bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary table 8 from A Mutant p53-Dependent Embryonic Stem Cell Gene Signature Is Associated with Augmented Tumorigenesis of Stem Cells
Authors: Koifman Gabriela , Shetzer Yoav , Eizenberger Shay , Solomon Hilla , Rotkopf Ron , Molchadsky Alina , Lonetto Giuseppe , Goldfinger Naomi , Rotter Varda
Published: April 2023

Differential expression of the p53 Mut MSC TL ESC signature and mutant dependent ESC genes in human tumors harboring mutant p53 missense mutations versus the rest of tumor samples. This analysis was based on datasets provided by TCGA.
Supplementary table 4 from A Mutant p53-Dependent Embryonic Stem Cell Gene Signature Is Associated with Augmented Tumorigenesis of Stem Cells
Authors: Koifman Gabriela , Shetzer Yoav , Eizenberger Shay , Solomon Hilla , Rotkopf Ron , Molchadsky Alina , Lonetto Giuseppe , Goldfinger Naomi , Rotter Varda
Published: April 2023

Differential genes between p53 Mut MSC TL and KO MSC TL sub-clones. The table contains genes that had at least 10 reads in the RNA sequencing analysis. p53 Mut MSC TL ESC-like genes, ESC genes and PRC2 target genes are indicated and can be filtered.
Supplementary table 2 from A Mutant p53-Dependent Embryonic Stem Cell Gene Signature Is Associated with Augmented Tumorigenesis of Stem Cells
Authors: Koifman Gabriela , Shetzer Yoav , Eizenberger Shay , Solomon Hilla , Rotkopf Ron , Molchadsky Alina , Lonetto Giuseppe , Goldfinger Naomi , Rotter Varda
Published: April 2023

Differential genes between pMSCs and their derived TLs (MSC TLs). The table contains genes that had at least 10 reads in the RNA sequencing analysis. CSC genes, ESC genes, shared target genes of Nanog, Sox2 and Oct4 or of Nanog, Sox2, Oct4, Dax1 and Nac1 and genes induced by the reprogramming process are indicated and can be filtered.
Supplementary Figure S3 from Replication Protein A Availability during DNA Replication Stress Is a Major Determinant of Cisplatin Resistance in Ovarian Cancer Cells
Authors: Bélanger François , Fortier Emile , Dubé Maxime , Lemay Jean-François , Buisson Rémi , Masson Jean-Yves , Elsherbiny Abdelhamid , Costantino Santiago , Carmona Euridice , Mes-Masson Anne-Marie , Wurtele Hugo , Drobetsky Elliot
Published: April 2023

Supplementary Figure S3 shows expression of BRCA1, BRCA2, and Rad51 in ovarian cancer cell lines.
Supplementary Figure S1A-C from Preclinical Evaluation of the Hsp70 Peptide Tracer TPP-PEG24-DFO[89Zr] for Tumor-Specific PET/CT Imaging
Authors: Stangl Stefan , Tei Lorenzo , De Rose Francesco , Reder Sybille , Martinelli Jonathan , Sievert Wolfgang , Shevtsov Maxim , Öllinger Rupert , Rad Roland , Schwaiger Markus , D'Alessandria Calogero , Multhoff Gabriele
Published: April 2023

Schematic representation of the synthesis of TPP-DFO, TPP-PEG24-DFO, TPP-PEG24-FITC
Supplementary Figure Legends from LRRC15 Is a Novel Mesenchymal Protein and Stromal Target for Antibody–Drug Conjugates
Authors: Purcell James W. , Tanlimco Sonia G. , Hickson Jonathan , Fox Melvin , Sho Mien , Durkin Lisa , Uziel Tamar , Powers Rick , Foster Kelly , McGonigal Thomas , Kumar Subashri , Samayoa Josue , Zhang Dong , Palma Joann P. , Mishra Sasmita , Hollenbaugh Diane , Gish Kurt , Morgan-Lappe Susan E. , Hsi Eric D. , Chao Debra T.
Published: April 2023

Supplementary Figure Legends
Supplementary Methods from Modulating Bone Marrow Hematopoietic Lineage Potential to Prevent Bone Metastasis in Breast Cancer
Authors: Ubellacker Jessalyn M. , Baryawno Ninib , Severe Nicolas , DeCristo Molly J. , Sceneay Jaclyn , Hutchinson John N. , Haider Marie-Therese , Rhee Catherine S. , Qin Yuanbo , Gregory Walter M. , Garrido-Castro Ana C. , Holen Ingunn , Brown Janet E. , Coleman Robert E. , Scadden David T. , McAllister Sandra S.
Published: April 2023

Detailed information for controls and experiments to support primary data
Table S2. from Glycoprotein nmb Is Exposed on the Surface of Dormant Breast Cancer Cells and Induces Stem Cell–like Properties
Authors: Chen Chen , Okita Yukari , Watanabe Yukihide , Abe Fumie , Fikry Muhammad Ali , Ichikawa Yumu , Suzuki Hiroyuki , Shibuya Akira , Kato Mitsuyasu
Published: April 2023

Summary of statistical analysis related to Figure 7.
Supplementary files from Novel Richter Syndrome Xenograft Models to Study Genetic Architecture, Biology, and Therapy Responses
Authors: Vaisitti Tiziana , Braggio Esteban , Allan John N. , Arruga Francesca , Serra Sara , Zamò Alberto , Tam Wayne , Chadburn Amy , Furman Richard R. , Deaglio Silvia
Published: April 2023

This file contains supplemental additional experimental procedures, relevant references and 7 supplementary figures, including: S1 "Expression of EBV in RS samples"; S2 "Schematic representation of the RS-PDX models"; S3 "Disease engraftment and distribution of RS1316 i.v. model"; S4 "Phenotypic analysis of primary and derived-RS-PDXs"; S5 "Schematic diagram of proteins and corresponding mutations"; S6 "Differentially expressed genes in primary and RS-PDX"; S7 "Schematic sketch of the main mutated genes in our RS models and core signaling pathways they belong to and play a critical role". Supplementary tables contain additional information on sequencing results performed on primary and PDX-RS models.
Figure S2 from Epigenetic Regulation of CXCL12 Plays a Critical Role in Mediating Tumor Progression and the Immune Response In Osteosarcoma
Authors: Li Binghao , Wang Zhan , Wu Hao , Xue Mingfeng , Lin Peng , Wang Shengdong , Lin Nong , Huang Xin , Pan Weibo , Liu Meng , Yan Xiaobo , Qu Hao , Sun Lingling , Li Hengyuan , Wu Yan , Teng Wangsiyuan , Wang Zenan , Zhou Xingzhi , Chen Huabiao , Poznansky Mark C. , Ye Zhaoming
Published: April 2023

Supplementary figure S2. Gating strategies for flow cytometry analyses.
Table S7 from Canonical Wnt Signaling Remodels Lipid Metabolism in Zebrafish Hepatocytes following Ras Oncogenic Insult
Authors: Yao Yuxiao , Sun Shaoyang , Wang Jingjing , Fei Fei , Dong Zhaoru , Ke Ai-Wu , He Ruoyu , Wang Lei , Zhang Lili , Ji Min-Biao , Li Qiang , Yu Min , Shi Guo-Ming , Fan Jia , Gong Zhiyuan , Wang Xu
Published: April 2023

Full list of gene expression, gene ontologies, and KEGG pathway information in 6 dpf control, Tg(Myc), Tg(Kras), and Tg(Myc&Kras) larvae
Table S5 from Canonical Wnt Signaling Remodels Lipid Metabolism in Zebrafish Hepatocytes following Ras Oncogenic Insult
Authors: Yao Yuxiao , Sun Shaoyang , Wang Jingjing , Fei Fei , Dong Zhaoru , Ke Ai-Wu , He Ruoyu , Wang Lei , Zhang Lili , Ji Min-Biao , Li Qiang , Yu Min , Shi Guo-Ming , Fan Jia , Gong Zhiyuan , Wang Xu
Published: April 2023

List of normalized amounts of lipids species with variable importance (VIP) 1 in 6 dpf control, Tg(Myc), Tg(Kras), and Tg(Myc&Kras) larvae
Table S4 from Canonical Wnt Signaling Remodels Lipid Metabolism in Zebrafish Hepatocytes following Ras Oncogenic Insult
Authors: Yao Yuxiao , Sun Shaoyang , Wang Jingjing , Fei Fei , Dong Zhaoru , Ke Ai-Wu , He Ruoyu , Wang Lei , Zhang Lili , Ji Min-Biao , Li Qiang , Yu Min , Shi Guo-Ming , Fan Jia , Gong Zhiyuan , Wang Xu
Published: April 2023

List of percentage proportions of lipid categories and classes in 6 dpf control, Tg(Myc), Tg(Kras), and Tg(Myc&Kras) larvae
Figure S5 from EGFR Cooperates with EGFRvIII to Recruit Macrophages in Glioblastoma
Authors: An Zhenyi , Knobbe-Thomsen Christiane B. , Wan Xiaohua , Fan Qi Wen , Reifenberger Guido , Weiss William A.
Published: April 2023

A, CCL2, CD90/THY1 and SOX1 genes are induced by EGFR and EGFRvIII from RNA-sequencing analysis. B, qRT-PCR of indicated genes in GBM6 and GBM39 grown in stem cell media or differentiating media.
Supplementary Table S8 from Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations
Authors: Sowalsky Adam G. , Ye Huihui , Bhasin Manoj , Van Allen Eliezer M. , Loda Massimo , Lis Rosina T. , Montaser-Kouhsari Laleh , Calagua Carla , Ma Fen , Russo Joshua W. , Schaefer Rachel J. , Voznesensky Olga S. , Zhang Zhenwei , Bubley Glenn J. , Montgomery Bruce , Mostaghel Elahe A. , Nelson Peter S. , Taplin Mary-Ellen , Balk Steven P.
Published: April 2023

Mutations in 3 cases with only 1 focus dissected
Figure S3 from EGFR Cooperates with EGFRvIII to Recruit Macrophages in Glioblastoma
Authors: An Zhenyi , Knobbe-Thomsen Christiane B. , Wan Xiaohua , Fan Qi Wen , Reifenberger Guido , Weiss William A.
Published: April 2023

A-C, Western blotting confirming knockout or knockdown of CCL2/KRAS. D, Transwell migration assay showing attraction of macrophages (macrophage line: MV-4-11) in response to conditioned media from Ctrl siRNA and KRAS siRNA cells treated with a CCL2 neutralizing antibody (1μg/ml).
Supplementary Table S7 from Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations
Authors: Sowalsky Adam G. , Ye Huihui , Bhasin Manoj , Van Allen Eliezer M. , Loda Massimo , Lis Rosina T. , Montaser-Kouhsari Laleh , Calagua Carla , Ma Fen , Russo Joshua W. , Schaefer Rachel J. , Voznesensky Olga S. , Zhang Zhenwei , Bubley Glenn J. , Montgomery Bruce , Mostaghel Elahe A. , Nelson Peter S. , Taplin Mary-Ellen , Balk Steven P.
Published: April 2023

Unique somatic mutations
Figure S2 from EGFR Cooperates with EGFRvIII to Recruit Macrophages in Glioblastoma
Authors: An Zhenyi , Knobbe-Thomsen Christiane B. , Wan Xiaohua , Fan Qi Wen , Reifenberger Guido , Weiss William A.
Published: April 2023

Quantification of other cytokines upregulated by EGFR and EGFRvIII in cytokine array.
Supplementary Materials and Methods from The E2F1–miR-520/372/373–SPOP Axis Modulates Progression of Renal Carcinoma
Authors: Ding Meng , Lu Xiaolan , Wang Cheng , Zhao Quan , Ge Jingping , Xia Qiuyuan , Wang Junjun , Zen Ke , Zhang Chen-Yu , Zhang Chunni
Published: April 2023

Supplementary Materials and Methods provide detail materials and methods of migration and invasion assays, luciferase reporter assay, luciferase transduced cell generation, and in vivo assay.
Table S2 from Optimized Dosing Schedule Based on Circadian Dynamics of Mouse Breast Cancer Stem Cells Improves the Antitumor Effects of Aldehyde Dehydrogenase Inhibitor
Authors: Matsunaga Naoya , Ogino Takashi , Hara Yukinori , Tanaka Takahiro , Koyanagi Satoru , Ohdo Shigehiro
Published: April 2023

Time-dependently expressed genes in ALDH-negative 4T1 cells implanted in mice.
Table S1 from Optimized Dosing Schedule Based on Circadian Dynamics of Mouse Breast Cancer Stem Cells Improves the Antitumor Effects of Aldehyde Dehydrogenase Inhibitor
Authors: Matsunaga Naoya , Ogino Takashi , Hara Yukinori , Tanaka Takahiro , Koyanagi Satoru , Ohdo Shigehiro
Published: April 2023

Primer sequences for quantitative PCR analysis
Figure S6 from Tobacco Carcinogen–Induced Production of GM-CSF Activates CREB to Promote Pancreatic Cancer
Authors: Srinivasan Supriya , Totiger Tulasigeri , Shi Chanjuan , Castellanos Jason , Lamichhane Purushottam , Dosch Austin R. , Messaggio Fanuel , Kashikar Nilesh , Honnenahally Kumaraswamy , Ban Yuguang , Merchant Nipun B. , VanSaun Michael , Nagathihalli Nagaraj S.
Published: April 2023

Figure S6 shows recGM-CSF and CREBi treatment and colony formation and PKT mouse weight.
Figure S5 from Tobacco Carcinogen–Induced Production of GM-CSF Activates CREB to Promote Pancreatic Cancer
Authors: Srinivasan Supriya , Totiger Tulasigeri , Shi Chanjuan , Castellanos Jason , Lamichhane Purushottam , Dosch Austin R. , Messaggio Fanuel , Kashikar Nilesh , Honnenahally Kumaraswamy , Ban Yuguang , Merchant Nipun B. , VanSaun Michael , Nagathihalli Nagaraj S.
Published: April 2023

Figure S5 shows Ingenuity Pathway Analysis (IPA) summary
Fig. S7-S10 from Optimized Dosing Schedule Based on Circadian Dynamics of Mouse Breast Cancer Stem Cells Improves the Antitumor Effects of Aldehyde Dehydrogenase Inhibitor
Authors: Matsunaga Naoya , Ogino Takashi , Hara Yukinori , Tanaka Takahiro , Koyanagi Satoru , Ohdo Shigehiro
Published: April 2023

Supplementary Fig. 7 shows the transcriptional regulation of Wnt10a by clock gene products. Supplementary Fig. 8 shows the down-regulation of Wnt10a in Aldh3a1::Luc-expressing 4T1 cells. Supplementary Fig. 9 Unedited full blots of Supplementary Fig. 8. Supplementary Fig. 10 shows the comparison of mRNA levels of Aldh3a1, Clock, Bnal1 and Rev-erbα between ALDH-positive and negative 4T1 cells which was isolated from 4T1 tumor implanted in BALB/c female mice, and influence of overexpression of Aldh3a1 on the temporal expression of clock genes.
Figure S2 from Tobacco Carcinogen–Induced Production of GM-CSF Activates CREB to Promote Pancreatic Cancer
Authors: Srinivasan Supriya , Totiger Tulasigeri , Shi Chanjuan , Castellanos Jason , Lamichhane Purushottam , Dosch Austin R. , Messaggio Fanuel , Kashikar Nilesh , Honnenahally Kumaraswamy , Ban Yuguang , Merchant Nipun B. , VanSaun Michael , Nagathihalli Nagaraj S.
Published: April 2023

Figure S2 shows GM-CSF and nicotine acetylcholine receptor expression in PDAC cells
Merged pdf from ErbB3 Targeting Enhances the Effects of MEK Inhibitor in Wild-Type BRAF/NRAS Melanoma
Authors: Capparelli Claudia , Purwin Timothy J. , Heilman Shea A. , Chervoneva Inna , McCue Peter A. , Berger Adam C. , Davies Michael A. , Gershenwald Jeffrey E. , Krepler Clemens , Aplin Andrew E.
Published: April 2023

Article File and Figures
Supplemental Figure Legends from Long-Chain n-3 Fatty Acids Attenuate Oncogenic KRas-Driven Proliferation by Altering Plasma Membrane Nanoscale Proteolipid Composition
Authors: Fuentes Natividad R. , Mlih Mohamed , Barhoumi Rola , Fan Yang-Yi , Hardin Paul , Steele Trevor J. , Behmer Spencer , Prior Ian A. , Karpac Jason , Chapkin Robert S.
Published: April 2023

Contains the legend text for supplemental figures 1, quantitative pERK analysis images.Supplemental figures 2, pERK Western. Supplemental figures 3, Drosophila corn oil FLIM-FRET.
Table S1 and S2 from Zebrafish: Speeding Up the Cancer Drug Discovery Process
Authors: Letrado Patricia , de Miguel Irene , Lamberto Iranzu , Díez-Martínez Roberto , Oyarzabal Julen
Published: April 2023

This file contains supplemental tables of advantages and disadvantages of methods developed to induce cancer in zebrafish and the advantages and disadvantages of using embryo or adult stage in research assays
Supplementary tables from IFNγ PET Imaging as a Predictive Tool for Monitoring Response to Tumor Immunotherapy
Authors: Gibson Heather M. , McKnight Brooke N. , Malysa Agnes , Dyson Greg , Wiesend Wendy N. , McCarthy Claire E. , Reyes Joyce , Wei Wei-Zen , Viola-Villegas Nerissa T.
Published: April 2023

Primer sequences and biodistribution data for the anti-IFN-gamma PET tracer are shown.
Supplementary Method S1 from Combined MR Imaging of Oxygen Consumption and Supply Reveals Tumor Hypoxia and Aggressiveness in Prostate Cancer Patients
Authors: Hompland Tord , Hole Knut Håkon , Ragnum Harald Bull , Aarnes Eva-Katrine , Vlatkovic Ljiljana , Lie A. Kathrine , Patzke Sebastian , Brennhovd Bjørn , Seierstad Therese , Lyng Heidi
Published: April 2023

Diffusion weighted image (DWI) analysis.
Table S2 from Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer
Authors: Xiao Lanbo , Tien Jean C. , Vo Josh , Tan Mengyao , Parolia Abhijit , Zhang Yajia , Wang Lisha , Qiao Yuanyuan , Shukla Sudhanshu , Wang Xiaoju , Zheng Heng , Su Fengyun , Jing Xiaojun , Luo Esther , Delekta Andrew , Juckette Kristin M. , Xu Alice , Cao Xuhong , Alva Ajjai S. , Kim Youngsoo , MacLeod A. Robert , Chinnaiyan Arul M.
Published: April 2023

Supplementary Table 2 Cell-titer Glo raw data from epigenetic inhibitor screen.
Table S1 from Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer
Authors: Xiao Lanbo , Tien Jean C. , Vo Josh , Tan Mengyao , Parolia Abhijit , Zhang Yajia , Wang Lisha , Qiao Yuanyuan , Shukla Sudhanshu , Wang Xiaoju , Zheng Heng , Su Fengyun , Jing Xiaojun , Luo Esther , Delekta Andrew , Juckette Kristin M. , Xu Alice , Cao Xuhong , Alva Ajjai S. , Kim Youngsoo , MacLeod A. Robert , Chinnaiyan Arul M.
Published: April 2023

Supplementary Table 1: List of the compounds in the epigenetic inhibitor library.
Table S4 from IL1 Receptor Antagonist Controls Transcriptional Signature of Inflammation in Patients with Metastatic Breast Cancer
Authors: Wu Te-Chia , Xu Kangling , Martinek Jan , Young Robyn R. , Banchereau Romain , George Joshy , Turner Jacob , Kim Kyung In , Zurawski Sandra , Wang Xuan , Blankenship Derek , Brookes Hannah M. , Marches Florentina , Obermoser Gerlinde , Lavecchio Elizabeth , Levin Maren K. , Bae Sookyoung , Chung Cheng-Han , Smith Jennifer L. , Cepika Alma-Martina , Oxley Kyp L. , Snipes George J. , Banchereau Jacques , Pascual Virginia , O'Shaughnessy Joyce , Palucka A. Karolina
Published: April 2023

Key resource table
Supplementary Figures from Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer
Authors: Xiao Lanbo , Tien Jean C. , Vo Josh , Tan Mengyao , Parolia Abhijit , Zhang Yajia , Wang Lisha , Qiao Yuanyuan , Shukla Sudhanshu , Wang Xiaoju , Zheng Heng , Su Fengyun , Jing Xiaojun , Luo Esther , Delekta Andrew , Juckette Kristin M. , Xu Alice , Cao Xuhong , Alva Ajjai S. , Kim Youngsoo , MacLeod A. Robert , Chinnaiyan Arul M.
Published: April 2023

This file includes Supplementary Figures S1-S8. Figure S1: Inhibition of EPZ6438 and ASO-EZH2 sensitizes enzalutamide-resistant LNCaP cells to enzalutamide or ASO-AR. Figure S2: Design and validation of sgRNA targeting EZH2. Figure S3: Growth inhibitory effect of Enzalutamide in EZH2 loss-of-function CRPC cell lines. Figure S4: Knockdown efficiency of ASO-AR and ASO-EZH2 in CRPC cell lines. Figures S5: EZH2 ASOs inhibit proliferation of LNCaP-abl cells. Figure S6: EZH2 ASOs synergize with ASO-AR to inhibit growth of prostate cancer cells in soft-agar colony formation assay and Cell-titer Glo assay. Figure S7: Loss-of-function of EZH2 alters AR cistrome. Figure S8: Tumor characterization of xenografted study.
Supplementary Figure legends from Heterozygosity of Chaperone Grp78 Reduces Intestinal Stem Cell Regeneration Potential and Protects against Adenoma Formation
Authors: van Lidth de Jeude Jooske F. , Spaan Claudia N. , Meijer Bartolomeus J. , Smit Wouter L. , Soeratram Tanya T.D. , Wielenga Mattheus C.B. , Westendorp B. Florien , Lee Amy S. , Meisner Sander , Vermeulen Jacqueline L.M. , Wildenberg Manon E. , van den Brink Gijs R. , Muncan Vanesa , Heijmans Jarom
Published: April 2023

Supplementary Figure legends
Supplementary Fig. S1 from CAMKK2 Promotes Prostate Cancer Independently of AMPK via Increased Lipogenesis
Authors: Penfold Lucy , Woods Angela , Muckett Phillip , Nikitin Alexander Yu. , Kent Tera R. , Zhang Shuai , Graham Rebecca , Pollard Alice , Carling David
Published: April 2023

Representative images of prostates from wild type, Pten and Pten;Camkk2 mice, and associated histology.
Supplementary Figure S4 from p63-Dependent Dickkopf3 Expression Promotes Esophageal Cancer Cell Proliferation via CKAP4
Authors: Kajiwara Chihiro , Fumoto Katsumi , Kimura Hirokazu , Nojima Satoshi , Asano Keita , Odagiri Kazuki , Yamasaki Makoto , Hikita Hayato , Takehara Tetsuo , Doki Yuichiro , Morii Eiichi , Kikuchi Akira
Published: April 2023

Structure of p63 family proteins.
Fig, S4 from RIPK1 Binds MCU to Mediate Induction of Mitochondrial Ca2+ Uptake and Promotes Colorectal Oncogenesis
Authors: Zeng Fanxin , Chen Xiao , Cui Weiyi , Wen Wei , Lu Fujian , Sun Xueting , Ma Dongwei , Yuan Ye , Li Zezhong , Hou Ning , Zhao Hong , Bi Xinyu , Zhao Jianjun , Zhou Jianguo , Zhang Yan , Xiao Rui-Ping , Cai Jianqiang , Zhang Xiuqin
Published: April 2023

Figure S4. Mass Spectra shows Interactions between RIPK1 and MCU. (A) Coomassie blue staining with co-immunoprecipitation of RIPK1 from human tissue. (B) The sequence of MCU, yellow sign shows that the peptides are detected.
Supplementary Data from Measurement of Plasma Cell-Free Mitochondrial Tumor DNA Improves Detection of Glioblastoma in Patient-Derived Orthotopic Xenograft Models
Authors: Mair Richard , Mouliere Florent , Smith Christopher G. , Chandrananda Dineika , Gale Davina , Marass Francesco , Tsui Dana W.Y. , Massie Charles E. , Wright Alan J. , Watts Colin , Rosenfeld Nitzan , Brindle Kevin M.
Published: April 2023

This file presents demographic information across the different PDOX populations.
Supplementary materials and methods from APC/C-CDH1–Regulated IDH3β Coordinates with the Cell Cycle to Promote Cell Proliferation
Authors: Wu Qingnan , Zhang Weimin , Xue Liyan , Wang Yan , Fu Ming , Ma Liying , Song Yongmei , Zhan Qi-Min
Published: April 2023

Quantitative real-time PCR analysisï¼ŒProliferation assay and colony formation assayï¼ŒCell cycle analysisï¼ŒMetabolite measurement.
Supplementary Tables from In Vivo Modeling of Chemoresistant Neuroblastoma Provides New Insights into Chemorefractory Disease and Metastasis
Authors: Yogev Orli , Almeida Gilberto S. , Barker Karen T. , George Sally L. , Kwok Colin , Campbell James , Zarowiecki Magdalena , Kleftogiannis Dimitrios , Smith Laura M. , Hallsworth Albert , Berry Philip , Möcklinghoff Till , Webber Hannah T. , Danielson Laura S. , Buttery Bliss , Calton Elizabeth A. , da Costa Barbara M. , Poon Evon , Jamin Yann , Lise Stefano , Veal Gareth J. , Sebire Neil , Robinson Simon P. , Anderson John , Chesler Louis
Published: April 2023

Table S1. RNA sequencing sample overview and accession numbers Table S2. RNA sequencing sample mapping statistics and raw read counts Table S3. RNA sequencing differential expression results Table S4. RNA sequencing GSEA results Table S5. Mouse-Human homologous gene list for the Th-MYCNCPM32 amplified copy number region on chromosome 11. Table S6. WES coverage statistics and read counts. Table S7. GSEA for KEGG pathways.
Supplementary Fig. 4 from In Vivo Modeling of Chemoresistant Neuroblastoma Provides New Insights into Chemorefractory Disease and Metastasis
Authors: Yogev Orli , Almeida Gilberto S. , Barker Karen T. , George Sally L. , Kwok Colin , Campbell James , Zarowiecki Magdalena , Kleftogiannis Dimitrios , Smith Laura M. , Hallsworth Albert , Berry Philip , Möcklinghoff Till , Webber Hannah T. , Danielson Laura S. , Buttery Bliss , Calton Elizabeth A. , da Costa Barbara M. , Poon Evon , Jamin Yann , Lise Stefano , Veal Gareth J. , Sebire Neil , Robinson Simon P. , Anderson John , Chesler Louis
Published: April 2023

Th-MYCNCPM32 tumors and derived cell lines show enhancement of mesenchymal markers.
Supplementary Fig. 3 from In Vivo Modeling of Chemoresistant Neuroblastoma Provides New Insights into Chemorefractory Disease and Metastasis
Authors: Yogev Orli , Almeida Gilberto S. , Barker Karen T. , George Sally L. , Kwok Colin , Campbell James , Zarowiecki Magdalena , Kleftogiannis Dimitrios , Smith Laura M. , Hallsworth Albert , Berry Philip , Möcklinghoff Till , Webber Hannah T. , Danielson Laura S. , Buttery Bliss , Calton Elizabeth A. , da Costa Barbara M. , Poon Evon , Jamin Yann , Lise Stefano , Veal Gareth J. , Sebire Neil , Robinson Simon P. , Anderson John , Chesler Louis
Published: April 2023

Resistant tumors show recurrent copy number aberrations and a tendency towards the neuroblastoma mesenchymal gene expression signature.
Supplementary Data from In Vivo Modeling of Chemoresistant Neuroblastoma Provides New Insights into Chemorefractory Disease and Metastasis
Authors: Yogev Orli , Almeida Gilberto S. , Barker Karen T. , George Sally L. , Kwok Colin , Campbell James , Zarowiecki Magdalena , Kleftogiannis Dimitrios , Smith Laura M. , Hallsworth Albert , Berry Philip , Möcklinghoff Till , Webber Hannah T. , Danielson Laura S. , Buttery Bliss , Calton Elizabeth A. , da Costa Barbara M. , Poon Evon , Jamin Yann , Lise Stefano , Veal Gareth J. , Sebire Neil , Robinson Simon P. , Anderson John , Chesler Louis
Published: April 2023

Supplementary materials and methods Supplementary figures legends
Supplementary figures legends from Spindle Assembly Checkpoint Inhibition Can Resensitize p53-Null Stem Cells to Cancer Chemotherapy
Authors: Liu Changlong , Banister Carolyn E. , Buckhaults Phillip J.
Published: April 2023

Supplementary figures legends
Supplementary Data from Hypermethylation of SHISA3 Promotes Nasopharyngeal Carcinoma Metastasis by Reducing SGSM1 Stability
Authors: Zhang Jian , Li Ying-Qin , Guo Rui , Wang Ya-Qin , Zhang Pan-Pan , Tang Xin-Ran , Wen Xin , Hong Xiao-Hong , Lei Yuan , He Qing-Mei , Yang Xiao-Jing , Sun Ying , Ma Jun , Liu Na
Published: April 2023

Supplementary Tables S1-S5: -Table S1. Primers used in this study. Table S2. Antibodies used in this study. Table S3. Sequencing of anti-SHISA3 immunoprecipitation complex by mass spectrometry. Table S4. Sequencing of anti-SGSM1 immunoprecipitation complex by mass spectrometry. Table S5. The possible ubiquitination sites of SGSM1 C-terminal.
Legend for Supplementary tables from Vitamin D–VDR Signaling Inhibits Wnt/β-Catenin–Mediated Melanoma Progression and Promotes Antitumor Immunity
Authors: Muralidhar Sathya , Filia Anastasia , Nsengimana Jérémie , Poźniak Joanna , O'Shea Sally J. , Diaz Joey M. , Harland Mark , Randerson-Moor Juliette A. , Reichrath Jörg , Laye Jonathan P. , van der Weyden Louise , Adams David J. , Bishop D.T. , Newton-Bishop Julia
Published: April 2023

Legend for Supplementary tables
Figure S3 from Tumor Angiogenesis Is Differentially Regulated by Phosphorylation of Endothelial Cell Focal Adhesion Kinase Tyrosines-397 and -861
Authors: Pedrosa Ana-Rita , Bodrug Natalia , Gomez-Escudero Jesus , Carter Edward P. , Reynolds Louise E. , Georgiou Paraskivi Natalia , Fernandez Isabelle , Lees Delphine M. , Kostourou Vassiliki , Alexopoulou Annika N. , Batista Silvia , Tavora Bernardo , Serrels Bryan , Parsons Maddy , Iskratsch Thomas , Hodivala-Dilke Kairbaan M.
Published: April 2023

Supplementary Figure 3. Levels of tumour hypoxia are enhanced in ECCre+;FAK397F/397F mice and blood vessel density reduced in early stage CMT19T tumours in ECCre+;FAKY861F/Y861F mice.
Supplementary Table S1 from Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods
Authors: Jiménez-Sánchez Alejandro , Cast Oliver , Miller Martin L.
Published: April 2023

Supplementary Table 1: A) TME cell estimation method information. B) Benchmarking dataset information. C) Cell type inclusion for multiple linear regression analyses. D) TME cell estimation method to ground truth cell type matching for cell type-specific benchmarking experiments.
Supplementary Table S3 from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

GC PDXs are annotated for: CNV of HER2, EGFR, FGFR2, MET, KRAS ({greater than or equal to}8 gene copies); COSMIC Mutations/Frameshifts (Allelic frequency >0.3)
Supplementary Figure S3 from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

ROC curves of Lee MSI signature predicting MSI genetic status in PDXs and TCGA samples cohorts.
Supplementary Figure S2 from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

Organoids contain few or no stroma component and when reinjected in mice originated tumors resembling the corresponding PDXs.
Table S2 from Metabolic Reprogramming by MYCN Confers Dependence on the Serine-Glycine-One-Carbon Biosynthetic Pathway
Authors: Xia Yingfeng , Ye Bingwei , Ding Jane , Yu Yajie , Alptekin Ahmet , Thangaraju Muthusamy , Prasad Puttur D. , Ding Zhi-Chun , Park Eun Jeong , Choi Jeong-Hyeon , Gao Bei , Fiehn Oliver , Yan Chunhong , Dong Zheng , Zha Yunhong , Ding Han-Fei
Published: April 2023

Functional annotation of NCT503-responsive genes
supplementary material and methods from S100A10 Is a Critical Mediator of GAS6/AXL–Induced Angiogenesis in Renal Cell Carcinoma
Authors: Xiao Yiren , Zhao Hongjuan , Tian Lei , Nolley Rosalie , Diep Anh N. , Ernst Anne , Fuh Katherine C. , Miao Yu Rebecca , von Eyben Rie , Leppert John T. , Brooks James D. , Peehl Donna M. , Giaccia Amato J. , Rankin Erinn B.
Published: April 2023

Document contains supplementary material and method
Figure S4 from S100A10 Is a Critical Mediator of GAS6/AXL–Induced Angiogenesis in Renal Cell Carcinoma
Authors: Xiao Yiren , Zhao Hongjuan , Tian Lei , Nolley Rosalie , Diep Anh N. , Ernst Anne , Fuh Katherine C. , Miao Yu Rebecca , von Eyben Rie , Leppert John T. , Brooks James D. , Peehl Donna M. , Giaccia Amato J. , Rankin Erinn B.
Published: April 2023

Cabozantinib therapy inhibits ccRCC tumor growth.
Supplementary Material from MUC1-C Activates the NuRD Complex to Drive Dedifferentiation of Triple-Negative Breast Cancer Cells
Authors: Hata Tsuyoshi , Rajabi Hasan , Takahashi Hidekazu , Yasumizu Yota , Li Wei , Jin Caining , Long Mark D. , Hu Qiang , Liu Song , Fushimi Atsushi , Yamashita Nami , Kui Ling , Hong Deli , Yamamoto Masaaki , Miyo Masaaki , Hiraki Masayuki , Maeda Takahiro , Suzuki Yozo , Samur Mehmet K. , Kufe Donald
Published: April 2023

Supplementary Figures S1-S11 and Tables S1-S2. Supplemental Figure S1. Treatment of BT-549/tet-CshRNA and SUM149/tet-CshRNA cells with DOX has no apparent effect on MTA1, MBD3, CHD4 or HDAC1 expression. Supplemental Figure S2. Targeting MUC1-C with a different shRNA is associated with downregulation of MTA1, MBD3 and CHD4 expression. Supplemental Figure S3. Targeting MUC1-C in luminal MCF-7, T47D and ZR-75-1 BC cells has no detectable effect on MTA1, MBD3 or CHD4 expression. Supplemental Figure S4. Targeting MYC with a different shRNA or treatment with the JQ1 inhibitor is associated with downregulation of MTA1, MBD3 and CHD4 expression. Supplemental Figure S5. Association of MUC1-C with MYC and MTA1 in the presence of ethidium bromide to inhibit non-specific association of proteins and nucleic acids. Supplemental Figure S6. MUC1-C CQC motif binds directly to the MYC HLH-LZ domain. Supplemental Figure S7. ChIP studies performed on regions upstream to the MTA1 and MBD3 promoters. Supplemental Figure S8. ChIP studies performed on the ESR1 promoter. Supplemental Figure S9. MUC1-C regulates the Hallmark Estrogen Response Early and Late gene sets in BT-549 cells. Supplemental Figure S10. MUC1-C regulates the Hallmark Estrogen Response Early and Late gene sets in SUM149 cells. Supplemental Figure S11. Silencing MUC1-C regulates the expression of luminal and basal markers. Supplemental Figure S12. Expression of MTA1 and MBD3 correlates negatively with that of FOXA1 and GATA3 in breast cancers. Supplemental Table S1. Primers used for qRT-PCR analysis. Supplemental Table S2. Primers used for ChIP-PCR analysis.
Figure S6 from The Deubiquitylase OTUB1 Mediates Ferroptosis via Stabilization of SLC7A11
Authors: Liu Tong , Jiang Le , Tavana Omid , Gu Wei
Published: April 2023

The loss of OTUB1 induces ferroptosis in T24 cells
Supplementary Table 3 from An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation
Authors: Aqaqe Nasma , Yassin Muhammad , Yassin Abed Alkader , Ershaid Nour , Katz-Even Chen , Zipin-Roitman Adi , Kugler Eitan , Lechman Eric R. , Gan Olga I. , Mitchell Amanda , Dick John E. , Izraeli Shai , Milyavsky Michael
Published: April 2023

Supplementary Table 3
Figure S1 from The Deubiquitylase OTUB1 Mediates Ferroptosis via Stabilization of SLC7A11
Authors: Liu Tong , Jiang Le , Tavana Omid , Gu Wei
Published: April 2023

SLC3A2 is present in the SLC7A11 complex
Supplementary Table 1 from An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation
Authors: Aqaqe Nasma , Yassin Muhammad , Yassin Abed Alkader , Ershaid Nour , Katz-Even Chen , Zipin-Roitman Adi , Kugler Eitan , Lechman Eric R. , Gan Olga I. , Mitchell Amanda , Dick John E. , Izraeli Shai , Milyavsky Michael
Published: April 2023

Supplementary Table 1
Supplementary Data from An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation
Authors: Aqaqe Nasma , Yassin Muhammad , Yassin Abed Alkader , Ershaid Nour , Katz-Even Chen , Zipin-Roitman Adi , Kugler Eitan , Lechman Eric R. , Gan Olga I. , Mitchell Amanda , Dick John E. , Izraeli Shai , Milyavsky Michael
Published: April 2023

Supplementary figure legends and full list of materials and methods references
Movie S3 from Assessment of Tumor Redox Status through (S)-4-(3-[18F]fluoropropyl)-L-Glutamic Acid PET Imaging of System xc− Activity
Authors: McCormick Patrick N. , Greenwood Hannah E. , Glaser Matthias , Maddocks Oliver D.K. , Gendron Thibault , Sander Kerstin , Gowrishankar Gayatri , Hoehne Aileen , Zhang Tong , Shuhendler Adam J. , Lewis David Y. , Berndt Mathias , Koglin Norman , Lythgoe Mark F. , Gambhir Sanjiv S. , Årstad Erik , Witney Timothy H.
Published: April 2023

Movie S3
Tables S1-S4 from DNA Methylation Controls Metastasis-Suppressive 14q32-Encoded miRNAs
Authors: Oshima Go , Poli Elizabeth C. , Bolt Michael J. , Chlenski Alexandre , Forde Martin , Jutzy Jessica M.S. , Biyani Neha , Posner Mitchell C. , Pitroda Sean P. , Weichselbaum Ralph R. , Khodarev Nikolai N.
Published: April 2023

Supplementary Tables S1-S4 show primers and gRNAs used in CRISPR/cas9 experiments and differential expression of 14q32 microRNAs in DKO mice and after treatment by 5-Aza-dC.
Figure S7 from DNA Methylation Controls Metastasis-Suppressive 14q32-Encoded miRNAs
Authors: Oshima Go , Poli Elizabeth C. , Bolt Michael J. , Chlenski Alexandre , Forde Martin , Jutzy Jessica M.S. , Biyani Neha , Posner Mitchell C. , Pitroda Sean P. , Weichselbaum Ralph R. , Khodarev Nikolai N.
Published: April 2023

Colo320 cells have limited response to 5-Aza-dC treatment and fail to produce liver metastases in vivo
Figure S4 from DNA Methylation Controls Metastasis-Suppressive 14q32-Encoded miRNAs
Authors: Oshima Go , Poli Elizabeth C. , Bolt Michael J. , Chlenski Alexandre , Forde Martin , Jutzy Jessica M.S. , Biyani Neha , Posner Mitchell C. , Pitroda Sean P. , Weichselbaum Ralph R. , Khodarev Nikolai N.
Published: April 2023

Viability of HCT116-L2T cells after treatment with 5-aza-dC
Supplementary Figures S1-S10. from Differential Subcellular Localization Regulates Oncogenic Signaling by ROS1 Kinase Fusion Proteins
Authors: Neel Dana S. , Allegakoen David V. , Olivas Victor , Mayekar Manasi K. , Hemmati Golzar , Chatterjee Nilanjana , Blakely Collin M. , McCoach Caroline E. , Rotow Julia K. , Le Anh , Karachaliou Niki , Rosell Rafael , Riess Jonathan W. , Nichols Robert , Doebele Robert C. , Bivona Trever G.
Published: April 2023

Figure S1: Prevalence of N-terminal fusion partners and ROS1 exonic breakpoints; Figure S2: Activation of STAT3 and IRS1 by ROS1 fusions; Figure S3: Effects of MEK activation in ROS1 fusion oncoprotein-expressing cellular models; Figure S4: JAK/STAT pathway activation is unable to rescue ROS1 fusion-positive patient-derived cells from crizotinib sensitivity; Figure S5: Effects of MAPK pathway suppression by SHP2 inhibitor treatment in ROS1-fusion oncoprotein expressing patient-derived NSCLC cell lines; Figure S6: SHP2 interacts with phospho-SDC4-ROS1; Figure S7: ROS1 exonic breakpoint does not determine the fusion protein's ability to engage the MAPK pathway; Figure S8: Localization of ROS1 in patient-derived cell lines reveals differential subcellular localization of the different ROS1 fusion oncoproteins; Figure S9: Growth of positive and negative control NIH-3T3 cells in vivo; Figure S10: MAPK pathway activation is higher in SDC4-ROS1- and SLC34A2-ROS1-driven tumors
Table S3 from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Table S3 contains normalized cell viability values of 4x4 combination experiments (original data of Fig. S2).
Supplementary Table S6 from Immuno-oncological Efficacy of RXDX-106, a Novel TAM (TYRO3, AXL, MER) Family Small-Molecule Kinase Inhibitor
Authors: Yokoyama Yumi , Lew Erin D. , Seelige Ruth , Tindall Elizabeth A. , Walsh Colin , Fagan Patrick C. , Lee Jack Y. , Nevarez Robin , Oh Joanne , Tucker Kathleen D. , Chen Marissa , Diliberto Amy , Vaaler Heather , Smith Kristen M. , Albert Amanda , Li Gary , Bui Jack D.
Published: April 2023

GO analysis of RNA-Seq data from the MC38 combination study
Table S2 from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Table S2 contains normalized cell viability values of single agent dose-response curves of 18 compounds employed in the screen (original data of Fig. S1).
Supplementary Table S5 from Immuno-oncological Efficacy of RXDX-106, a Novel TAM (TYRO3, AXL, MER) Family Small-Molecule Kinase Inhibitor
Authors: Yokoyama Yumi , Lew Erin D. , Seelige Ruth , Tindall Elizabeth A. , Walsh Colin , Fagan Patrick C. , Lee Jack Y. , Nevarez Robin , Oh Joanne , Tucker Kathleen D. , Chen Marissa , Diliberto Amy , Vaaler Heather , Smith Kristen M. , Albert Amanda , Li Gary , Bui Jack D.
Published: April 2023

Listed are the Top 100 genes significantly upregulated or downregulated over time in the MC38 model by RXDX-106 treatment relative to vehicle.
Table S1 from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Table S1 complements the Material and Methods part listing cell lines and growing conditions, primer sequences, antibodies, compounds and their concentrations.
Supplementary Table S2 from BRCA1 Deficiency Upregulates NNMT, Which Reprograms Metabolism and Sensitizes Ovarian Cancer Cells to Mitochondrial Metabolic Targeting Agents
Authors: Kanakkanthara Arun , Kurmi Kiran , Ekstrom Thomas L. , Hou Xiaonan , Purfeerst Emma R. , Heinzen Ethan P. , Correia Cristina , Huntoon Catherine J. , O'Brien Daniel , Wahner Hendrickson Andrea E. , Dowdy Sean C. , Li Hu , Oberg Ann L. , Hitosugi Taro , Kaufmann Scott H. , Weroha S. John , Karnitz Larry M.
Published: April 2023

Excel data file of NNMT and CDK12 protein levels in HGSOC tumors from patients.
Figure S1 from Prolactin Promotes Fibrosis and Pancreatic Cancer Progression
Authors: Tandon Manuj , Coudriet Gina M. , Criscimanna Angela , Socorro Mairobys , Eliliwi Mouhanned , Singhi Aatur D. , Cruz-Monserrate Zobeida , Bailey Peter , Lotze Michael T. , Zeh Herbert , Hu Jing , Goffin Vincent , Gittes George K. , Biankin Andrew V. , Esni Farzad
Published: April 2023

Prolactin does not promote activation of Jak2 signaling pathway in BxPC3 cell line, which lacks PRLR expression.
Supplementary Figure 3 from Secretion of Acid Sphingomyelinase and Ceramide by Endothelial Cells Contributes to Radiation-Induced Intestinal Toxicity
Authors: Leonetti Daniela , Estéphan Hala , Ripoche Natacha , Dubois Nolwenn , Aguesse Audrey , Gouard Sébastien , Brossard Lisa , Chiavassa Sophie , Corre Isabelle , Pecqueur Claire , Neunlist Michel , Hadchity Elie , Gaugler Marie-Hélène , Mahé Maxime M. , Paris François
Published: April 2023

SupFigure3
Figure S15 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Kv3.3 immunostaining of proprioceptive sensory neurons receptor endings and cell bodies
Figure S14 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Heat-map distribution of significantly differentially expressed genes specific to neuron neuronal excitability
Figure S11 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

vGlut1 immunostaining of proprioceptive sensory neurons receptor endings.
Figure S1 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Immunohistochemical and morphological analyses of healthy and tumor bearing colons
Figure S3 from Infiltrating Mast Cell–Mediated Stimulation of Estrogen Receptor Activity in Breast Cancer Cells Promotes the Luminal Phenotype
Authors: Majorini Maria Teresa , Cancila Valeria , Rigoni Alice , Botti Laura , Dugo Matteo , Triulzi Tiziana , De Cecco Loris , Fontanella Enrico , Jachetti Elena , Tagliabue Elda , Chiodoni Claudia , Tripodo Claudio , Colombo Mario P. , Lecis Daniele
Published: April 2023

The presence of MCs positively correlates with the expression of ER-dependent genes. Each scatter plot graph shows the correlation between CPA3 expression and selected genes evaluated in tumors obtained from patients of the GHEA cohort.
Combined Supplementary Figures from IL26, a Noncanonical Mediator of DNA Inflammatory Stimulation, Promotes TNBC Engraftment and Progression in Association with Neutrophils
Authors: Trotter Timothy N. , Shuptrine Casey W. , Tsao Li-Chung , Marek Robert D. , Acharya Chaitanya , Wei Jun-Ping , Yang Xiao-Yi , Lei Gangjun , Wang Tao , Lyerly Herbert Kim , Hartman Zachary C.
Published: April 2023

SF1: IL-26 protein or mRNA expression in human cell lines and clinical samples; SF2: Single-cell profiling of CD4+ TH17 cells in TNBC patients; SF3: Confirmation of IL-26 knockdown in MDA-MB-231 cells; SF4: In vitro proliferation and in vivo metastasis of IL-26 knockdown MDA-MB-231 cells; SF5: Gene expression profiling of IL-26 knockdown MDA-MB-231 tumors; SF6: IL-26 knockdown in SUM159 and MDA-MB-468 cells and in vitro phenotyping; SF7: Western blot confirmation of IL-26 knock-in E0771 cells and IL-26 upregulation after growth in vivo; SF8: IL-26 knock-in E0771 tumors progress more rapidly than control in an immune competent setting; SF9: Stat3 activation by IL-26 is dependent on human IL10RB and IL20RA; SF10: DNA-bound IL-26 elicits inflammatory signaling in human and mouse immune cells; SF11: Confirmation of mouse neutrophil enrichment; SF12: Confirmation of Anti-Ly6G antibody depletion of mouse neutrophils; SF13: Inflammatory cytokine expression in MDA-MB-231 parental and MDA-MB-231 LM2 lung-metastatic subclone; SF14: CRISPR knockdown of IL-6, IL-8, and Cxcl1 in MDA-MB-231 LM2 CRISPR 3x cell lines/lung metastases and correlation of CRISPR 3x primary tumor volume with metastasis; SF15: IL-26 signature and Neutrophil enrichment score are significantly correlated in METABRIC dataset; SF16: T cell ELISPOT response to IL-26 vaccination in vivo.
Table S2 from Transcriptomics Associates Molecular Features with 18F-Fluorocholine PET/CT Imaging Phenotype and Its Potential Relationship to Survival in Hepatocellular Carcinoma
Authors: Kwee Sandi A. , Tiirikainen Maarit , Sato Miles M. , Acoba Jared D. , Wei Runmin , Jia Wei , Le Marchand Loic , Wong Linda L.
Published: April 2023

GSEA using mSigDB CGP collection
Supplementary Figures 1-6; Supplementary Methods and Materials; Supplementary References from TAp63-Regulated miRNAs Suppress Cutaneous Squamous Cell Carcinoma through Inhibition of a Network of Cell-Cycle Genes
Authors: Davis Andrew John , Tsinkevich Maksym , Rodencal Jason , Abbas Hussein A. , Su Xiao-hua , Gi Young-Jin , Fang Bin , Rajapakshe Kimal , Coarfa Cristian , Gunaratne Preethi H. , Koomen John M. , Tsai Kenneth Y. , Flores Elsa R.
Published: April 2023

This file contains the following: Supplementary Figure 1: Representative H&E staining and immunohistochemistry for keratin 5 of a metastasis in the lung of a tumor-bearing TAp63-/- mouse. Supplementary Figure 2: TAp63-deficient tumors exhibit deregulated mRNA and miRNA expression. Supplementary Figure 3: TAp63-regulated miR-30c-2* and miR-497-5p suppresses cuSCC through induction of cell death and cell cycle arrest. Supplementary Figure 4: Identification of miRNA targets through the use of TMT-LC-MS/MS. Supplementary Figure 5: Inhibition of miR-30c-2-3p and miR-497-5p targets affects cuSCC cell proliferation and survival. Supplementary Figure 6: AURKA is a viable therapeutic target in cuSCC. Supplementary Methods and Materials. Supplementary References.
Supplementary Data from Inhibition of miR-328–3p Impairs Cancer Stem Cell Function and Prevents Metastasis in Ovarian Cancer
Authors: Srivastava Amit K. , Banerjee Ananya , Cui Tiantian , Han Chunhua , Cai Shurui , Liu Lu , Wu Dayong , Cui Ri , Li Zaibo , Zhang Xiaoli , Xie Guozhen , Selvendiran Karuppaiyah , Patnaik Srinivas , Karpf Adam R. , Liu Jinsong , Cohn David E. , Wang Qi-En
Published: April 2023

microRNA expression assay, primers and antibodies used in this study, as well as supplementary tables and figures showing the relationship among miR328, ERK, and ROS in CSCs.