 500 mW/cm (S5); Gross sections and high-resolution H&E stained tissues following transpleural PTT at 500 mW/cm in rabbit with IV-administration of 20 mg/kg porphysome (S6).
Supplementary Table 3- Tumor incidence of CD24 negative & CD24 positive cell populations from Inflammation Triggers Zeb1-Dependent Escape from Tumor Latency
Authors: De Cock Jasmine M. , Shibue Tsukasa , Dongre Anushka , Keckesova Zuzana , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Summary of tumor incidences at limiting dilutions for CD24negative and CD24positive cell populations
Supplementary Material from Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy
Authors: Ingle James N. , Xie Fang , Ellis Matthew J. , Goss Paul E. , Shepherd Lois E. , Chapman Judith-Anne W. , Chen Bingshu E. , Kubo Michiaki , Furukawa Yoichi , Momozawa Yukihide , Stearns Vered , Pritchard Kathleen I. , Barman Poulami , Carlson Erin E. , Goetz Matthew P. , Weinshilboum Richard M. , Kalari Krishna R. , Wang Liewei
Published: April 2023

Provides supplementary information related to this manuscript.
Supplementary Table 2- Incidence of orthotopic tumor formation and spontaneous metastasis in D2A1-d & parental D2A1 cells from Inflammation Triggers Zeb1-Dependent Escape from Tumor Latency
Authors: De Cock Jasmine M. , Shibue Tsukasa , Dongre Anushka , Keckesova Zuzana , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Summary of incidence of orthotopic tumor formation and spontaneous metastasis at limiting dilutions
Supplementary Figure S5 from Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy
Authors: Ingle James N. , Xie Fang , Ellis Matthew J. , Goss Paul E. , Shepherd Lois E. , Chapman Judith-Anne W. , Chen Bingshu E. , Kubo Michiaki , Furukawa Yoichi , Momozawa Yukihide , Stearns Vered , Pritchard Kathleen I. , Barman Poulami , Carlson Erin E. , Goetz Matthew P. , Weinshilboum Richard M. , Kalari Krishna R. , Wang Liewei
Published: April 2023

Knock down of MIR2052HG decreased androstenedione-induced and E2-induced proliferation in MCF7/AC1 cells.
Supplementary Figure Legends from Inflammation Triggers Zeb1-Dependent Escape from Tumor Latency
Authors: De Cock Jasmine M. , Shibue Tsukasa , Dongre Anushka , Keckesova Zuzana , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Detailed description of supplementary figures
Supplemental Figure S1 from Functional Flow Patterns and Static Blood Pooling in Tumors Revealed by Combined Contrast-Enhanced Ultrasound and Photoacoustic Imaging
Authors: Bar-Zion Avinoam , Yin Melissa , Adam Dan , Foster F. Stuart
Published: April 2023

Construction of the composite histological images.
Supplementary Figure S7 from Metastatic Progression of Prostate Cancer Is Mediated by Autonomous Binding of Galectin-4-O-Glycan to Cancer Cells
Authors: Tsai Chin-Hsien , Tzeng Sheue-Fen , Chao Tai-Kuang , Tsai Chia-Yun , Yang Yu-Chih , Lee Ming-Ting , Hwang Jiuan-Jiuan , Chou Yu-Ching , Tsai Mong-Hsun , Cha Tai-Lung , Hsiao Pei-Wen
Published: April 2023

The expression of inherent RTKs ligands and galectins in PCa.
Supplementary Figure S6 from Metastatic Progression of Prostate Cancer Is Mediated by Autonomous Binding of Galectin-4-O-Glycan to Cancer Cells
Authors: Tsai Chin-Hsien , Tzeng Sheue-Fen , Chao Tai-Kuang , Tsai Chia-Yun , Yang Yu-Chih , Lee Ming-Ting , Hwang Jiuan-Jiuan , Chou Yu-Ching , Tsai Mong-Hsun , Cha Tai-Lung , Hsiao Pei-Wen
Published: April 2023

Galectin-4 enhances the tumorigenicity of 22Rv1 and PC-3 cells.
Supplementary Figure S5 from Metastatic Progression of Prostate Cancer Is Mediated by Autonomous Binding of Galectin-4-O-Glycan to Cancer Cells
Authors: Tsai Chin-Hsien , Tzeng Sheue-Fen , Chao Tai-Kuang , Tsai Chia-Yun , Yang Yu-Chih , Lee Ming-Ting , Hwang Jiuan-Jiuan , Chou Yu-Ching , Tsai Mong-Hsun , Cha Tai-Lung , Hsiao Pei-Wen
Published: April 2023

The effect of non-glaectin-4 control on RTKs phosphorylation and invasion.
Supporting Figure legends from Targeting BRK-Positive Breast Cancers with Small-Molecule Kinase Inhibitors
Authors: Jiang Jie , Gui Fu , He Zhixiang , Li Li , Li Yunzhan , Li Shunying , Wu Xinrui , Deng Zhou , Sun Xihuan , Huang Xiaoxing , Huang Wei , Han Shang , Zhang Ting , Wang Zheng , Jiao Bo , Song Siyang , Wang Hongrui , Chen Lanfen , Zhou Dawang , Liu Qiang , Ren Ruibao , Zhang Jianming , Deng Xianming
Published: April 2023

Supplementary figure legends
Supplementary Figure S1 from Metastatic Progression of Prostate Cancer Is Mediated by Autonomous Binding of Galectin-4-O-Glycan to Cancer Cells
Authors: Tsai Chin-Hsien , Tzeng Sheue-Fen , Chao Tai-Kuang , Tsai Chia-Yun , Yang Yu-Chih , Lee Ming-Ting , Hwang Jiuan-Jiuan , Chou Yu-Ching , Tsai Mong-Hsun , Cha Tai-Lung , Hsiao Pei-Wen
Published: April 2023

Characterization of 22Rv1-derived sublines for invasion activity and galectin-4 expression level.
Supplementary figure 3 from Differential Effects of IL6 and Activin A in the Development of Cancer-Associated Cachexia
Authors: Chen Justin L. , Walton Kelly L. , Qian Hongwei , Colgan Timothy D. , Hagg Adam , Watt Matthew J. , Harrison Craig A. , Gregorevic Paul
Published: April 2023

Titrating rAAV6:IL-6 doses in wild type mice to elevate circulating levels of IL-6. High doses of rAAV6:IL-6 result in cachexia.
Supplemental Materials and Methods from Cardiolipins Are Biomarkers of Mitochondria-Rich Thyroid Oncocytic Tumors
Authors: Zhang Jialing , Yu Wendong , Ryu Seung Woo , Lin John , Buentello Gerardo , Tibshirani Robert , Suliburk James , Eberlin Livia S.
Published: April 2023

This supplemental file contains detailed descriptions of the methods employed in the research reported in the main manuscript, including the methods used for molecular imaging experiments using DESI-MS, immunohistochemistry and immunofluorescence assays, mitochondria isolation and analysis, and histopathologic evaluation of tissue samples.
Supplementary data from A Cell-Penetrating Peptide Targeting AAC-11 Specifically Induces Cancer Cells Death
Authors: Jagot-Lacoussiere Léonard , Kotula Ewa , Villoutreix Bruno O. , Bruzzoni-Giovanelli Heriberto , Poyet Jean-Luc
Published: April 2023

This file contains the supplementary Table S1, which contains the amino-acid sequences of the peptides used in the study, the supplementary Figure S1 which shows that RT53 increases drug-induced cell death and disrupts endogenous AAC-11-Acinus interaction and the supplementary Figure S2 which shows that RT53 does not induce detectable cytochrome c, AIF and Smac release from isolated mitochondria and does not accumulate in mitochondria
Figure S1 from Tissue-Specific Signaling Networks Rewired by Major Somatic Mutations in Human Cancer Revealed by Proteome-Wide Discovery
Authors: Zhao Junfei , Cheng Feixiong , Zhao Zhongming
Published: April 2023

Manhattan plot of putative significantly mutated proteins identified in single cancer type analysis.
Supplemental Figure S3 from Impaired Planar Germ Cell Division in the Testis, Caused by Dissociation of RHAMM from the Spindle, Results in Hypofertility and Seminoma
Authors: Li Huaibiao , Frappart Lucien , Moll Jürgen , Winkler Anne , Kroll Torsten , Hamann Jana , Kufferath Iris , Groth Marco , Taudien Stefan , Schütte Moritz , Yaspo Marie-Laure , Heuer Heike , Lange Bodo M.H. , Platzer Matthias , Zatloukal Kurt , Herrlich Peter , Ploubidou Aspasia
Published: April 2023

Analysis of mouse sperm parameters; Localization of - undifferentiated vs. differentiating - spermatogonia and of activated ERK1/2 in the seminiferous tubule.
supporting data from Multifunctional Telodendrimer Nanocarriers Restore Synergy of Bortezomib and Doxorubicin in Ovarian Cancer Treatment
Authors: Wang Lili , Shi Changying , Wright Forrest A. , Guo Dandan , Wang Xu , Wang Dongliang , Wojcikiewicz Richard J.H. , Luo Juntao
Published: April 2023

Supplementary information contains materials, spectroscopic characterization, telodendrimer synthesis; Figures S1-S24 for synthetic pathway, NMR spectra, MALDI-TOF MS spectra, spectrometry studies, drug release, cellular uptake; Table S1-S2 for synergistic cytotoxicity and blood cell counting studies.
Supplemental Figure S1 from Impaired Planar Germ Cell Division in the Testis, Caused by Dissociation of RHAMM from the Spindle, Results in Hypofertility and Seminoma
Authors: Li Huaibiao , Frappart Lucien , Moll Jürgen , Winkler Anne , Kroll Torsten , Hamann Jana , Kufferath Iris , Groth Marco , Taudien Stefan , Schütte Moritz , Yaspo Marie-Laure , Heuer Heike , Lange Bodo M.H. , Platzer Matthias , Zatloukal Kurt , Herrlich Peter , Ploubidou Aspasia
Published: April 2023

Its centrosome-targeting domain is indispensable for RHAMM spindle localization and it contributes to maintenance of spindle integrity in vitro.
Supplementary Methods from Stomach-Specific Activation of Oncogenic KRAS and STAT3-Dependent Inflammation Cooperatively Promote Gastric Tumorigenesis in a Preclinical Model
Authors: Thiem Stefan , Eissmann Moritz F. , Elzer Joachim , Jonas Anna , Putoczki Tracy L. , Poh Ashleigh , Nguyen Paul , Preaudet Adele , Flanagan Dustin , Vincan Elizabeth , Waring Paul , Buchert Michael , Jarnicki Andrew , Ernst Matthias
Published: April 2023

Extended methods and materials are provided as a supplement to the methods section in the main manuscript and to describe additional methods from the supplementary data.
Supplemental Figures from Stromal-Based Signatures for the Classification of Gastric Cancer
Authors: Uhlik Mark T. , Liu Jiangang , Falcon Beverly L. , Iyer Seema , Stewart Julie , Celikkaya Hilal , O'Mahony Marguerita , Sevinsky Christopher , Lowes Christina , Douglass Larry , Jeffries Cynthia , Bodenmiller Diane , Chintharlapalli Sudhakar , Fischl Anthony , Gerald Damien , Xue Qi , Lee Jee-yun , Santamaria-Pang Alberto , Al-Kofahi Yousef , Sui Yunxia , Desai Keyur , Doman Thompson , Aggarwal Amit , Carter Julia H. , Pytowski Bronislaw , Jaminet Shou-ching , Ginty Fiona , Nasir Aejaz , Nagy Janice A. , Dvorak Harold F. , Benjamin Laura E.
Published: April 2023

These figures contain extensions of data that would not fit in the primary manuscript but are important for a complete understanding of the work. These include analysis of other data sets, correlations between genomic profiling our stromal subtyping and information on bioinformatics and animal models.
Supplemental Figures 1 through 9 and Supplemental Tables 1 and 2 from Stromal-Based Signatures for the Classification of Gastric Cancer
Authors: Uhlik Mark T. , Liu Jiangang , Falcon Beverly L. , Iyer Seema , Stewart Julie , Celikkaya Hilal , O'Mahony Marguerita , Sevinsky Christopher , Lowes Christina , Douglass Larry , Jeffries Cynthia , Bodenmiller Diane , Chintharlapalli Sudhakar , Fischl Anthony , Gerald Damien , Xue Qi , Lee Jee-yun , Santamaria-Pang Alberto , Al-Kofahi Yousef , Sui Yunxia , Desai Keyur , Doman Thompson , Aggarwal Amit , Carter Julia H. , Pytowski Bronislaw , Jaminet Shou-ching , Ginty Fiona , Nasir Aejaz , Nagy Janice A. , Dvorak Harold F. , Benjamin Laura E.
Published: April 2023

These figures contain extensions of data that would not fit in the primary manuscript but are important for a complete understanding of the work. These include analysis of other data sets, correlations between genomic profiling our stromal subtyping and information on bioinformatics and animal models.
Table S5. List of proteins associated with tumor fragmentation. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

The table shows the list of proteins correlating with TF scores as a continuous response with a FDR<0.05, by Significance Analysis of Microarrays.
Supplementary Figure 1: THelper gating strategy from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Flow cytometry gating strategy to identify memory CD4 T cell subpopulations through chemokine receptor expression.
Supplementary Materials and Methods from Interleukin-30 Promotes Breast Cancer Growth and Progression
Authors: Airoldi Irma , Cocco Claudia , Sorrentino Carlo , Angelucci Domenico , Di Meo Serena , Manzoli Lamberto , Esposito Silvia , Ribatti Domenico , Bertolotto Maria , Iezzi Laura , Natoli Clara , Di Carlo Emma
Published: April 2023

Supplementary Materials and Methods
Legend to Supplement Figures from Anticancer Effects of Targeting Hsp70 in Tumor Stromal Cells
Authors: Gabai Vladimir L. , Yaglom Julia A. , Wang Yongmei , Meng Le , Shao Hao , Kim Geunwon , Colvin Teresa , Gestwicki Jason , Sherman Michael Y.
Published: April 2023

Legend to Supplement Figures
Supplementary figures 1-4 from Targetable T-type Calcium Channels Drive Glioblastoma
Authors: Zhang Ying , Cruickshanks Nichola , Yuan Fang , Wang Baomin , Pahuski Mary , Wulfkuhle Julia , Gallagher Isela , Koeppel Alexander F. , Hatef Sarah , Papanicolas Christopher , Lee Jeongwu , Bar Eli E. , Schiff David , Turner Stephen D. , Petricoin Emanuel F. , Gray Lloyd S. , Abounader Roger
Published: April 2023

Supplementary figures: 1): molecular structure of mibefradil, 2) Mibefradil effects on HIFs, 3) effects of sh-RNA inhibition of Cav3.2 in GSCs, 4) Schematic summary of the findings.
Supplementary Table 2 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

Cell lines were treated with the indicated compounds for 96 h and then growth determined. Results represent the mean {plus minus} SD of 2-4 experiments in which each condition was assayed in triplicate.
Supplementary Figure 3 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

A. Tumors were undetectable at 4 weeks by IVIS imaging when b-AP15 was administered from day 1 after injecting A673 cells expressing GFP-luciferase. NSG mice bearing A673 xenografts were treated with DMSO, bortezomib or b-AP15 after they reached 80-100mm3 and weekly tumor size measurements were taken. B. b-AP15 slowed the growth of the established A673 xenografts and C. prolonged survival of A673 tumor bearing mice compared to bortezomib. D. VLX-1570 and b-AP15 treatment did not cause significant weight loss in xenograft models. (two way Anova with Tukey's multiple comparison test).
Supplementary Figure Legends from Efficacy of Adoptive T-cell Therapy Is Improved by Treatment with the Antioxidant N-Acetyl Cysteine, Which Limits Activation-Induced T-cell Death
Authors: Scheffel Matthew J. , Scurti Gina , Simms Patricia , Garrett-Mayer Elizabeth , Mehrotra Shikhar , Nishimura Michael I. , Voelkel-Johnson Christina
Published: April 2023

Legends for Supplementary Figures 1 and 2
Supplemental Methods from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

General Procedures for synthesis of 2,6-Bis-arylidenepiperidone scaffold
Figure S2 from Individualized Breast Cancer Characterization through Single-Cell Analysis of Tumor and Adjacent Normal Cells
Authors: Anjanappa Manjushree , Cardoso Angelo , Cheng Lijun , Mohamad Safa , Gunawan Andrea , Rice Susan , Dong Yan , Li Lang , Sandusky George E. , Srour Edward F. , Nakshatri Harikrishna
Published: April 2023

Figure S2 shows unsupervised clustering of PAM50 genes examined in all cells of patient 1
Supplementary Figure Legends from EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition
Authors: Hsu Ya-Ting , Osmulski Pawel , Wang Yao , Huang Yi-Wen , Liu Lu , Ruan Jianhua , Jin Victor X. , Kirma Nameer B. , Gaczynska Maria E. , Huang Tim Hui-Ming
Published: April 2023

Supplementary Figure Legends Fig S1-S9
Supplemental Table 2 from Lipocalin-2 Promotes Pancreatic Ductal Adenocarcinoma by Regulating Inflammation in the Tumor Microenvironment
Authors: Gomez-Chou Sobeyda B. , Swidnicka-Siergiejko Agnieszka Katarzyna , Badi Niharika , Chavez-Tomar Myrriah , Lesinski Gregory B. , Bekaii-Saab Tanios , Farren Matthew R. , Mace Thomas A. , Schmidt Carl , Liu Yan , Deng Defeng , Hwang Rosa F. , Zhou Liran , Moore Todd , Chatterjee Deyali , Wang Huamin , Leng Xiaohong , Arlinghaus Ralph B. , Logsdon Craig D. , Cruz-Monserrate Zobeida
Published: April 2023

Supplementary Table 2. List of human (h) and mouse (m) primer sequences used in study.
Suppl Video 1 from Monocyte Induction of E-Selectin–Mediated Endothelial Activation Releases VE-Cadherin Junctions to Promote Tumor Cell Extravasation in the Metastasis Cascade
Authors: Häuselmann Irina , Roblek Marko , Protsyuk Darya , Huck Volker , Knopfova Lucia , Grässle Sandra , Bauer Alexander T. , Schneider Stefan W. , Borsig Lubor
Published: April 2023

Suppl Video: Tumor cells (green) and monocytes (white) are seeded on a confluent endothelial monolayer (red) on a 3-D collagen matrix.
Supplementary Materials and Methods and Supplementary Figure Legends from Loss of the Methyl-CpG–Binding Protein ZBTB4 Alters Mitotic Checkpoint, Increases Aneuploidy, and Promotes Tumorigenesis
Authors: Roussel-Gervais Audrey , Naciri Ikrame , Kirsh Olivier , Kasprzyk Laetitia , Velasco Guillaume , Grillo Giacomo , Dubus Pierre , Defossez Pierre-Antoine
Published: April 2023

Supplementary methods and supplementary figure legends
Table S2 from Regeneration of CD8αβ T Cells from T-cell–Derived iPSC Imparts Potent Tumor Antigen-Specific Cytotoxicity
Authors: Maeda Takuya , Nagano Seiji , Ichise Hiroshi , Kataoka Keisuke , Yamada Daisuke , Ogawa Seishi , Koseki Haruhiko , Kitawaki Toshio , Kadowaki Norimitsu , Takaori-Kondo Akifumi , Masuda Kyoko , Kawamoto Hiroshi
Published: April 2023

IC50 of regenerated CTLs
Table S1 from Regeneration of CD8αβ T Cells from T-cell–Derived iPSC Imparts Potent Tumor Antigen-Specific Cytotoxicity
Authors: Maeda Takuya , Nagano Seiji , Ichise Hiroshi , Kataoka Keisuke , Yamada Daisuke , Ogawa Seishi , Koseki Haruhiko , Kitawaki Toshio , Kadowaki Norimitsu , Takaori-Kondo Akifumi , Masuda Kyoko , Kawamoto Hiroshi
Published: April 2023

TCR sequence of original and regenerated CTL
Supplementary Table 5 from Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Comparison of predictive value of DNF versus published methods
Supplementary Methods from Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

This file contains a detailed description of the methods used to reproduce published algorithms for drug clustering.
Figure S5. BRD4 regulates migration and invasion through Notch signaling. from BRD4 Regulates Breast Cancer Dissemination through Jagged1/Notch1 Signaling
Authors: Andrieu Guillaume , Tran Anna H. , Strissel Katherine J. , Denis Gerald V.
Published: April 2023

(A-C) Migration (left panels) and invasion (right panels) assays were conducted using MCF-7 cells under (A) BRD4 over-expression, (B) treatment with IL-6 (50 ng/ml for 24h), (C) BRD4 over-expression and treatment with DAPT (10 microM for 16 h). Bars show means {plus minus} SEM of three independent experiments. Statistical analyses were performed by using Student's t test or one-way ANOVA. (D) Jagged1 and mRNA expression were measured in MDA-MB-231 cells 48h after transfection with the indicated plasmids. Statistical analyses were performed by using one-way ANOVA.
Supplementary Figure S2 from Incipient Melanoma Brain Metastases Instigate Astrogliosis and Neuroinflammation
Authors: Schwartz Hila , Blacher Eran , Amer Malak , Livneh Nir , Abramovitz Lilach , Klein Anat , Ben-Shushan Dikla , Soffer Shelly , Blazquez Raquel , Barrantes-Freer Alonso , Müller Meike , Müller-Decker Karin , Stein Reuven , Tsarfaty Galia , Satchi-Fainaro Ronit , Umansky Viktor , Pukrop Tobias , Erez Neta
Published: April 2023

Supplementary Figure S2: Molecular analysis of mCherry enables detection of micrometastases
Supplementary Information from Increased T-cell Infiltration Elicited by Erk5 Deletion in a Pten-Deficient Mouse Model of Prostate Carcinogenesis
Authors: Loveridge Carolyn J. , Mui Ernest J. , Patel Rachana , Tan Ee Hong , Ahmad Imran , Welsh Michelle , Galbraith Julie , Hedley Ann , Nixon Colin , Blyth Karen , Sansom Owen , Leung Hing Y.
Published: April 2023

This file contains Supplementary Materials and Methods, Supplementary Figures, Legends to Supplementary Figures and Supplementary Tables. Figure S1 shows histopathological analysis of Ptenfl/fl and Ptenfl/fl Erk5fl/fl tumours at 3 and 9-10 month fixed time points and demonstrates that there is reduced %Ki67 positive nuclei in Ptenfl/fl Erk5fl/fl tumours at the 9-10 month time point. There is very little T lymphocyte infiltration at the 3 month time point but significant T lymphocyte infiltration is observed at the later time point. Figure S2 shows Western Blot and QPCR data to validate that P1 and PE cells are null for PTEN and ERK5 protein and Erk5 mRNA transcript where expected. Also shown is IHC staining demonstrating increased immunoreactivity for CCL5 and CXCL10 in Ptenfl/fl Erk5fl/fl compared to Ptenfl/fl tumours and that CCR5 and CXCR3 immunoreactivity is detected in the tumour epithelium and immune cells present in the stroma of Ptenfl/fl Erk5fl/fl tumours. Figure S3 shows IHC staining for CD45 demonstrating significant lymphocyte infiltration in Ptenfl/fl and Ptenfl/fl Erk5fl/fl tumours. Also shown is dual IHC staining for CD3/CD4 revealing a high degree of CD4 reactivity within the lymphoid aggregates of Ptenfl/fl Erk5fl/fl tumours.
Supplementary Methods and Table Legends from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Authors: Vaughan Liwen , Glänzel Wolfgang , Korch Christopher , Capes-Davis Amanda
Published: April 2023

Contains the Supplementary Methods and the legends to accompany the Supplementary Tables.
Supplementary Methods from Long Noncoding RNA GCASPC, a Target of miR-17-3p, Negatively Regulates Pyruvate Carboxylase–Dependent Cell Proliferation in Gallbladder Cancer
Authors: Ma Ming-zhe , Zhang Yan , Weng Ming-zhe , Wang Shou-hua , Hu Ye , Hou Zhao-yuan , Qin Yi-yu , Gong Wei , Zhang Yong-Jie , Kong Xiang , Wang Jian-dong , Quan Zhi-wei
Published: April 2023

Supplementary Methods. Description of additional methods and procedures used in the study.
Supplementary Figure S1 from miR-9 and miR-200 Regulate PDGFRβ-Mediated Endothelial Differentiation of Tumor Cells in Triple-Negative Breast Cancer
Authors: D'Ippolito Elvira , Plantamura Ilaria , Bongiovanni Lucia , Casalini Patrizia , Baroni Sara , Piovan Claudia , Orlandi Rosaria , Gualeni Ambra V. , Gloghini Annunziata , Rossini Anna , Cresta Sara , Tessari Anna , De Braud Filippo , Di Leva Gianpiero , Tripodo Claudio , Iorio Marilena V.
Published: April 2023

MiR-9 regulates PDGFRbeta expression in TNBC cell lines
Table S5 from Western Diet Deregulates Bile Acid Homeostasis, Cell Proliferation, and Tumorigenesis in Colon
Authors: Dermadi Denis , Valo Satu , Ollila Saara , Soliymani Rabah , Sipari Nina , Pussila Marjaana , Sarantaus Laura , Linden Jere , Baumann Marc , Nyström Minna
Published: April 2023

Table S5. Ingenuity Pathway Analysis network scores and details
Supplementary Figure S3 from Enhanced Detection of Cancer Biomarkers in Blood-Borne Extracellular Vesicles Using Nanodroplets and Focused Ultrasound
Authors: Paproski Robert J. , Jovel Juan , Wong Gane Ka-Shu , Lewis John D. , Zemp Roger J.
Published: April 2023

Determining if the remaining microbubbles within the unpurified nanodroplet solution significantly contribute to enhancing ultrasound-mediated vesicle release.
Supplementary Material from Mathematical Modeling of Cancer Immunotherapy and Its Synergy with Radiotherapy
Authors: Serre Raphael , Benzekry Sebastien , Padovani Laetitia , Meille Christophe , André Nicolas , Ciccolini Joseph , Barlesi Fabrice , Muracciole Xavier , Barbolosi Dominique
Published: April 2023

The Supplementary Material section contains detailed mathematical information related to the model presented in the article.
Supplementary Figure 5 from Nucleolin Targeting Impairs the Progression of Pancreatic Cancer and Promotes the Normalization of Tumor Vasculature
Authors: Gilles Maud-Emmanuelle , Maione Federica , Cossutta Mélissande , Carpentier Gilles , Caruana Laure , Di Maria Silvia , Houppe Claire , Destouches Damien , Shchors Ksenya , Prochasson Christopher , Mongelard Fabien , Lamba Simona , Bardelli Alberto , Bouvet Philippe , Couvelard Anne , Courty José , Giraudo Enrico , Cascone Ilaria
Published: April 2023

N6L and angiogenic molecules regulation.
Supplementary Figures 1 through 10 from Heterogeneous Stromal Signaling within the Tumor Microenvironment Controls the Metastasis of Pancreatic Cancer
Authors: Rucki Agnieszka A. , Foley Kelly , Zhang Pingbo , Xiao Qian , Kleponis Jennifer , Wu Annie A. , Sharma Rajni , Mo Guanglan , Liu Angen , Van Eyk Jennifer , Jaffee Elizabeth M. , Zheng Lei
Published: April 2023

Supplemental Figure S1. Inhibition of Src and IGF-1R kinases results in decreased phosphorylation of AnxA2 at Tyrosine 23 on the cell surface of PDAC cells. Supplemental Figure S2. Inhibition of EGFR kinase does not affect phosphorylation of AnxA2 at tyrosine 23 in human PDAC cells. Supplemental Figure S3. shRNA knockdown of AnxA2 in human PDAC cells and HGF and IGF-1 in hCAFs. Supplemental Figure S4. Cell invasion and proliferation are not affected by inhibitor treatment (PDAC cells) nor IGF-1/HGF knockdown (hCAFs). Supplemental Figure S5. IGF-1 and HGF secreted by hCAFs regulate AnxA2 phosphorylation in human PDAC cells in co-culture and serum factors can compensate for c-Met and Hh mediated inhibition of AnxA2 phosphorylation in single human PDAC culture Supplemental Figure S6. Amount of HGF, Shh and IGF-1 ligands present in serum used for cell culture is dependent of the amount of FBS in media. Supplemental Figure S7. AnxA2 has at least 14 different tyrosine sites that are predicted targets for Src and IGF-1R activity and tyrosine 199 and tyrosine 333 on cell surface AnxA2 are the predominant phosphorylation sites detected by mass spectrometry. Supplemental Figure S8. Mass spectrometry analysis of AnxA2 phosphorylation regulated by IGF-1 and HGF secreted by hCAFs via Src and IGF-1R. Supplemental Figure S9. In vivo targeting of stromal signals in KPC mouse models of PDAC suppresses hCAF activation, AnxA2 phosphorylation, and the epithelial to mesenchymal transition (EMT). Supplemental Figure S10. IGF-1 expression in primary murine PDACs correlates positively with Shh and negatively with HGF expression in those tumors.
Supplemental Table 4 from Evaluation of Alternative In Vivo Drug Screening Methodology: A Single Mouse Analysis
Authors: Murphy Brendan , Yin Han , Maris John M. , Kolb E. Anders , Gorlick Richard , Reynolds C. Patrick , Kang Min H. , Keir Stephen T. , Kurmasheva Raushan T. , Dvorchik Igor , Wu Jianrong , Billups Catherine A. , Boateng Nana , Smith Malcolm A. , Lock Richard B. , Houghton Peter J.
Published: April 2023

Exomic mutations in 'best' and 'worst' xenograft models.
Supplemental Tables from FGF2 from Marrow Microenvironment Promotes Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia
Authors: Traer Elie , Martinez Jacqueline , Javidi-Sharifi Nathalie , Agarwal Anupriya , Dunlap Jennifer , English Isabel , Kovacsovics Tibor , Tyner Jeffrey W. , Wong Melissa , Druker Brian J.
Published: April 2023

Supplemental Tables 1-4 are included in this file: Supplemental Table 1. Calculation of combination indexes to evaluate synergy. Supplemental Table 2. Genes tested with OHSU Knight Diagnostic Labs Supplemental Table 3. Patient characteristics studied by immunohistochemistry Supplemental Table 4. Resistance mediated by FGF2 or FL does not affect response to SYK inhibitor PRT062607.
Supplementary Table S5 from Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma
Authors: Lamy Philippe , Nordentoft Iver , Birkenkamp-Demtröder Karin , Thomsen Mathilde Borg Houlberg , Villesen Palle , Vang Søren , Hedegaard Jakob , Borre Michael , Jensen Jørgen Bjerggaard , Høyer Søren , Pedersen Jakob Skou , Ørntoft Torben F. , Dyrskjøt Lars
Published: April 2023

Mutations included in the 1530 amplicons target panel.
Supplymentary Table 1-9 from Dysregulation of RUNX2/Activin-A Axis upon miR-376c Downregulation Promotes Lymph Node Metastasis in Head and Neck Squamous Cell Carcinoma
Authors: Chang Wei-Min , Lin Yuan-Feng , Su Chia-Yi , Peng Hsuan-Yu , Chang Yu-Chan , Lai Tsung-Ching , Wu Guan-Hsun , Hsu Yuan-Ming , Chi Li-Hsing , Hsiao Jenn-Ren , Chen Chi-Long , Chang Jang-Yang , Shieh Yi-Shing , Hsiao Michael , Shiah Shine-Gwo
Published: April 2023

Supplementary Table 1. Antibodies and Primer list Supplementary Table 2. IPA results for HNSCC upstream transcriptional regulators Supplementary Table 3. Clinical characteristics of RUNX2 in validation HNSCC cohort Supplementary Table 4. Lung colony formation abilities among HNSCC cells Supplementary Table 5. Relative expression and hazard ratio of RUNX2 target genes in GSE37991 HNSCC cohort and TCGA HNSCC cohort Supplementary Table 6. Clinical characteristics of RUNX2 and INHBA expression among TCGA HNSCC cohort Supplementary Table 7. Prediction binding affinity between 14q32.2 miRNAs and RUNX2 3'-UTR in HNSCC Supplement Table 8. Transcription factor 3'UTR miR-376c MRE analysis and binding prediction analysis of INHBA promoter. Supplementary Table 9. IPA Interaction analysis between RUNX2 and TFs and revealed differential expressed genes in GSE37991 HNSCC patients
Supplymentary Figure 1-7 from Dysregulation of RUNX2/Activin-A Axis upon miR-376c Downregulation Promotes Lymph Node Metastasis in Head and Neck Squamous Cell Carcinoma
Authors: Chang Wei-Min , Lin Yuan-Feng , Su Chia-Yi , Peng Hsuan-Yu , Chang Yu-Chan , Lai Tsung-Ching , Wu Guan-Hsun , Hsu Yuan-Ming , Chi Li-Hsing , Hsiao Jenn-Ren , Chen Chi-Long , Chang Jang-Yang , Shieh Yi-Shing , Hsiao Michael , Shiah Shine-Gwo
Published: April 2023

Supplementary Figure 1. RUNX2 is nucleus location protein among HNSCC cells. Supplementary Figure 2. RUNX2 was a poor prognostic marker in HNSCC. Supplementary Figure 3. Lung colony formation ability of HNSCC cells. Supplementary Figure 4. RUNX2 and its regulation targets, INHBA, promoted HNSCC invasion and migration assay in HNSCC cells. Supplementary Figure 5. The TCGA-HNSCC dataset shows the positive correlation between RUNX2 and INHBA and their prognostic value. Supplementary Figure 6. Ectopic anti-miR-376c-3p increases RUNX2 3'-UTR reporter assay in Ca9-22 cells. Supplementary Figure 7Knockdown RUNX2 prevent anti-miR-376c-3p induced cell migration and invasion ablilties in Ca9-22 cells.
Supplementary Data from Recurrent Loss of STING Signaling in Melanoma Correlates with Susceptibility to Viral Oncolysis
Authors: Xia Tianli , Konno Hiroyasu , Barber Glen N.
Published: April 2023

Supplementary Figure S1, dsDNA90 Transfection efficiency in melanoma cells; Supplementary Figure S2, si-STING effect on melanoma cells; Supplementary Figure S3, Cisplatin treatment in melanoma cells and cGAS immuoblot verification; Supplementary Figure S4, additional immunofluorescence analysis in melanoma cells; Supplementary Figure S5, schematic diagram of predicted CpG islands in STING promoter; Supplementary Figure S6, vaccinia virus treatment in melanoma cells; Supplementary Figure S7, HSV1γ34.5 treatment on MeWo xenograft in vivo; Supplementary Table S1, IHC analysis of STING and cGAS in Melanoma Tissue Microarray; Supplementary Table S2, sequencing of STING in Melanoma Cell Lines; Supplementary Table S3, sequencing of cGAS in Melanoma Cell Lines.
Supplementary Figure S6 from PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells
Authors: Kaur Amanpreet , Denisova Oxana V. , Qiao Xi , Jumppanen Mikael , Peuhu Emilia , Ahmed Shafiq U. , Raheem Olayinka , Haapasalo Hannu , Eriksson John , Chalmers Anthony J. , Laakkonen Pirjo , Westermarck Jukka
Published: April 2023

PME-1 and HDAC4 expression can predict glioma patient response to kinase inhibitors. Supplementary figure related to Figure 6.
Supplementary Figure S4 from PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells
Authors: Kaur Amanpreet , Denisova Oxana V. , Qiao Xi , Jumppanen Mikael , Peuhu Emilia , Ahmed Shafiq U. , Raheem Olayinka , Haapasalo Hannu , Eriksson John , Chalmers Anthony J. , Laakkonen Pirjo , Westermarck Jukka
Published: April 2023

HDAC4 is a PME-1 regulated target involved in GBM cell kinase inhibitor resistance. Supplementary figure related to Figure 4.
Supplementary Methods and Reference from Assessing Immune-Related Adverse Events of Efficacious Combination Immunotherapies in Preclinical Models of Cancer
Authors: Liu Jing , Blake Stephen J. , Harjunpää Heidi , Fairfax Kirsten A. , Yong Michelle C.R. , Allen Stacey , Kohrt Holbrook E. , Takeda Kazuyoshi , Smyth Mark J. , Teng Michele W.L.
Published: April 2023

Description of additional methods and procedures used in the study. Also includes Supplementary Reference.
Supplementary Table S1: Frequencies of gains and losses for selected genes in both OUH and TCGA cohorts. from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

The table shows the genes, chromosomal location and frequency of deletion and amplification of genes in OUH (PAs (n=54), cell lines (n=3) and IPMN (n=3) and TCGA data sets (n=127).
Supplementary Figure S4. Correlation between genome instability index (GII) and ploidy. from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

4A) Scatter plot shows the correlation between GII and ploidy of the tumors in OUH cohort. 4B) Scatter plot shows the correlation between GII and ploidy of the tumors in TCGA cohort. The x-axis represent the genome instability index while the y-axis represent the ploidy of the tumors
Supplementary Figure S1. Heatmap shows the cytobands amplified and deleted in OUH and TCGA cohort. from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

1a) Amplification and deletion of cytobands in OUH cohort. 1b) Amplification and deletion of cytobands in TCGA cohort. The rows represent the cytobands while the columns represent the samples. The color bars on y-axis represent the chromosomes. The red color in the heatmap represents the amplification, green color represent the deletion while black represent the normal state.
Figure S3 from Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand
Published: April 2023

Analysis of TIC markers
Figure S2 from Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand
Published: April 2023

Quantification of Western and IHC images
Figure S5. The small molecule inhibitor C 021 specifically inhibits Treg migration to CCR4 cognate chemokines. from CCL2 Produced by the Glioma Microenvironment Is Essential for the Recruitment of Regulatory T Cells and Myeloid-Derived Suppressor Cells
Authors: Chang Alan L. , Miska Jason , Wainwright Derek A. , Dey Mahua , Rivetta Claudia V. , Yu Dou , Kanojia Deepak , Pituch Katarzyna C. , Qiao Jian , Pytel Peter , Han Yu , Wu Meijing , Zhang Lingjiao , Horbinski Craig M. , Ahmed Atique U. , Lesniak Maciej S.
Published: April 2023

(A) Sorted Tregs were placed the upper chamber of a 3.0 microm pore cell culture insert with or without 5 microM of the small molecule antagonist C 021 and chemokine-containing media was placed in the well. Migration index was determined after 4 hours through flow cytometric analysis. (B) A similar migration assay was performed as in A, except CCL21 and 10% FBS were used in the bottom chamber as a non-specific positive control. Data are representative of 3 independent experiments. Data are represented as mean {plus minus} SEM; *P < 0.05, by Student's t test.
Supplementary Table S4 from JARID1B Enables Transit between Distinct States of the Stem-like Cell Population in Oral Cancers
Authors: Facompre Nicole D. , Harmeyer Kayla M. , Sole Xavier , Kabraji Sheheryar , Belden Zachary , Sahu Varun , Whelan Kelly , Tanaka Koji , Weinstein Gregory S. , Montone Kathleen T. , Roesch Alexander , Gimotty Phyllis A. , Herlyn Meenhard , Rustgi Anil K. , Nakagawa Hiroshi , Ramaswamy Sridhar , Basu Devraj
Published: April 2023

Shared genes up-regulated in both G0-like and JARID1Bhigh cells compared with the bulk population.
Supplementary Figure S2 from Autocrine BMP-4 Signaling Is a Therapeutic Target in Colorectal Cancer
Authors: Yokoyama Yuichiro , Watanabe Toshiaki , Tamura Yusuke , Hashizume Yoshinobu , Miyazono Kohei , Ehata Shogo
Published: April 2023

Effect of BMP inhibitors on proliferation of cancer cells (related to Figure 4).
Table S2 from The Damaging Effect of Passenger Mutations on Cancer Progression
Authors: McFarland Christopher D. , Yaglom Julia A. , Wojtkowiak Jonathan W. , Scott Jacob G. , Morse David L. , Sherman Michael Y. , Mirny Leonid A.
Published: April 2023

Table S2 - Summary of Mice Tumors analyzed in this study
Supplementary Table 3 from A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers
Authors: Guo Theresa , Sakai Akihiro , Afsari Bahman , Considine Michael , Danilova Ludmila , Favorov Alexander V. , Yegnasubramanian Srinivasan , Kelley Dylan Z. , Flam Emily , Ha Patrick K. , Khan Zubair , Wheelan Sarah J. , Gutkind J. Silvio , Fertig Elana J. , Gaykalova Daria A. , Califano Joseph
Published: April 2023

List of 109 validated junctions associated with splice variants with location, gene symbol and category.
Cell line authentication UM-SCC-047 from A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers
Authors: Guo Theresa , Sakai Akihiro , Afsari Bahman , Considine Michael , Danilova Ludmila , Favorov Alexander V. , Yegnasubramanian Srinivasan , Kelley Dylan Z. , Flam Emily , Ha Patrick K. , Khan Zubair , Wheelan Sarah J. , Gutkind J. Silvio , Fertig Elana J. , Gaykalova Daria A. , Califano Joseph
Published: April 2023

Cell line authentication for UM-SCC-047
Figure S5 Tumour growth upon ATRi and Gemcitabine Treatment in Allografts model from ATM Deficiency Generating Genomic Instability Sensitizes Pancreatic Ductal Adenocarcinoma Cells to Therapy-Induced DNA Damage
Authors: Perkhofer Lukas , Schmitt Anna , Romero Carrasco Maria Carolina , Ihle Michaela , Hampp Stephanie , Ruess Dietrich Alexander , Hessmann Elisabeth , Russell Ronan , Lechel André , Azoitei Ninel , Lin Qiong , Liebau Stefan , Hohwieler Meike , Bohnenberger Hanibal , Lesina Marina , Algül Hana , Gieldon Laura , Schröck Evelin , Gaedcke Jochen , Wagner Martin , Wiesmüller Lisa , Sipos Bence , Seufferlein Thomas , Reinhardt Hans Christian , Frappart Pierre-Olivier , Kleger Alexander
Published: April 2023

Tumour growth upon ATRi and Gemcitabine Treatment in Allografts model
Supplementary Tables from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
Authors: Etemadmoghadam Dariush , Azar Walid J. , Lei Ying , Moujaber Tania , Garsed Dale W. , Kennedy Catherine J. , Fereday Sian , Mitchell Chris , Chiew Yoke-Eng , Hendley Joy , Sharma Raghwa , Harnett Paul R. , Li Jason , Christie Elizabeth L. , Patch Ann-Marie , George Joshy , Au-Yeung George , Mir Arnau Gisela , Holloway Timothy P. , Semple Timothy , Pearson John V. , Waddell Nicola , Grimmond Sean M. , Köbel Martin , Rizos Helen , Lomakin Ivan B. , Bowtell David D.L. , deFazio Anna
Published: April 2023

Supplementary Table S1. Patient characteristics; Supplementary Table S2. Ki67 proliferation index; Supplementary Table S3. WES and WGS performance statistics; Supplementary Table S4. Amplicon sequencing primers; Supplementary Table S5. High confidence variants from exome and whole genome sequencing; Supplementary Table S6. Summary of SNVs and indels by sample; Supplementary Table S7. Significantly mutated genes (MuSiC output); Supplementary Table S8. Somatic variants in recurrently mutated genes; Supplementary Table S9. Validation cohort variants; Supplementary Table S10. TP53 variants in validation cohort; Supplementary Table S11. EIF1AX mutations reported in cancer