bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S4 from Mesenchymal Stem Cells Promote Hepatocarcinogenesis via lncRNA–MUF Interaction with ANXA2 and miR-34a
Authors: Yan Xinlong , Zhang Dongdong , Wu Wei , Wu Shuheng , Qian Jingfeng , Hao Yajing , Yan Fang , Zhu Pingping , Wu Jiayi , Huang Guanling , Huang Yinghui , Luo Jianjun , Liu Xinhui , Liu Benyu , Chen Xiaomin , Du Ying , Chen Runsheng , Fan Zusen
Published: March 2023

LncRNA-MUF acts as a ceRNA to modulate the function of miR-34a.
Figure S4 and Legend from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains the results of studies with Eo771 cells stably expressing MUC1-C (S4A and S4B), demonstrating that treatment of these cells with JQ1 (S4C), BAY-11-7085 (S4D) or GO-203/NPs (S4E) decreases PD-L1 expression.
Figure S1 and Legend from MUC1-C Induces PD-L1 and Immune Evasion in Triple-Negative Breast Cancer
Authors: Maeda Takahiro , Hiraki Masayuki , Jin Caining , Rajabi Hasan , Tagde Ashujit , Alam Maroof , Bouillez Audrey , Hu Xiufeng , Suzuki Yozo , Miyo Masaaki , Hata Tsuyoshi , Hinohara Kunihiko , Kufe Donald
Published: March 2023

This file contains the results of studies with DOX-treated (i) BT-549 cells expressing a tet-CshRNA or tet-MUC1shRNA (S1A-S1D), (ii) MDA-MB-231 cells expressing a tet-CshRNA (S1E), and (iii) SUM-159 cells expressing a tet-MUC1shRNA (S1F).
Supplementary Tables I-IV from FLT3 and JAK2 Mutations in Acute Myeloid Leukemia Promote Interchromosomal Homologous Recombination and the Potential for Copy Neutral Loss of Heterozygosity
Authors: Gaymes Terry J. , Mohamedali Azim , Eiliazadeh Anthony L. , Darling David , Mufti Ghulam J.
Published: March 2023

Table I: Mutation screening in primary NK-AML Table II: HR repair activity in primary NK-AML Table III: HR repair in FLT3-ITD cell lines Table IV: Mutation rate and frequency in FLT3-ITD cells
Supplementary figure 4 from Prominent Oncogenic Roles of EVI1 in Breast Carcinoma
Authors: Wang Hui , Schaefer Thorsten , Konantz Martina , Braun Martin , Varga Zsuzsanna , Paczulla Anna M. , Reich Selina , Jacob Francis , Perner Sven , Moch Holger , Fehm Tanja N. , Kanz Lothar , Schulze-Osthoff Klaus , Lengerke Claudia
Published: March 2023

EVI1 affects cell cycle regulatory molecules in BC.
Supplemental Table S1 from The NCI-60 Methylome and Its Integration into CellMiner
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Rajapakse Vinodh , Luna Augustin , Kohn Kurt W. , Stevenson Holly , Wang Yonghong , Heyn Holger , Nogales Vanesa , Moran Sebastian , Goldstein David J. , Doroshow James H. , Meltzer Paul S. , Esteller Manel , Pommier Yves
Published: March 2023

128,394 probes used for the determination of gene methylation levels.
Supplementary Tables S1-S7 from A Transposon-based Analysis Reveals RASA1 Is Involved in Triple-Negative Breast Cancer
Authors: Suárez-Cabrera Cristian , Quintana Rita M. , Bravo Ana , Casanova M. Llanos , Page Angustias , Alameda Josefa P. , Paramio Jesús M. , Maroto Alicia , Salamanca Javier , Dupuy Adam J. , Ramírez Angel , Navarro Manuel
Published: March 2023

Table in gff3 format showing all the transposon insertions in breast tumors as detected by gCIS analysis (S1); Clinical data for 32 human breast tumors (S2); Scoring of the immunohistochemical staining of human breast tumors with RASA1, TP53 and NF1 antibodies (S3); Association of RASA1 and NF1 expression with clinical-pathological characteristics of patients described in supplementary Table S2 (S4); Analysis of RASA1 putative copy number alterations in the breast invasive carcinoma dataset using cBioportal (S5); Analysis of RASA1 putative copy loss and TP53 mutations in the breast invasive carcinoma dataset using cBioportal (S6); Analysis of NF1 putative copy number alterations in the breast invasive carcinoma dataset using cBioportal (S7).
Supplemental Figure S2 from The NCI-60 Methylome and Its Integration into CellMiner
Authors: Reinhold William C. , Varma Sudhir , Sunshine Margot , Rajapakse Vinodh , Luna Augustin , Kohn Kurt W. , Stevenson Holly , Wang Yonghong , Heyn Holger , Nogales Vanesa , Moran Sebastian , Goldstein David J. , Doroshow James H. , Meltzer Paul S. , Esteller Manel , Pommier Yves
Published: March 2023

Relationship between methylation and lack of SLFN11 and MGMT expression in the NCI-60.
Supplementary data from MicroRNA-194 Promotes Prostate Cancer Metastasis by Inhibiting SOCS2
Authors: Das Rajdeep , Gregory Philip A. , Fernandes Rayzel C. , Denis Iza , Wang Qingqing , Townley Scott L. , Zhao Shuang G. , Hanson Adrienne R. , Pickering Marie A. , Armstrong Heather K. , Lokman Noor A. , Ebrahimie Esmaeil , Davicioni Elai , Jenkins Robert B. , Karnes R. Jeffrey , Ross Ashley E. , Den Robert B. , Klein Eric A. , Chi Kim N. , Ramshaw Hayley S. , Williams Elizabeth D. , Zoubeidi Amina , Goodall Gregory J. , Feng Felix Y. , Butler Lisa M. , Tilley Wayne D. , Selth Luke A.
Published: March 2023

This files contains 1 Supplementary Table and 11 Supplementary Figures. The Supplementary Table shows Univariate and multivariate Cox proportional hazard analysis of prostate tumor levels of miR-194 and Gleason score/grade in relation to recurrence-free interval after radical prostatectomy in the TCGA cohort. The Supplementary Figures collectively include data that supports the key finding of this study; namely, that miR-194 is an important driver of prostate cancer metastasis.
Supplementary Methods from MYC Inhibition Depletes Cancer Stem-like Cells in Triple-Negative Breast Cancer
Authors: Yang Aimin , Qin Shenghui , Schulte Bradley A. , Ethier Stephen P. , Tew Kenneth D. , Wang Gavin Y.
Published: March 2023

Additional methods on drug screen, CSC sorting, real-time PCR, flow cytometric apoptosis assay and immunohistochemical (IHC) analysis are provided.
Supplementary Figures and Legends from MYC Inhibition Depletes Cancer Stem-like Cells in Triple-Negative Breast Cancer
Authors: Yang Aimin , Qin Shenghui , Schulte Bradley A. , Ethier Stephen P. , Tew Kenneth D. , Wang Gavin Y.
Published: March 2023

The Supplementary Figures and Legends provide additional information on Flow Cytometry gating strategy for TNBC CSC sorting, the effects of C1572 on additional TNBC cells, the evidence that C1572 reversibly inhibits MYC, comparing the effectiveness of C1572 and JQ1 at inhibiting MYC, and the impact of C1572 on body weight change in mice.
Figure S3 from Emergence of High-Avidity Melan-A–Specific Clonotypes as a Reflection of Anti–PD-1 Clinical Efficacy
Authors: Simon Sylvain , Vignard Virginie , Varey Emilie , Parrot Tiphaine , Knol Anne-Chantal , Khammari Amir , Gervois Nadine , Lang Francois , Dreno Brigitte , Labarriere Nathalie
Published: March 2023

Figure S3 documents PD-1, TIGIT and PD-1/TIGIT co-expression on all the main VÃŸ subtypes, from all Melan-A specific T cell populations, at rest.
Figure S2 from Emergence of High-Avidity Melan-A–Specific Clonotypes as a Reflection of Anti–PD-1 Clinical Efficacy
Authors: Simon Sylvain , Vignard Virginie , Varey Emilie , Parrot Tiphaine , Knol Anne-Chantal , Khammari Amir , Gervois Nadine , Lang Francois , Dreno Brigitte , Labarriere Nathalie
Published: March 2023

Figure S2 documents PD-1, TIGIT and PD-1/TIGIT co-expression on whole peripheral CD8+ T cells from HLA-A2 melanoma patients, before and after PD-1 therapy.
Figures S1-S6 from SKP2 Activation by Thyroid Hormone Receptor β2 Bypasses Rb-Dependent Proliferation in Rb-Deficient Cells
Authors: Xu Xiaoliang L. , Li Zhengke , Liu Aihong , Fan Xianqun , Hu Dan-ning , Qi Dong-Lai , Chitty David W. , Jia Renbing , Qui Jianping , Wang Justin Q. , Sharaf Jake , Zou Jun , Weiss Rebecca , Huang Hongyan , Joseph Walter J. , Ng Lily , Rosen Richard , Shen Binghui , Reid Mark W. , Forrest Douglas , Abramson David H. , Singer Samuel , Cobrinik David , Jhanwar Suresh C.
Published: March 2023

Figure S1. TRβ2 and TRβ1 inversely regulate retinoblastoma cell proliferation and cell cycle progression.Figure S2. Pituitary anterior lobe and intermediate lobe markers and Trβ isoforms expressed in pituitary tumors in Rb1+/- mice of different Trβ genetic backgrounds.Figure S3. EMI1 mediates TRβ2 regulation of SKP2.Figure S4. Rescue of Rb knockdown-induced cell cycle arrest and SKP2 down-regulation by ectopic Rb expression.Figure S5. Gene expression changes in response to RB1-KD in synchronized SKN-BE(2) neuroblastoma cells.Figure S6. TRβ1 and TRβ2 regulate proliferation and SKP2 and p27 expression in Rb-deficient MXF8000 myxofibrosarcoma cells.
Figure S1 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

DHHC3 expression in malignant and metastatic human breast cancer subtypes and effects on breast tumor growth are shown.
Supplementary Fig. 2 from A Novel Mouse Model to Study Image-Guided, Radiation-Induced Intestinal Injury and Preclinical Screening of Radioprotectors
Authors: Verginadis Ioannis I. , Kanade Rahul , Bell Brett , Koduri Sravya , Ben-Josef Edgar , Koumenis Constantinos
Published: March 2023

Supplementary Fig. 2 - Harvesting and processing of intestinal tissue segments.
Supplementary Table 1 from Systematic In Vivo Inactivation of Chromatin-Regulating Enzymes Identifies Setd2 as a Potent Tumor Suppressor in Lung Adenocarcinoma
Authors: Walter David M. , Venancio Olivia S. , Buza Elizabeth L. , Tobias John W. , Deshpande Charuhas , Gudiel A. Andrea , Kim-Kiselak Caroline , Cicchini Michelle , Yates Travis J. , Feldser David M.
Published: March 2023

Supplementary Table 1: Ingenuity Pathway Analysis results for Arid1a vs. GFP tumors.
Supplemental Figures 1 through 3 from Quantitative Fluorescence Microscopy Measures Vascular Pore Size in Primary and Metastatic Brain Tumors
Authors: Mittapalli Rajendar K. , Adkins Chris E. , Bohn Kaci. A. , Mohammad Afroz S. , Lockman Julie A. , Lockman Paul R.
Published: March 2023

Supplementary figures showing representative histology and tracer distribution in the brain tumor models.
Supplementary tables from Zeb1 in Stromal Myofibroblasts Promotes Kras-Driven Development of Pancreatic Cancer
Authors: Sangrador Irene , Molero Xavier , Campbell Fiona , Franch-Expósito Sebastià , Rovira-Rigau Maria , Samper Esther , Domínguez-Fraile Manuel , Fillat Cristina , Castells Antoni , Vaquero Eva C.
Published: March 2023

Antibodies used for immunohistochemistry and immunofluorescence (Table 1), and for western blot (Table 2)
Figure S9-S14 from New Generation Nanomedicines Constructed from Self-Assembling Small-Molecule Prodrugs Alleviate Cancer Drug Toxicity
Authors: Wang Hangxiang , Lu Zhongjie , Wang Lijiang , Guo Tingting , Wu Jiaping , Wan Jianqin , Zhou Liqian , Li Hui , Li Zhen , Jiang Donghai , Song Penghong , Xie Haiyang , Zhou Lin , Xu Xiao , Zheng Shusen
Published: March 2023

Histological analysis of tumors and major organs
Supplementary Materials and Methods, Supplementary Figures 1 through 3 and Supplementary Tables 1 through 5 from Aberrant SYK Kinase Signaling Is Essential for Tumorigenesis Induced by TSC2 Inactivation
Authors: Cui Ye , Steagall Wendy K. , Lamattina Anthony M. , Pacheco-Rodriguez Gustavo , Stylianou Mario , Kidambi Pranav , Stump Benjamin , Golzarri Fernanda , Rosas Ivan O. , Priolo Carmen , Henske Elizabeth P. , Moss Joel , El-Chemaly Souheil
Published: March 2023

Supplementary methods. Supplementary Figure S1. R406 and rapamycin induce G1 cell cycle arrest in TSC2- cells. Supplementary Figure S2. Densitometric analysis of phospho-Syk and Syk, related to Fig. 4D. Supplementary Figure S3. TSC2 deficiency leads to upregulation of MCP-1 gene expression in vitro. Supplementary Table S1. Characteristics of subjects who were part of the longitudinal studies, related to Fig.6B. Supplementary Table S2. Characteristics of healthy volunteers and LAM subjects whose PBMCs were studied, related to Fig.6C. Supplementary Table S3. siRNA sequences. Supplementary Table S4. Complete list of antibodies. Supplementary Table S5. Real-time PCR primer sequences.
Supplemental figure 4 from Selective Reversible Inhibition of Autophagy in Hypoxic Breast Cancer Cells Promotes Pulmonary Metastasis
Authors: Dower Christopher M. , Bhat Neema , Wang Edward W. , Wang Hong-Gang
Published: March 2023

Differential gene expression and pathway analysis
Supplementary figures from PI-273, a Substrate-Competitive, Specific Small-Molecule Inhibitor of PI4KIIα, Inhibits the Growth of Breast Cancer Cells
Authors: Li Jiangmei , Gao Zhen , Zhao Dan , Zhang Lunfeng , Qiao Xinhua , Zhao Yingying , Ding Hong , Zhang Panpan , Lu Junyan , Liu Jia , Jiang Hualiang , Luo Cheng , Chen Chang
Published: March 2023

Suppl. Fig. 1 First-round screening of PI4KIIα inhibitors;Suppl. Fig. 2 Second-round screening of PI4KIIα inhibitors;Suppl. Fig.3. Direct interaction between PI-273 analogs and PI4KIIα;Suppl. Fig. 4. PI-273 resistance screens using CRISPR-Cas9;Suppl. Fig.5. Generate and identify PI4KIIα knock out MCF-7 cells;Suppl. Fig. 6. Effects of PI-273 and its analogs on PI4KIIα downstream signaling pathways;Suppl. Fig. 7. PI4KIIα is required for the regulation of PI-273 on signaling transduction in breast cancer cells;Suppl. Fig. 8. PI-273 inhibits the proliferation of breast cancer cells.;Suppl. Fig. 9 Anti-tumor effect of PI-273 in an MCF-7-induced xenograft model;Suppl. Fig. 10 Inhibitory effect of 100 μM PIK inhibitors on PI4KIIα.
Supplemental Tables S1-S11 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks
Authors: Kelley Dylan Z. , Flam Emily L. , Izumchenko Evgeny , Danilova Ludmila V. , Wulf Hildegard A. , Guo Theresa , Singman Dzov A. , Afsari Bahman , Skaist Alyza M. , Considine Michael , Welch Jane A. , Stavrovskaya Elena , Bishop Justin A. , Westra William H. , Khan Zubair , Koch Wayne M. , Sidransky David , Wheelan Sarah J. , Califano Joseph A. , Favorov Alexander V. , Fertig Elana J. , Gaykalova Daria A.
Published: March 2023

Table S1. Clinical data for patient-derived PDX1, PDX2, UPPP1, and UPPP2 samples used for ChIP-based analysis. Table S2. ChIP-DNA qRT-PCR primers-probe sequence Table S3. Sample-specific enrichment of H3K4me3 histone mark at 5''UTR of individual genes. Table S4. Sample-specific enrichment of H3K27ac histone mark at 5''UTR of individual genes. Table S5. Sample-specific enrichment of H3K9ac histone mark at 5''UTR of individual genes. Table S6. Sample-specific enrichment of H3K9me3 histone mark at 5''UTR of individual genes. Table S7. Gene set enrichment analysis of genes linked to H3K27ac-enrichment specific for tumor samples. Table S8. Gene set enrichment analysis of genes linked to H3K27ac-enrichment specific for normal samples. Table S9. Gene set enrichment analysis of genes linked to H3K4me3-enrichment specific for tumor samples. Table S10. Gene set enrichment analysis of genes linked to H3K4me3-enrichment specific for normal samples. Table S11. Correlation of H3K27ac-enriched with genes differentially regulated in HPV-KRT and HPV-IMU.
Table S2 from Blocking Myristoylation of Src Inhibits Its Kinase Activity and Suppresses Prostate Cancer Progression
Authors: Kim Sungjin , Alsaidan Omar Awad , Goodwin Octavia , Li Qianjin , Sulejmani Essilvo , Han Zhen , Bai Aiping , Albers Thomas , Beharry Zanna , Zheng Y. George , Norris James S. , Szulc Zdzislaw M. , Bielawska Alicja , Lebedyeva Iryna , Pegan Scott D. , Cai Houjian
Published: March 2023

Data collection and refinement statistics (molecular replacement)
Supplementary Movie 1 from Sustained Adrenergic Signaling Promotes Intratumoral Innervation through BDNF Induction
Authors: Allen Julie K. , Armaiz-Pena Guillermo N. , Nagaraja Archana S. , Sadaoui Nouara C. , Ortiz Tatiana , Dood Robert , Ozcan Merve , Herder Danielle M. , Haemmerle Monika , Gharpure Kshipra M. , Rupaimoole Rajesha , Previs Rebecca A. , Wu Sherry Y. , Pradeep Sunila , Xu Xiaoyun , Han Hee Dong , Zand Behrouz , Dalton Heather J. , Taylor Morgan , Hu Wei , Bottsford-Miller Justin , Moreno-Smith Myrthala , Kang Yu , Mangala Lingegowda S. , Rodriguez-Aguayo Cristian , Sehgal Vasudha , Spaeth Erika L. , Ram Prahlad T. , Wong Stephen T.C. , Marini Frank C. , Lopez-Berestein Gabriel , Cole Steve W. , Lutgendorf Susan K. , De Biasi Mariella , Sood Anil K.
Published: March 2023

CARS imaging of ex vivo ovarian cancer samples
Supplementary Table S12 from Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation
Authors: Guo Yucheng , Nie Qing , MacLean Adam L. , Li Yanda , Lei Jinzhi , Li Shao
Published: March 2023

Cancer risks from 1 to 30 years obtained from simulation under different protocols of periodic acute inflammation.
Table S1 from Tumorigenic and Antiproliferative Properties of the TALE-Transcription Factors MEIS2D and MEIS2A in Neuroblastoma
Authors: Groß Anja , Schulz Catrine , Kolb Jasmine , Koster Jan , Wehner Sibylle , Czaplinski Sebastian , Khilan Abdulghani , Rohrer Hermann , Harter Patrick N. , Klingebiel Thomas , Langer Julian D. , Geerts Dirk , Schulte Dorothea
Published: March 2023

This table contains antibody information and primer sequences.
Supplementary Table S10 from Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation
Authors: Guo Yucheng , Nie Qing , MacLean Adam L. , Li Yanda , Lei Jinzhi , Li Shao
Published: March 2023

Mutation rate of the 20 biological processes.
Supplemental method from Tumorigenic and Antiproliferative Properties of the TALE-Transcription Factors MEIS2D and MEIS2A in Neuroblastoma
Authors: Groß Anja , Schulz Catrine , Kolb Jasmine , Koster Jan , Wehner Sibylle , Czaplinski Sebastian , Khilan Abdulghani , Rohrer Hermann , Harter Patrick N. , Klingebiel Thomas , Langer Julian D. , Geerts Dirk , Schulte Dorothea
Published: March 2023

This file contains detailed information on the mass spectrometry approach.
Supplementary (Model description, Parameter values, Model implementation,Experimental data analysis, Supporting Tables S1-S3 and Supporting Figures S1-S19) from Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation
Authors: Guo Yucheng , Nie Qing , MacLean Adam L. , Li Yanda , Lei Jinzhi , Li Shao
Published: March 2023

This Supplementary file includes: (1) Model description, Parameter values, Model implementation, and Experimental data analysis. (2) Supporting Tables S1-S3. Table S1: The influence between gene mutation type and cell function; Table S2: Parameters used model simulation; and Table S3: Parameters for simplifying success DNA repair probability. (3) Supporting Figures S1-S19. Figure S1: Illustration of the model; Figure S2: The inflammatory score divided into mild, moderate, and severe; Figure S3: Illustration of the DNA damage/repair module; Figure S4: Cell fate decision after DNA damage; Figure S5: The functions for the probability of successful repair and the number of un-repaired damage locus obtained from stochastic simulation; Figure S6: Flow chart of the numerical scheme of the simulation process; Figure S7: Population dynamics with three stages; Figure S8: Major pathways responsible to the process from inflammation to tumorigenesis; Figure S9: Mutations rates of the 20 classes biological processes; Figure S10: Effects of inflammation on population size and DNA damage; Figure S11: Population dynamics with different inflammation conditions; Figure S12: Evolution dynamics from 2 sample runs; Figure S13: Evolution dynamics from under various inflammation conditions; Figure S14: Evolution dynamics from 1 sample runs occurs to a single stem cell; Figure S15: Evolution dynamics from 1 sample runs for a group of stem cells; Figure S16: Summary of the double mutations present at the three time points. Figure S17: Evolution dynamics from 4 sample runs; Figure S18: Evolution dynamics under 5-15 protocols, periodic acute inflammation attacks; and Figure S19: Evolution dynamics under 0-15 protocols, periodic acute inflammation attacks.
Supplementary Material from ERα Binding by Transcription Factors NFIB and YBX1 Enables FGFR2 Signaling to Modulate Estrogen Responsiveness in Breast Cancer
Authors: Campbell Thomas M. , Castro Mauro A. A. , de Oliveira Kelin Gonçalves , Ponder Bruce A. J. , Meyer Kerstin B.
Published: March 2023

Supplementary Material: Figure S1: Nuclear localisation and fluorescent properties of FRET constructs Figure S2: Quantification of FRET experiment Figure S3: Relative mRNA expression of ESR1 target genes Figure S4: Characterisation of MCF-7 clones overexpressing NFIB and YBX1 Figure S5: Separated growth curves shown in Figure 4 Figure S6: Kaplan-Meier survival curves for breast cancer cases stratified by YBX1 expression Figure S7: Response of breast cancer PDX models to tamoxifen treatment Table S1: Primers used in RT-PCR Table S2: Antibodies used in Western blots
Supplementary Table S1 from Targeting CDK6 and BCL2 Exploits the “MYB Addiction” of Ph+ Acute Lymphoblastic Leukemia
Authors: De Dominici Marco , Porazzi Patrizia , Soliera Angela Rachele , Mariani Samanta A. , Addya Sankar , Fortina Paolo , Peterson Luke F. , Spinelli Orietta , Rambaldi Alessandro , Martinelli Giovanni , Ferrari Anna , Iacobucci Ilaria , Calabretta Bruno
Published: March 2023

Primary human Ph+ ALL samples information.
Supplementary Figure S1-10 from Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle–Related Transcription and Attenuated Androgen Response
Authors: Horning Aaron M. , Wang Yao , Lin Che-Kuang , Louie Anna D. , Jadhav Rohit R. , Hung Chia-Nung , Wang Chiou-Miin , Lin Chun-Lin , Kirma Nameer B. , Liss Michael A. , Kumar Addanki P. , Sun LuZhe , Liu Zhijie , Chao Wei-Ting , Wang Qianben , Jin Victor X. , Chen Chun-Liang , Huang Tim H.-M.
Published: March 2023

Supplementary Figure S1: Time-course expression analysis of LNCaP cells reveals dynamic and heterogeneous responses to androgen stimulation. Supplementary Figure S2: Cell cycle progression of LNCaP cells treated with or without R1881 after cell synchronization by double thymidine block (DTB). Supplementary Figure S3: The summary of aligned and unaligned single-cell RNA-seq reads counts. Supplementary Figure S4: Correlation of single-cell RNA-seq ensemble reads with representative bulk RNA-seq reads. Supplementary Figure S5: Venn diagrams illustrating the comparison of differentially expressed genes found in single- and bulk-cell LNCaP experiments. Supplementary Figure S6: The Mclust algorithm defines likely subgroups using a "model-based" approach. Supplementary Figure S7: Each cell within each subcluster exhibits a similar gene expression profile. Supplementary Figure S8: Gleason score and biochemical recurrence status compared to each subcluster''s gene expression profile. Supplementary Figure S9: Differential expression of 10 genes in LNCaP''s 8.1 subpopulation of cells. Supplementary Figure S10: High single-cell expression of 10 genes in PC3 similar to 12hr-R1881 LNCaP cells.
Figure S2 from Mitotic Phosphorylation of SENP3 Regulates DeSUMOylation of Chromosome-Associated Proteins and Chromosome Stability
Authors: Wei Bo , Huang Chao , Liu Bin , Wang Yang , Xia Nansong , Fan Qiuju , Chen Guo-Qiang , Cheng Jinke
Published: March 2023

Phosphorylation regulates SENP3 de-SUMOylation activity
Figure S1 from Mitotic Phosphorylation of SENP3 Regulates DeSUMOylation of Chromosome-Associated Proteins and Chromosome Stability
Authors: Wei Bo , Huang Chao , Liu Bin , Wang Yang , Xia Nansong , Fan Qiuju , Chen Guo-Qiang , Cheng Jinke
Published: March 2023

SENP3 is phosphorylated at the G2/M phase.
Supplementary figure from ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients
Authors: Bertrand Denis , Drissler Sibyl , Chia Burton K. , Koh Jia Yu , Li Chenhao , Suphavilai Chayaporn , Tan Iain Beehuat , Nagarajan Niranjan
Published: March 2023

Supplementary figures showing additional comparisons and benchmarks for ConsensusDriver.
Figure S1-S3 from Metformin-Induced Reduction of CD39 and CD73 Blocks Myeloid-Derived Suppressor Cell Activity in Patients with Ovarian Cancer
Authors: Li Lifeng , Wang Liping , Li Jieyao , Fan Zhirui , Yang Li , Zhang Zhen , Zhang Chaoqi , Yue Dongli , Qin Guohui , Zhang Tengfei , Li Feng , Chen Xinfeng , Ping Yu , Wang Dan , Gao Qun , He Qianyi , Huang Lan , Li Hong , Huang Jianmin , Zhao Xuan , Xue Wenhua , Sun Zhi , Lu Jingli , Yu Jane J. , Zhao Jie , Zhang Bin , Zhang Yi
Published: March 2023

Supplementary Fig.1.Increased MDSCs levels in peripheral blood and tumor from OC patients.Supplementary Fig.2.Characterization of phenotype and immunosuppressive activity of MDSCs in OC patients.Supplementary Fig.3.Phenotypic analysis of MDSCs following metformin treatment.
Supplementary Table 5 from Energy Balance Modulation Impacts Epigenetic Reprogramming, ERα and ERβ Expression, and Mammary Tumor Development in MMTV-neu Transgenic Mice
Authors: Rossi Emily L. , Dunlap Sarah M. , Bowers Laura W. , Khatib Subreen A. , Doerstling Steven S. , Smith Laura A. , Ford Nikki A. , Holley Darcy , Brown Powel H. , Estecio Marcos R. , Kusewitt Donna F. , deGraffenried Linda A. , Bultman Scott J. , Hursting Stephen D.
Published: March 2023

RNA-seq summary
Table S3 from Circulating Tumor Cells Undergoing EMT Provide a Metric for Diagnosis and Prognosis of Patients with Hepatocellular Carcinoma
Authors: Qi Lu-Nan , Xiang Bang-De , Wu Fei-Xiang , Ye Jia-Zhou , Zhong Jian-Hong , Wang Yan-Yan , Chen Yuan-Yuan , Chen Zu-Shun , Ma Liang , Chen Jie , Gong Wen-Feng , Han Ze-Guang , Lu Yan , Shang Jin-Jie , Li Le-Qun
Published: March 2023

112 HCC Patients' characteristics
Supplementary Figure Legends from Circulating Tumor Cells Undergoing EMT Provide a Metric for Diagnosis and Prognosis of Patients with Hepatocellular Carcinoma
Authors: Qi Lu-Nan , Xiang Bang-De , Wu Fei-Xiang , Ye Jia-Zhou , Zhong Jian-Hong , Wang Yan-Yan , Chen Yuan-Yuan , Chen Zu-Shun , Ma Liang , Chen Jie , Gong Wen-Feng , Han Ze-Guang , Lu Yan , Shang Jin-Jie , Li Le-Qun
Published: March 2023

legends
Supp Figure Legend from Energy Balance Modulation Impacts Epigenetic Reprogramming, ERα and ERβ Expression, and Mammary Tumor Development in MMTV-neu Transgenic Mice
Authors: Rossi Emily L. , Dunlap Sarah M. , Bowers Laura W. , Khatib Subreen A. , Doerstling Steven S. , Smith Laura A. , Ford Nikki A. , Holley Darcy , Brown Powel H. , Estecio Marcos R. , Kusewitt Donna F. , deGraffenried Linda A. , Bultman Scott J. , Hursting Stephen D.
Published: March 2023

Supp Figure Legend from Energy Balance Modulation Impacts Epigenetic Reprogramming, ERα and ERβ Expression, and Mammary Tumor Development in MMTV-neu Transgenic Mice
Supplementary Figures S1-S9 from Keratin 19 Expression in Hepatocellular Carcinoma Is Regulated by Fibroblast-Derived HGF via a MET-ERK1/2-AP1 and SP1 Axis
Authors: Rhee Hyungjin , Kim Hye-Young , Choi Ji-Hye , Woo Hyun Goo , Yoo Jeong Eun , Nahm Ji Hae , Choi Jin-Sub , Park Young Nyun
Published: March 2023

Supplementary Figures S1-S9 S1: The representative case showing CD90 expression. Morphology and character of hepatic stellate cell lines. S2: The expression change of KRT19 following S3I-201, TPA, U0126, and SCH772984. The transfection efficiency of HCC cell lines. S3: The HGF concentrations in conditioned media from hTERT-HSC, LX-2, and primary human hepatic stellate cells. Western blot analysis of hepatocellular carcinoma cell lines, showing expression of phospho-MET, MET, phsopho-ERK1/2, and KRT19. mRNA and protein expression of KRT19 in HepG2 and SNU475 cells, following transient expression of MET. S4: Morphologic changes in HepG2 and SNU423 induced by conditioned media (CM) from inducible HGF knockdown stable cell lines established from hTERT-HSC: shHGF-1 and shHGF-2. mRNA expression levels of KRT19 and morphologic changes in HepG2 and SNU423, following CM treatment combined with hepatocyte growth factor (HGF) neutralizing antibody. S5: The gene knock-down efficiencies of two pooled siRNAs targeting JUN, JUND, FOSL1, or FOSL2. The gene knock-down efficiencies of siRNAs targeting JUN or FOSL1. S6: Expression of HGF in hepatic stellate cell line of hTERT-HSC, and HCC cell lines of HepG2 and SNU423. Distribution of HGF and MET expression in HepG2 cells, at various time points after conditioned media (CM) treatment. S7: S7. Increased KRT19 expression and nuclear translocation of ERK1/2, phospho-ERK1/2, FOSL1, phospho-FOSL1 after the conditioned media treatment in HepG2. Rapid decline in phosphor-MET levels after removal of conditioned media. S8: Schematic representation of regulatory mechanism of KRT19 gene by cancer-associated fibroblast (CAF) derived HGF via MET-ERK1/2- AP1 and SP1 axis. S9: Conservation of AP1 and SP1 binding sites in KRT19 promoter.
supplementary information from Visualization of Breast Cancer Metabolism Using Multimodal Nonlinear Optical Microscopy of Cellular Lipids and Redox State
Authors: Hou Jue , Williams Joshua , Botvinick Elliot L. , Potma Eric O. , Tromberg Bruce J.
Published: March 2023

additional experiment results, table and figures.
Supplementary video 1 from Visualization of Breast Cancer Metabolism Using Multimodal Nonlinear Optical Microscopy of Cellular Lipids and Redox State
Authors: Hou Jue , Williams Joshua , Botvinick Elliot L. , Potma Eric O. , Tromberg Bruce J.
Published: March 2023

The 3D reconstruction of T47D cancer acinus in the control group.
Supplementary Figures 1-4 from Synthetic Lethality of PARP Inhibitors in Combination with MYC Blockade Is Independent of BRCA Status in Triple-Negative Breast Cancer
Authors: Carey Jason. P.W. , Karakas Cansu , Bui Tuyen , Chen Xian , Vijayaraghavan Smruthi , Zhao Yang , Wang Jing , Mikule Keith , Litton Jennifer K. , Hunt Kelly K. , Keyomarsi Khandan
Published: March 2023

Supplementary Figure 1 Comparison of 24h, 72-h and continuous HTSA in PARPi treated cells Supplementary Figure 2 HTSA versus MTT proliferation assays Supplementary Figure 3 PARPi sensitivity and resistance in breast cancer cells Supplementary Figure 4 Cell-cycle changes following PARP inhibitor treated sensitive (MB436, HCC1806) versus resistant (MB231, SUM149) breast cancer cells.
Figure S1 from Osteoblast-Secreted Factors Mediate Dormancy of Metastatic Prostate Cancer in the Bone via Activation of the TGFβRIII–p38MAPK–pS249/T252RB Pathway
Authors: Yu-Lee Li-Yuan , Yu Guoyu , Lee Yu-Chen , Lin Song-Chang , Pan Jing , Pan Tianhong , Yu Kai-Jie , Liu Bin , Creighton Chad J. , Rodriguez-Canales Jaime , Villalobos Pamela A. , Wistuba Ignacio I. , de Nadal Eulalia , Posas Francesc , Gallick Gary E. , Lin Sue-Hwa
Published: March 2023

DiO-labeling of C4-2B4 PCa cells.
Supplementary Methods from The Inhibitory NKR-P1B:Clr-b Recognition Axis Facilitates Detection of Oncogenic Transformation and Cancer Immunosurveillance
Authors: Tanaka Miho , Fine Jason H. , Kirkham Christina L. , Aguilar Oscar A. , Belcheva Antoaneta , Martin Alberto , Ketela Troy , Moffat Jason , Allan David S.J. , Carlyle James R.
Published: March 2023

Supplementary Methods describing intronic qRT-PCR, dual luciferase reporter assay, and CRISPR/Cas9 generation of ERK2-deficient cells.
Table S1 from A Pyrrole-Imidazole Polyamide Is Active against Enzalutamide-Resistant Prostate Cancer
Authors: Kurmis Alexis A. , Yang Fei , Welch Timothy R. , Nickols Nicholas G. , Dervan Peter B.
Published: March 2023

GSEA of gene expression signatures in LREX' and LNCaP cells using Hallmark pathways
Table S3 from NK-cell Editing Mediates Epithelial-to-Mesenchymal Transition via Phenotypic and Proteomic Changes in Melanoma Cell Lines
Authors: Huergo-Zapico Leticía , Parodi Monica , Cantoni Claudia , Lavarello Chiara , Fernández-Martínez Juan L. , Petretto Andrea , DeAndrés-Galiana Enrique J. , Balsamo Mirna , López-Soto Alejandro , Pietra Gabriella , Bugatti Mattia , Munari Enrico , Marconi Marcella , Mingari Maria Cristina , Vermi William , Moretta Lorenzo , González Segundo , Vitale Massimo
Published: March 2023

Supplementary Table S3
Figure S1 from A Pyrrole-Imidazole Polyamide Is Active against Enzalutamide-Resistant Prostate Cancer
Authors: Kurmis Alexis A. , Yang Fei , Welch Timothy R. , Nickols Nicholas G. , Dervan Peter B.
Published: March 2023

Nuclear uptake of ARE-1-FITC
Supplementary figures from PDSS2 Deficiency Induces Hepatocarcinogenesis by Decreasing Mitochondrial Respiration and Reprogramming Glucose Metabolism
Authors: Li Yan , Lin Shuhai , Li Lei , Tang Zhi , Hu Yumin , Ban Xiaojiao , Zeng Tingting , Zhou Ying , Zhu Yinghui , Gao Song , Deng Wen , Zhang Xiaoshi , Xie Dan , Yuan Yunfei , Huang Peng , Li Jinjun , Cai Zongwei , Guan Xin-Yuan
Published: March 2023

Supplementary figure 1. PDSS2 and CoQ10 in HCC tissues and cell lines. Supplementary figure 2. PDSS2 reintroduction enhanced mitochondrial respiration. Supplementary figure 3. PDSS2 reintroduction inhibited tumor cell growth. Supplementary figure 4. PDSS2 arrested cell cycle and inhibited xenograft growth in vivo. Supplementary figure 5. PDSS2 deficiency was established in MIHA cells. Supplementary figure 6. PDSS2 deficiency affected cell growth. Supplementary figure 7. PDSS2 variants and sequence analysis of PDSS2 and PDSS2-Del2.
Supplementary Figures S1 through S7 from CD39 Expression Defines Cell Exhaustion in Tumor-Infiltrating CD8+ T Cells
Authors: Canale Fernando P. , Ramello María C. , Núñez Nicolás , Furlan Cintia L. Araujo , Bossio Sabrina N. , Serrán Melisa Gorosito , Boari Jimena Tosello , del Castillo Andrés , Ledesma Marta , Sedlik Christine , Piaggio Eliane , Gruppi Adriana , Rodríguez Eva V. Acosta , Montes Carolina L.
Published: March 2023

(1) Figure S1. Expression of CD39 and CD73 on CD8+T cells from different cancer models and tumor-free mice. (2) Figure S2. Expression of CD39 and CD73 on tumor-infiltrating CD45+ cells. Frequency of CD39high CD8+ TILs in tumors with different immunogenicity. (3) Figure S3. Functionality of CD39high CD8+ TILs in tumors with different immunogenicity. Expression of iRs and TFs on CD8+ T cells. (4) Figure S4. Phenotype of exhausted CD8+ T cells after re-stimulation. Data related to co-culture experiments. (5) Figure S5. Identification of tumor-infiltrating CD39+CD4+ Tconv cells. Characterization of CD39+CD8+ T cells from breast cancer patients. (6) Figure S6. Phenotypic and functional study of CD39+CD8+ T cells from melanoma patients. (7) Figure S7. Functional study of CD39+CD8+ T cells induced in vitro. Localization of CD39+CD45+ cells in hypoxic foci.
Supplementary figure S4 from CD4+ T-cell–Mediated Rejection of MHC Class II–Positive Tumor Cells Is Dependent on Antigen Secretion and Indirect Presentation on Host APCs
Authors: Haabeth Ole Audun W. , Fauskanger Marte , Manzke Melanie , Lundin Katrin U. , Corthay Alexandre , Bogen Bjarne , Tveita Anders A.
Published: March 2023

Flow cytometry characterization of tumor-infiltrating CD11b+ cells, and mean MHC II expression levels on CD11b+ cells isolated from tumors following challenge with the A20 lymphoma variants F9 or F59.
Fig. S3 from The FACT inhibitor CBL0137 Synergizes with Cisplatin in Small-Cell Lung Cancer by Increasing NOTCH1 Expression and Targeting Tumor-Initiating Cells
Authors: De Sarmishtha , Lindner Daniel J. , Coleman Claire J. , Wildey Gary , Dowlati Afshin , Stark George R.
Published: March 2023

Supplementary Fig S3. CBL0137 inhibits FACT function in SCLC TICs. A, SSRP1 levels were determined by Western analysis in CD133high or CD133low cells from H82 or H526. Î²-actin was used as a loading control. B, H82 CD133high cells were treated with 1 ÂµM CBL0137 for different times. Soluble and chromatin bound SSRP1 levels were detected by immunoblotting.
Fig. S2 from The FACT inhibitor CBL0137 Synergizes with Cisplatin in Small-Cell Lung Cancer by Increasing NOTCH1 Expression and Targeting Tumor-Initiating Cells
Authors: De Sarmishtha , Lindner Daniel J. , Coleman Claire J. , Wildey Gary , Dowlati Afshin , Stark George R.
Published: March 2023

Supplementary Fig S2. SCLC TICs are enriched for stem cell markers. A, B, C, Expression levels of SOX2, NANOG and OCT4 mRNAs in CD133high and CD133low H82 (A) and H526 (B) cells or CD44high and CD44low H446 (C) cells. D, Levels of SOX2 and OCT4, determined by Western analysis in CD133high and CD133low H82 and H526 cells or CD44high and CD44low H446 cells.
Supplemental Tables from Multikinase Inhibitor CT-707 Targets Liver Cancer by Interrupting the Hypoxia-Activated IGF-1R–YAP Axis
Authors: Zhu Hong , Wang Dan-Dan , Yuan Tao , Yan Fang-Jie , Zeng Chen-Ming , Dai Xiao-Yang , Chen Zi-bo , Chen Ying , Zhou Tianyi , Fan Guang-Han , Ying Meidan , Cao Ji , Luo Peihua , Liu Xi-Jie , Hu Yuandong , Peng Yong , He Qiaojun , Yang Bo
Published: March 2023

Supplemental Table 1. The primer sequences for qRT-PCR assay Supplemental Table 2. The targeting sequences for siRNA Supplemental Table 3. The list of compounds for YAP-TEADs luciferase screening
Supplementary Data from Expression of Long Noncoding RNA YIYA Promotes Glycolysis in Breast Cancer
Authors: Xing Zhen , Zhang Yanyan , Liang Ke , Yan Liang , Xiang Yu , Li Chunlai , Hu Qingsong , Jin Feng , Putluri Vasanta , Putluri Nagireddy , Coarfa Cristian , Sreekumar Arun , Park Peter K. , Nguyen Tina K. , Wang Shouyu , Zhou Jianwei , Zhou Yan , Marks Jeffrey R. , Hawke David H. , Hung Mien-Chie , Yang Liuqing , Han Leng , Ying Haoqiang , Lin Chunru
Published: March 2023

Supplementary Figure and Supplementary Figure legend
Figure S3B from eIF5A-PEAK1 Signaling Regulates YAP1/TAZ Protein Expression and Pancreatic Cancer Cell Growth
Authors: Strnadel Jan , Choi Sunkyu , Fujimura Ken , Wang Huawei , Zhang Wei , Wyse Meghan , Wright Tracy , Gross Emilie , Peinado Carlos , Park Hyun Woo , Bui Jack , Kelber Jonathan , Bouvet Michael , Guan Kun-Liang , Klemke Richard L.
Published: March 2023

Informatics analyses of cytoskeleton proteins altered in PEAK1-depleted PDAC cells
Suppl Table S2 from PPARδ Elicits Ligand-Independent Repression of Trefoil Factor Family to Limit Prostate Cancer Growth
Authors: Martín-Martín Natalia , Zabala-Letona Amaia , Fernández-Ruiz Sonia , Arreal Leire , Camacho Laura , Castillo-Martin Mireia , Cortazar Ana R. , Torrano Verónica , Astobiza Ianire , Zúñiga-García Patricia , Ugalde-Olano Aitziber , Loizaga-Iriarte Ana , Unda Miguel , Valcárcel-Jiménez Lorea , Arruabarrena-Aristorena Amaia , Piva Marco , Sánchez-Mosquera Pilar , Aransay Ana M. , Gomez-Muñoz Antonio , Barrio Rosa , Sutherland James D. , Carracedo Arkaitz
Published: March 2023

Suppl Table S2
Supplementary Tables 1-5, 7, 9-12 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Authors: Löffler Markus W. , Kowalewski Daniel J. , Backert Linus , Bernhardt Jörg , Adam Patrick , Schuster Heiko , Dengler Florian , Backes Daniel , Kopp Hans-Georg , Beckert Stefan , Wagner Silvia , Königsrainer Ingmar , Kohlbacher Oliver , Kanz Lothar , Königsrainer Alfred , Rammensee Hans-Georg , Stevanović Stefan , Haen Sebastian P.
Published: March 2023

Supplementary Tables 1-5, 7, 9-12 containing: Suppl. Table 1: Sample characteristics; Suppl. Table 2: Patient characteristics; Suppl. Table 3: Control peptides Suppl. Table 4: Peptide-specific properties Suppl. Table 5: Over-represented Peptides HLA class I; Suppl. Table 7: Over-represented Peptides HLA class II; Suppl. Table 9: STRING results Suppl. Table 9: Protein-protein interactions (STRING) Suppl. Table 10: Over-represented pathways (STRING) Suppl. Table 11: Vaccine peptide selection Suppl. Table 12: Candidate vaccine peptides
Supplementary Table 6 from Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation
Authors: Löffler Markus W. , Kowalewski Daniel J. , Backert Linus , Bernhardt Jörg , Adam Patrick , Schuster Heiko , Dengler Florian , Backes Daniel , Kopp Hans-Georg , Beckert Stefan , Wagner Silvia , Königsrainer Ingmar , Kohlbacher Oliver , Kanz Lothar , Königsrainer Alfred , Rammensee Hans-Georg , Stevanović Stefan , Haen Sebastian P.
Published: March 2023

Statistics over-represented peptides HLA class I
Supplementary Material from Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs
Authors: Fang Fang , Cardenas Horacio , Huang Hao , Jiang Guanglong , Perkins Susan M. , Zhang Chi , Keer Harold N. , Liu Yunlong , Nephew Kenneth P. , Matei Daniela
Published: March 2023

Supplementary Material and Methods
Supplementary Table 1 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes
Authors: Abbas Hussein A. , Bui Ngoc Hoang Bao , Rajapakshe Kimal , Wong Justin , Gunaratne Preethi , Tsai Kenneth Y. , Coarfa Cristian , Flores Elsa R.
Published: March 2023

Normalized enriched scores from GSEA results across developmental and progression cancer signatures in light of TAp63 and Î"Np63 transcriptome profiles.
Supplementary File 2 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes
Authors: Abbas Hussein A. , Bui Ngoc Hoang Bao , Rajapakshe Kimal , Wong Justin , Gunaratne Preethi , Tsai Kenneth Y. , Coarfa Cristian , Flores Elsa R.
Published: March 2023

Tumor development and progression signatures of TCGA cancers.
Figure S3 from Acetylation within the N- and C-Terminal Domains of Src Regulates Distinct Roles of STAT3-Mediated Tumorigenesis
Authors: Huang Chao , Zhang Zhe , Chen Lihan , Lee Hank W. , Ayrapetov Marina K. , Zhao Ting C. , Hao Yimei , Gao Jinsong , Yang Chunzhang , Mehta Gautam U. , Zhuang Zhengping , Zhang Xiaoren , Hu Guohong , Chin Y. Eugene
Published: March 2023

Src global post-translational modifications are triggered by CBP
Supplementary Materials and Methods from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

Supplementary Materials and Methods section provides additional data on the protocols used in this manuscript including those pertaining to chemical and reagents, denervation, flow cytometry and sorting, immunohistochemistry and immunofluorescence, histopathologic analysis, genotyping and physiologic testing of denervation.
Supplemental Figure Legends from PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk
Authors: Sinha Smrita , Fu Ya-Yuan , Grimont Adrien , Ketcham Maren , Lafaro Kelly , Saglimbeni Joseph A. , Askan Gokce , Bailey Jennifer M. , Melchor Jerry P. , Zhong Yi , Joo Min Geol , Grbovic-Huezo Olivera , Yang In-Hong , Basturk Olca , Baker Lindsey , Park Young , Kurtz Robert C. , Tuveson David , Leach Steven D. , Pasricha Pankaj J.
Published: March 2023

Contains the figure legends for supplemental Figures S1-S8, Table S1 and Videos V1 and V2.
Supplemental Figures from Coactivation of Estrogen Receptor and IKKβ Induces a Dormant Metastatic Phenotype in ER-Positive Breast Cancer
Authors: El-Shennawy Lamiaa , Dubrovskyi Oleksii , Kastrati Irida , Danes Jeanne M. , Zhang Yiqun , Whiteley Herbert E. , Creighton Chad J. , Frasor Jonna
Published: March 2023

This file contains supplemental data related to T47D-CA-IKKβ and control cell lines, estrogen receptor expression, phosphorylation, and activity, cell morphology and EMT. Additional analysis of metastases and stem cell phenotypes are included.
Supplementary Data and Figures from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Supplementary methods contains additional information describing methods used and description of all supplemental data included. Supplemental Figures Supplemental Figure 1. Real human data clustered Supplemental Figure 2. Random human data clustered Supplemental Figure 3. Permuted human data clustered Supplemental Figure 4. Real mouse data clustered Supplemental Figure 5. Random mouse data clustered Supplemental Figure 6. Permuted mouse data clustered Supplemental Figure 7. Real dog data clustered Supplemental Figure 8. Random dog data clustered Supplemental Figure 9. Permuted dog data clustered Supplemental Figure 10. Examples of 4 immunohistochemistry groups Supplemental Figure 11. KM significance in real, random, and permuted human and dog datasets. Supplemental Figure 12. KM human cluster-1 Supplemental Figure 13. KM human cluster-4 Supplemental Figure 14. KM human cluster-8 Supplemental Figure 15. KM dog cluster-3 Supplemental Figure 16. GSE212257 Array cluster- 3 association with Outcome Supplemental Figure 17. GSE212257 Array cluster-5 association with Outcome Supplemental Figure 18. GSE212257 Array cluster-3 association with Metastasis Supplemental Figure 19. GSE212257 Array cluster-5 association with Metastasis Supplemental Figure 20. GSE212257 Array cluster-7 association with Metastasis Supplemental Figure 21. Cell Cycle GCESS plotted against Immune-1 and Immune-2 GCESS Supplemental Figure 22. Model depicting how immune cell components may be preventing the occurrence of metastasis in OS patients. Supplemental Figure 23. Flowchart of OS samples utilized in this work
Supplemental Figure Legends from Coactivation of Estrogen Receptor and IKKβ Induces a Dormant Metastatic Phenotype in ER-Positive Breast Cancer
Authors: El-Shennawy Lamiaa , Dubrovskyi Oleksii , Kastrati Irida , Danes Jeanne M. , Zhang Yiqun , Whiteley Herbert E. , Creighton Chad J. , Frasor Jonna
Published: March 2023

This document contains materials and methods for Immunofluorescence for ER and IKKβ, Western Blot for S305 and total ER, and Histology and Immunohistochemistry. This file also contains figure legends for supplemental figures 1 - 9.
Supplemental Table 1 from Comparative Transcriptome Analysis Quantifies Immune Cell Transcript Levels, Metastatic Progression, and Survival in Osteosarcoma
Authors: Scott Milcah C. , Temiz Nuri A. , Sarver Anne E. , LaRue Rebecca S. , Rathe Susan K. , Varshney Jyotika , Wolf Natalie K. , Moriarity Branden S. , O'Brien Timothy D. , Spector Logan G. , Largaespada David A. , Modiano Jaime F. , Subramanian Subbaya , Sarver Aaron L.
Published: March 2023

Sample clinical, outcome and sequencing metadata for human mouse and dog samples.
Supplemental Table S1 from YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells
Authors: Ooki Akira , Del Carmen Rodriguez Pena Maria , Marchionni Luigi , Dinalankara Wikum , Begum Asma , Hahn Noah M. , VandenBussche Christopher J. , Rasheed Zeshaan A. , Mao Shifeng , Netto George J. , Sidransky David , Hoque Mohammad O.
Published: March 2023

Supplemental Table S1. Relative expression of stem cell-related genes using RT2 profile PCR array.
Supplementary Figure S5 from Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors
Authors: Steinberg Shannon M. , Shabaneh Tamer B. , Zhang Peisheng , Martyanov Viktor , Li Zhenghui , Malik Brian T. , Wood Tamara A. , Boni Andrea , Molodtsov Aleksey , Angeles Christina V. , Curiel Tyler J. , Whitfield Michael L. , Turk Mary Jo
Published: March 2023

Depletion of intratumoral MDSC.