bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1 from The Epithelial–Stromal Microenvironment in Early Colonic Neoplasia
Authors: Ideta Takayasu , Li Boyang , Flynn Christopher , Igarashi Yuichi , Lowman Geoffrey , Looney Tim , Devers Thomas J. , Birk John , Forouhar Faripour , Giardina Charles , Rosenberg Daniel W.
Published: April 2023

Supplemental Figure S1. PCA analysis shows concordance between replicates and more variation within ACF samples. (A) PCA plot of all samples, colored individually. Each sample has two biological replicates marked by a triangle and a circle. (B) PCA plots of all epithelial or stromal samples, colored by ACF (red) or normal (blue). (C) Variation evaluated by distance to centroid within each condition, bar graph in right panel
Figure S4 from p53 Is Not Required for High CIN to Induce Tumor Suppression
Authors: Funk Laura C. , Wan Jun , Ryan Sean D. , Kaur Charanjeet , Sullivan Ruth , Roopra Avtar , Weaver Beth A.
Published: April 2023

Figure S4 shows detection of LOH in tumors from p53+/- animals.
Figure S1 from p53 Is Not Required for High CIN to Induce Tumor Suppression
Authors: Funk Laura C. , Wan Jun , Ryan Sean D. , Kaur Charanjeet , Sullivan Ruth , Roopra Avtar , Weaver Beth A.
Published: April 2023

Figure S1 shows that there are equivalent levels of CIN in p53-/- and CENP-E+/-;p53-/- lymphomas
Combined Supplementary Data from p53 Is Not Required for High CIN to Induce Tumor Suppression
Authors: Funk Laura C. , Wan Jun , Ryan Sean D. , Kaur Charanjeet , Sullivan Ruth , Roopra Avtar , Weaver Beth A.
Published: April 2023

This file contains 5 supplemental figures and 1 supplemental table
Supplementary Figure 3 from Comprehensive Molecular Profiling of Desmoplastic Small Round Cell Tumor
Authors: Slotkin Emily K. , Bowman Anita S. , Levine Max F. , Dela Cruz Filemon , Coutinho Diego F. , Sanchez Glorymar I. , Rosales Nestor , Modak Shakeel , Tap William D. , Gounder Mrinal M. , Thornton Katherine A. , Bouvier Nancy , You Daoqi , Gundem Gunes , Gerstle Justin T. , Heaton Todd E. , LaQuaglia Michael P. , Wexler Leonard H. , Meyers Paul A. , Kung Andrew L. , Papaemmanuil Elli , Zehir Ahmet , Ladanyi Marc , Shukla Neerav
Published: April 2023

Supplementary Figure 3 provides a breakdown of the structural variant types found via whole genome sequencing in DSRCT samples
Supplementary Tables 1-8 from MYC Activity Inference Captures Diverse Mechanisms of Aberrant MYC Pathway Activation in Human Cancers
Authors: Schaafsma Evelien , Zhao Yanding , Zhang Lanjing , Li Yong , Cheng Chao
Published: April 2023

Table S1. TCGA samples included in study. Table S2. Gene weights of MYC signatures. Table S3. Pre-ranked Gene Set Enrichment Analysis results of cancer type-specific MYC activity signatures. Table S4. MYC AUC characteristics. Table S5. Recurrent MYC mutations. Table S6. Multivariate Cox regression model assessing the relationship between patient prognosis and MYC activity scores, immune infiltration and expression of E2F family members in SKCM. Table S7. Prognostic results of individual datasets from GEO and PRECOG. Table S8. GEO and PRECOG datasets.
Supplemental Figure 2 from In Situ Analysis of N-Linked Glycans as Potential Biomarkers of Clinical Course in Human Prostate Cancer
Authors: Conroy Lindsey R. , Stanback Alexandra E. , Young Lyndsay E.A. , Clarke Harrison A. , Austin Grant L. , Liu Jinze , Allison Derek B. , Sun Ramon C.
Published: April 2023

Supplemental Figure 2. Prostate tumor tissue exhibits decreased abundance of selected N-glycans proportional to tumor grade.
Supplemental Figure 1 from In Situ Analysis of N-Linked Glycans as Potential Biomarkers of Clinical Course in Human Prostate Cancer
Authors: Conroy Lindsey R. , Stanback Alexandra E. , Young Lyndsay E.A. , Clarke Harrison A. , Austin Grant L. , Liu Jinze , Allison Derek B. , Sun Ramon C.
Published: April 2023

Supplemental Figure 1. Hematoxylin & Eosin (H&E) staining of the three prostate TMAs used for this study.
Supplementary Data S8 from The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics
Authors: Smith Kaitlyn H. , Budhraja Amit , Lynch John , Roberts Kathryn , Panetta John C. , Connelly Jon P. , Turnis Meghan E. , Pruett-Miller Shondra M. , Schuetz John D. , Mullighan Charles G. , Opferman Joseph T.
Published: April 2023

Densitometry for immunoblots
Supplementary File 1 from EMT-Derived Alterations in Glutamine Metabolism Sensitize Mesenchymal Breast Cells to mTOR Inhibition
Authors: Karvelsson Sigurdur Trausti , Sigurdsson Arnar , Seip Kotryna , Grinde Maria Tunset , Wang Qiong , Johannsson Freyr , Mælandsmo Gunhild Mari , Moestue Siver Andreas , Rolfsson Ottar , Halldorsson Skarphedinn
Published: April 2023

An R-script for the weighted correlation network analysis. This file is a .R file which can be opened in RStudio.
Supplementary Data S7 from The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics
Authors: Smith Kaitlyn H. , Budhraja Amit , Lynch John , Roberts Kathryn , Panetta John C. , Connelly Jon P. , Turnis Meghan E. , Pruett-Miller Shondra M. , Schuetz John D. , Mullighan Charles G. , Opferman Joseph T.
Published: April 2023

Synergy analysis of HRI activation ex vivo
Supplementary Figure 4 from EMT-Derived Alterations in Glutamine Metabolism Sensitize Mesenchymal Breast Cells to mTOR Inhibition
Authors: Karvelsson Sigurdur Trausti , Sigurdsson Arnar , Seip Kotryna , Grinde Maria Tunset , Wang Qiong , Johannsson Freyr , Mælandsmo Gunhild Mari , Moestue Siver Andreas , Rolfsson Ottar , Halldorsson Skarphedinn
Published: April 2023

UPLC-MS label enrichment in various metabolites after culturing of D492 and D492M with A) 1-13C-glutamine and B) 5-13C-glutamine for 6 hours. Results are shown as mean + standard deviation (n = 3).
Supplementary Data S1 from The Heme-Regulated Inhibitor Pathway Modulates Susceptibility of Poor Prognosis B-Lineage Acute Leukemia to BH3-Mimetics
Authors: Smith Kaitlyn H. , Budhraja Amit , Lynch John , Roberts Kathryn , Panetta John C. , Connelly Jon P. , Turnis Meghan E. , Pruett-Miller Shondra M. , Schuetz John D. , Mullighan Charles G. , Opferman Joseph T.
Published: April 2023

Stress pathways in cellular response to DHA
Video S3 from Hypoxic Induction of Exosome Uptake through Proteoglycan-Dependent Endocytosis Fuels the Lipid Droplet Phenotype in Glioma
Authors: Cerezo-Magaña Myriam , Christianson Helena C. , van Kuppevelt Toin H. , Forsberg-Nilsson Karin , Belting Mattias
Published: April 2023

High-resolution Airyscan live-cell confocal microscopy visualization of LD dynamics during reoxygenation. LD+ hypoxic glioma cells were imaged during 3 h of reoxygenation. The sequence was captured at 20 min interval during 3 h. Scale bar, 20 µm.
Video S2 from Hypoxic Induction of Exosome Uptake through Proteoglycan-Dependent Endocytosis Fuels the Lipid Droplet Phenotype in Glioma
Authors: Cerezo-Magaña Myriam , Christianson Helena C. , van Kuppevelt Toin H. , Forsberg-Nilsson Karin , Belting Mattias
Published: April 2023

High-resolution Airyscan live-cell confocal microscopy visualization of EV and CtxB co-internalization. The sequence was captured at 1.5 min interval for 45 min. Scale bar, 20 µm.
Supplementary Figure S3 from EWS-FLI1 and Menin Converge to Regulate ATF4 Activity in Ewing Sarcoma
Authors: Jiménez Jennifer A. , Apfelbaum April A. , Hawkins Allegra G. , Svoboda Laurie K. , Kumar Abhijay , Ruiz Ramon Ocadiz , Garcia Alessandra X. , Haarer Elena , Nwosu Zeribe C. , Bradin Joshua , Purohit Trupta , Chen Dong , Cierpicki Tomasz , Grembecka Jolanta , Lyssiotis Costas A. , Lawlor Elizabeth R.
Published: April 2023

Supplementary Figure S3. Timecourse for the effect of MI-503 on ATF4 in Ewing sarcoma cell lines.
Supplementary Figure S2 from EWS-FLI1 and Menin Converge to Regulate ATF4 Activity in Ewing Sarcoma
Authors: Jiménez Jennifer A. , Apfelbaum April A. , Hawkins Allegra G. , Svoboda Laurie K. , Kumar Abhijay , Ruiz Ramon Ocadiz , Garcia Alessandra X. , Haarer Elena , Nwosu Zeribe C. , Bradin Joshua , Purohit Trupta , Chen Dong , Cierpicki Tomasz , Grembecka Jolanta , Lyssiotis Costas A. , Lawlor Elizabeth R.
Published: April 2023

Supplementary Figure S2. Effect of shFLI1 knockdown in CHLA10 Ewing sarcoma cells and Publicly Available ChIP-seq of EWS-FLI1 at the ATF4 and SSP Gene Promoters.
Supplementary Figures 1-7 from AXL Is a Key Factor for Cell Plasticity and Promotes Metastasis in Pancreatic Cancer
Authors: Du Wenting , Phinney Natalie Z. , Huang Huocong , Wang Zhaoning , Westcott Jill , Toombs Jason E. , Zhang Yuqing , Beg Muhammad S. , Wilkie Thomas M. , Lorens James B. , Brekken Rolf A.
Published: April 2023

S1. Gene Ontology (GO) analysis of gene clusters from AXL-positive cancer cell populations based on scRNA-Seq data from Hosein et al (35). S2. Expression of Axl in tumors from WT and AXLLacZ/LacZ (AAKIC) KIC mice. S3. Tumor tissues from KIC and AxlLacZ/LacZ KIC mice were evaluated for indicated targets. S4. Flow cytometry of tumor-associated myeloid and lymphoid cells from KIC (n=11) and AxlLacZ/LacZ KIC (n=9). CD11b+ myeloid cells, CD4/CD3, and CD8/CD3 ratio were analyzed. 5. A) Cell proliferation was investigated in three different WT and AXL KO KPfC cells using MTS assay with eight technical replicates. B) Cell migration was investigated in three different WT and AXL KO KPfC cells by a "scratch" assay with three technical replicates. Monolayers of the indicated cells were wounded with a pipet tip. The cells were incubated in 1% serum media. Wound closure was monitored at 12, 24, and 36 hours and is reported as % wound closure. ***P < 0.001; ****P < 0.0001; by t-test. C) Colony formation (colonies/hpf) for three different WT and AXL KO KPfC cells with three technical replicates is shown by box plot (min to max). **P < 0.01; by t-test. S6. Expression of E-cadherin in WT and AXL KO KPfC cells. S7. A) WT and AxlLacZ/LacZ C57BL/6 mice orthotopically injected with 500,000 cells/mouse WT and AXL KO Pan02 cells were enrolled in a survival study. Groups were as follows: WT Pan02 cells in WT C57BL/6 mice (n=9); WT KPfC cells in AxlLacZ/LacZ C57BL/6 mice (n=7); AXL KO KPfC cells in WT C57BL/6 mice (n=6). B) 500,000 cells/mouse WT and AXL KO Pan02 cells were splenically injected into WT and AxlLacZ/LacZ C57BL/6 mice. Liver metastases were investigated 7 weeks after injection. Groups were as follows: WT Pan02 cells in WT C57BL/6 mice (n=8); WT KPfC cells in AxlLacZ/LacZ C57BL/6 mice (n=7); AXL KO KPfC cells in WT C57BL/6 mice (n=10); AXL KO KPfC cells in AxlLacZ/LacZ C57BL/6 mice (n=9). H&E and Alcian Blue stain were conducted in the liver tissues to confirm metastasis. Magnification, 10X. C) 1,000,000 cells/mouse WT and AXL KO Panc1 cells were orthotopically injected into NON SCID mice. Tumor weight were investigated 11 weeks after injection.
Figure S1 from TSC2 Interacts with HDLBP/Vigilin and Regulates Stress Granule Formation
Authors: Kosmas Kosmas , Filippakis Harilaos , Khabibullin Damir , Turkiewicz Michal , Lam Hilaire C. , Yu Jane , Kedersha Nancy L. , Anderson Paul J. , Henske Elizabeth P.
Published: April 2023

G3BP, vigilin and TSC2 colocalize in stress granules.
Figure S7 from Heparan Sulfate Synthesized by Ext1 Regulates Receptor Tyrosine Kinase Signaling and Promotes Resistance to EGFR Inhibitors in GBM
Authors: Ohkawa Yuki , Wade Anna , Lindberg Olle R. , Chen Katharine Y. , Tran Vy M. , Brown Spencer J. , Kumar Anupam , Kalita Mausam , James C. David , Phillips Joanna J.
Published: April 2023

Glypican-1 and Syndecan-1 are identified as heparan sulfate proteoglycans expressed on GBM43.
Figure S5 from Heparan Sulfate Synthesized by Ext1 Regulates Receptor Tyrosine Kinase Signaling and Promotes Resistance to EGFR Inhibitors in GBM
Authors: Ohkawa Yuki , Wade Anna , Lindberg Olle R. , Chen Katharine Y. , Tran Vy M. , Brown Spencer J. , Kumar Anupam , Kalita Mausam , James C. David , Phillips Joanna J.
Published: April 2023

Structures of polymeric heparin mimetics.
Figure S3 from Heparan Sulfate Synthesized by Ext1 Regulates Receptor Tyrosine Kinase Signaling and Promotes Resistance to EGFR Inhibitors in GBM
Authors: Ohkawa Yuki , Wade Anna , Lindberg Olle R. , Chen Katharine Y. , Tran Vy M. , Brown Spencer J. , Kumar Anupam , Kalita Mausam , James C. David , Phillips Joanna J.
Published: April 2023

HS expression on cells isolated from orthotopic tumors.
Supplementary Table S2 from A Novel Therapeutic Strategy Targeting the Mesenchymal Phenotype of Malignant Pleural Mesothelioma by Suppressing LSD1
Authors: Wirawan Aditya , Tajima Ken , Takahashi Fumiyuki , Mitsuishi Yoichiro , Winardi Wira , Hidayat Moulid , Hayakawa Daisuke , Matsumoto Naohisa , Izumi Kenta , Asao Tetsuhiko , Ko Ryo , Shimada Naoko , Takamochi Kazuya , Suzuki Kenji , Abe Masaaki , Hino Okio , Sekido Yoshitaka , Takahashi Kazuhisa
Published: April 2023

Supplementary Table S2 shows the chromatin accessibility with statistically significant changes in genome-wide ATAC-seq.
Supplementary Table S1 from Suppression of MET Signaling Mediated by Pitavastatin and Capmatinib Inhibits Oral and Esophageal Cancer Cell Growth
Authors: Xu Bo , Muramatsu Tomoki , Inazawa Johji
Published: April 2023

Table S1. Results of cell growth screening using an FDA-approved drug library in HOC313-LM cells.
Supplementary Figure S6 from A Novel Therapeutic Strategy Targeting the Mesenchymal Phenotype of Malignant Pleural Mesothelioma by Suppressing LSD1
Authors: Wirawan Aditya , Tajima Ken , Takahashi Fumiyuki , Mitsuishi Yoichiro , Winardi Wira , Hidayat Moulid , Hayakawa Daisuke , Matsumoto Naohisa , Izumi Kenta , Asao Tetsuhiko , Ko Ryo , Shimada Naoko , Takamochi Kazuya , Suzuki Kenji , Abe Masaaki , Hino Okio , Sekido Yoshitaka , Takahashi Kazuhisa
Published: April 2023

Supplementary Figure S6 shows that restoring MFGE8 abolishes apoptosis by re-activating the FAK-AKT pathway.
Table S6 from Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes
Authors: Hemming Matthew L. , Fan Changyu , Raut Chandrajit P. , Demetri George D. , Armstrong Scott A. , Sicinska Ewa , George Suzanne
Published: April 2023

Table S6. LMS and cell line transcript expression levels.
Table S5 from Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes
Authors: Hemming Matthew L. , Fan Changyu , Raut Chandrajit P. , Demetri George D. , Armstrong Scott A. , Sicinska Ewa , George Suzanne
Published: April 2023

Table S5. LMS subtype-specific transcript expression levels.
Table S4 from Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes
Authors: Hemming Matthew L. , Fan Changyu , Raut Chandrajit P. , Demetri George D. , Armstrong Scott A. , Sicinska Ewa , George Suzanne
Published: April 2023

Table S4. LMS RNA-seq samples.
Table S2 from Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes
Authors: Hemming Matthew L. , Fan Changyu , Raut Chandrajit P. , Demetri George D. , Armstrong Scott A. , Sicinska Ewa , George Suzanne
Published: April 2023

Table S2. cBioPortal cancer subtypes.
Supplementary Methods from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

Supplementary Methods
Figure S7 from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

Extended analysis of ShcD mRNA correlation and survival in the CGGA_325 dataset.
Figure S6 from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

Extended analysis of ShcD mRNA correlation and survival in the TCGA and CGGA_693 datasets.
Figure S3 from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

Stable T98G cells expressing ShcD-WT show increased invasion but fail to exhibit ShcD-Tie2 synergy.
Figure S2 from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

ShcD and Tie2 are expressed at low levels in glioma cell lines.
Figure S1 from Adaptor Protein ShcD/SHC4 Interacts with Tie2 Receptor to Synergistically Promote Glioma Cell Invasion
Authors: Tilak Manali , Alural Begüm , Wismer Sarah E. , Brasher Megan I. , New Laura A. , Sheridan Steven D. , Perlis Roy H. , Coppolino Marc G. , Lalonde Jasmin , Jones Nina
Published: April 2023

Extended analysis of ShcD mRNA expression in TCGA and CGGA_693 and CGGA_325 datasets.
Figure S1 from Mastermind Like Transcriptional Coactivator 3 (MAML3) Drives Neuroendocrine Tumor Progression
Authors: Alzofon Nathaniel , Koc Katrina , Panwell Kristin , Pozdeyev Nikita , Marshall Carrie B. , Albuja-Cruz Maria , Raeburn Christopher D. , Nathanson Katherine L. , Cohen Debbie L. , Wierman Margaret E. , Kiseljak-Vassiliades Katja , Fishbein Lauren
Published: April 2023

MAML3 in vitro cellular localization for QGP-1 and BON-1. Immunofluorescence of cells transfected with either FL or dEx1 MAML3 show nuclear localization of both constructs. FL MAML3 shows more punctate staining and dEx1 MAML3 shows more diffuse staining. No endogenous MAML3 could be found in transfected controls. (100x/1.30 oil Nikon Plan Fluor Objective, AlexaFluor546, Scale bar represents 10 Âµm)
FigureS6 from Adipokine Apelin/APJ Pathway Promotes Peritoneal Dissemination of Ovarian Cancer Cells by Regulating Lipid Metabolism
Authors: Dogra Samrita , Neelakantan Deepika , Patel Maulin M. , Griesel Beth , Olson Ann , Woo Sukyung
Published: April 2023

Effect of etomoxir on OvCa cell migration
FigureS3 from Adipokine Apelin/APJ Pathway Promotes Peritoneal Dissemination of Ovarian Cancer Cells by Regulating Lipid Metabolism
Authors: Dogra Samrita , Neelakantan Deepika , Patel Maulin M. , Griesel Beth , Olson Ann , Woo Sukyung
Published: April 2023

CD36 expression regulation in APJ cells
FigureS2 from Adipokine Apelin/APJ Pathway Promotes Peritoneal Dissemination of Ovarian Cancer Cells by Regulating Lipid Metabolism
Authors: Dogra Samrita , Neelakantan Deepika , Patel Maulin M. , Griesel Beth , Olson Ann , Woo Sukyung
Published: April 2023

Lipid droplet accumulation in APJ knockdown cells
Supplementary Figures 1-5 from Intraperitoneal Oil Application Causes Local Inflammation with Depletion of Resident Peritoneal Macrophages
Authors: Alsina-Sanchis Elisenda , Mülfarth Ronja , Moll Iris , Mogler Carolin , Rodriguez-Vita Juan , Fischer Andreas
Published: April 2023

S1. No changes in body weight of spleen histology. S2. Oil injection decreases the number of lymphocytes in peritoneal leverage. S3. Injection of saline does not generate inflammation in the peritoneum. S4. Macrophage foam cell formation upon contact with vegetal oils. S5. Macrophage cell death upon exposure to vegetal oils.
Supplementary Figure S2 from Platinum-Induced Ubiquitination of Phosphorylated H2AX by RING1A Is Mediated by Replication Protein A in Ovarian Cancer
Authors: Sriramkumar Shruthi , Matthews Timothy D. , Ghobashi Ahmed H. , Miller Samuel A. , VanderVere-Carozza Pamela S. , Pawelczak Katherine S. , Nephew Kenneth P. , Turchi John J. , O'Hagan Heather M.
Published: April 2023

RING1A monoubiquitinates phosphoH2AX at lysine 119 in response to cisplatin treatment
Supplementary Figure S1 from Platinum-Induced Ubiquitination of Phosphorylated H2AX by RING1A Is Mediated by Replication Protein A in Ovarian Cancer
Authors: Sriramkumar Shruthi , Matthews Timothy D. , Ghobashi Ahmed H. , Miller Samuel A. , VanderVere-Carozza Pamela S. , Pawelczak Katherine S. , Nephew Kenneth P. , Turchi John J. , O'Hagan Heather M.
Published: April 2023

RING1A mediates monoubiquitination of phosphoH2AX in response to carboplatin
Supplementary Tables 1-7 from Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System
Authors: Trinh Anne , Gil Del Alcazar Carlos R. , Shukla Sachet A. , Chin Koei , Chang Young Hwan , Thibault Guillaume , Eng Jennifer , Jovanović Bojana , Aldaz C. Marcelo , Park So Yeon , Jeong Joon , Wu Catherine , Gray Joe , Polyak Kornelia
Published: April 2023

Summary of Supplementary Tables Supplementary Table S1. Clinicopathological characteristics of patient cohort Supplementary Table S2. Antibody panel for cyclic IF Supplementary Table S3. Summary of mutations and neoantigen expression in the recurrence cohort (Related to 1C, 6A) Supplementary Table S4. Summary of altered pathways in DCIS/IDC (Fig 1F) Supplementary Table S5. Enriched gene sets between DCIS and IDC (Fig 3A) Supplementary Table S6. Identified chromosomal regions associated with immune changes (Related to Fig. 5) Supplementary Table S7. Mutational, neoantigen and rsSNP frequency of commonly mutated genes in TCGA and Abba cohorts (related to Fig 6C,E)
Supplementary Methods and Figures 1-5 from Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System
Authors: Trinh Anne , Gil Del Alcazar Carlos R. , Shukla Sachet A. , Chin Koei , Chang Young Hwan , Thibault Guillaume , Eng Jennifer , Jovanović Bojana , Aldaz C. Marcelo , Park So Yeon , Jeong Joon , Wu Catherine , Gray Joe , Polyak Kornelia
Published: April 2023

S1. Overview of patient cohort. S2. Whole exome sequencing of matched DCISand IDC transition. S3. Mutationalprofiling of the DCIS-to-IDC transition. S4.Phenotypic immune properties of patient cohort. S5.Immune-related genomicchanges and neoantigen load.
Supplementary Table from Gene Body Methylation of the Lymphocyte-Specific Gene CARD11 Results in Its Overexpression and Regulates Cancer mTOR Signaling
Authors: McGuire Michael H. , Dasari Santosh K. , Yao Hui , Wen Yunfei , Mangala Lingegowda S. , Bayraktar Emine , Ma Wencai , Ivan Cristina , Shoshan Einav , Wu Sherry Y. , Jonasch Eric , Bar-Eli Menashe , Wang Jing , Baggerly Keith A. , Sood Anil K.
Published: April 2023

Supplementary Table from Gene Body Methylation of the Lymphocyte-Specific Gene CARD11 Results in Its Overexpression and Regulates Cancer mTOR Signaling
Figure S2 from IQ Motif-Containing GTPase-Activating Protein 2 Inhibits Breast Cancer Angiogenesis by Suppressing VEGFR2–AKT Signaling
Authors: Kumar Dinesh , Patel Saket Awadhesbhai , Khan Rehan , Chawla Saurabh , Mohapatra Nachiketa , Dixit Manjusha
Published: April 2023

Effect of IQGAP2 expression on the other IQGAPs
Supplementary figures and figure legends 1-5 from Multiorgan Signaling Mobilizes Tumor-Associated Erythroid Cells Expressing Immune Checkpoint Molecules
Authors: Sano Yasuyo , Yoshida Toshimi , Choo Min-Kyung , Jiménez-Andrade Yanek , Hill Kathryn R. , Georgopoulos Katia , Park Jin Mo
Published: April 2023

Figure S1. Skin exposure to UVB induces splenic erythroid cell proliferation in mice. Figure S2. Skin exposure to UVB results in expansion of splenic cell populations with erythroid colony-forming potential. Figure S3. Administration of an anti-EPO antibody prevents UVB-responsive splenic erythroid expansion. Figure S4. Tumor growth induces splenic erythroid cell proliferation in mice. Figure S5. CD235A immunostaining identifies tumor-associated erythroid cells in human cancer tissues.
Supplementary Figure S3 from Aberrant Claudin-6–Adhesion Signaling Promotes Endometrial Cancer Progression via Estrogen Receptor α
Authors: Kojima Manabu , Sugimoto Kotaro , Kobayashi Makoto , Ichikawa-Tomikawa Naoki , Kashiwagi Korehito , Watanabe Takafumi , Soeda Shu , Fujimori Keiya , Chiba Hideki
Published: April 2023

S3. The SFK/PI3K-dependent AKT and SGK pathways are involved in the CLDN6-accelerated proliferation and migration of endometrial cancer cells.
Supplementary Table S3 from Cross-talk between YAP and RAR-RXR Drives Expression of Stemness Genes to Promote 5-FU Resistance and Self-Renewal in Colorectal Cancer Cells
Authors: Bauzone Marjolaine , Souidi Mouloud , Dessein Anne-Frédérique , Wisztorski Maxence , Vincent Audrey , Gimeno Jean-Pascal , Monté Didier , Van Seuningen Isabelle , Gespach Christian , Huet Guillemette
Published: April 2023

Supplementary Table S3 (Parts A and B) provides the classification of 115 YAP-binding partners according to several criteria related to the study
Supplementary Table S2 from Cross-talk between YAP and RAR-RXR Drives Expression of Stemness Genes to Promote 5-FU Resistance and Self-Renewal in Colorectal Cancer Cells
Authors: Bauzone Marjolaine , Souidi Mouloud , Dessein Anne-Frédérique , Wisztorski Maxence , Vincent Audrey , Gimeno Jean-Pascal , Monté Didier , Van Seuningen Isabelle , Gespach Christian , Huet Guillemette
Published: April 2023

Supplementary Table S2 presents the detailed proteomics of nuclear YAP-interactome identified in HT29-YAPdc cells
Supplementary Figure S1 from Cross-talk between YAP and RAR-RXR Drives Expression of Stemness Genes to Promote 5-FU Resistance and Self-Renewal in Colorectal Cancer Cells
Authors: Bauzone Marjolaine , Souidi Mouloud , Dessein Anne-Frédérique , Wisztorski Maxence , Vincent Audrey , Gimeno Jean-Pascal , Monté Didier , Van Seuningen Isabelle , Gespach Christian , Huet Guillemette
Published: April 2023

Supplementary Figure S1 identifies YAP/RXRalpha and YAP/RARgamma molecular complexes in HT29-YAPdc cells expressing activated nuclear YAP
Supplementary Table 1 from Metabolomics of Prostate Cancer Gleason Score in Tumor Tissue and Serum
Authors: Penney Kathryn L. , Tyekucheva Svitlana , Rosenthal Jacob , El Fandy Habiba , Carelli Ryan , Borgstein Stephanie , Zadra Giorgia , Fanelli Giuseppe Nicolò , Stefanizzi Lavinia , Giunchi Francesca , Pomerantz Mark , Peisch Samuel , Coulson Hannah , Lis Rosina , Kibel Adam S. , Fiorentino Michelangelo , Umeton Renato , Loda Massimo
Published: April 2023

Full results of 10-fold cross-validation performance assessment for all ML models and prediction tasks (mean +/- SD).
Table S4 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes
Authors: DelaCourt Andrew , Black Alyson , Angel Peggi , Drake Richard , Hoshida Yujin , Singal Amit , Lewin David , Taouli Bachir , Lewis Sara , Schwarz Myron , Fiel M. Isabel , Mehta Anand S.
Published: April 2023

N-glycan structures increased in non-tumor tissue cores compared to tumor tissue cores in the tissue micro-array
Table S3 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes
Authors: DelaCourt Andrew , Black Alyson , Angel Peggi , Drake Richard , Hoshida Yujin , Singal Amit , Lewin David , Taouli Bachir , Lewis Sara , Schwarz Myron , Fiel M. Isabel , Mehta Anand S.
Published: April 2023

Full list of glycans analyzed on the MALDI-TOF mass spectrometer
Table S4 from Fatty Acid Oxidation Is an Adaptive Survival Pathway Induced in Prostate Tumors by HSP90 Inhibition
Authors: Nassar Zeyad D. , Mah Chui Yan , Centenera Margaret M. , Irani Swati , Sadowski Martin C. , Scott Julia S. , Nguyen Elizabeth V. , Nagarajan Shilpa R. , Moldovan Max , Lynn David J. , Daly Roger J. , Hoy Andrew J. , Butler Lisa M.
Published: April 2023

Clinicopathological features of prostate cancer patients in the study
Supplementary Figure from Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer
Authors: El Ghamrasni Samah , Quevedo Rene , Hawley James , Mazrooei Parisa , Hanna Youstina , Cirlan Iulia , Zhu Helen , Bruce Jeff P. , Oldfield Leslie E. , Yang S.Y. Cindy , Guilhamon Paul , Reimand Jüri , Cescon Dave W. , Done Susan J. , Lupien Mathieu , Pugh Trevor J.
Published: April 2023

Supplementary Figure from Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast Cancer
Supplementary File 2 from Functional Hierarchy and Cooperation of EMT Master Transcription Factors in Breast Cancer Metastasis
Authors: Addison Joseph B. , Voronkova Maria A. , Fugett James H. , Lin Chen-Chung , Linville Nathaniel C. , Trinh Brandon , Livengood Ryan H. , Smolkin Matthew B. , Schaller Michael D. , Ruppert J. Michael , Pugacheva Elena N. , Creighton Chad J. , Ivanov Alexey V.
Published: April 2023

Correlation of expression of eight EMT-TFs with 100 core epithelial markers in normal breast tissue and primary breast tumors.
Supplementary File 1 from Functional Hierarchy and Cooperation of EMT Master Transcription Factors in Breast Cancer Metastasis
Authors: Addison Joseph B. , Voronkova Maria A. , Fugett James H. , Lin Chen-Chung , Linville Nathaniel C. , Trinh Brandon , Livengood Ryan H. , Smolkin Matthew B. , Schaller Michael D. , Ruppert J. Michael , Pugacheva Elena N. , Creighton Chad J. , Ivanov Alexey V.
Published: April 2023

Differential expression of 100 core epithelial genes in four breast cancer subtypes compared to normal breast tissue.
Supplementary Table 2 from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

Supplementary Table 2. Patient characteristics from (A) the primary breast cancer core biopsy study and (B) the primary breast cancer and regional node metastasis study.
Supplementary Figure and Table Legends from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

Supplementary Figure and Table Legends
Supplementary Figure 3 from ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression
Authors: Sheldon Helen , Bridges Esther , Silva Ildefonso , Masiero Massimo , Favara David M. , Wang Dian , Leek Russell , Snell Cameron , Roxanis Ioannis , Kreuzer Mira , Gileadi Uzi , Buffa Francesca M. , Banham Alison , Harris Adrian L.
Published: April 2023

S3. Expression of mcoEltd1 in 4T1 cells does not affect cell growth in vitro but increases tumour growth and metastasis.
Supplementary Data 2 from High Response Rate and Durability Driven by HLA Genetic Diversity in Patients with Kidney Cancer Treated with Lenvatinib and Pembrolizumab
Authors: Lee Chung-Han , DiNatale Renzo G. , Chowell Diego , Krishna Chirag , Makarov Vladimir , Valero Cristina , Vuong Lynda , Lee Mark , Weiss Kate , Hoen Doug , Morris Luc , Reznik Ed , Murray Samuel , Kotecha Ritesh , Voss Martin H. , Carlo Maria I. , Feldman Darren , Sachdev Pallavi , Adachi Yusuke , Minoshima Yukinori , Matsui Junji , Funahashi Yasuhiro , Nomoto Kenichi , Hakimi A. Ari , Motzer Robert J. , Chan Timothy A.
Published: April 2023

HLA class-I allele data along with mean HED values for the lenvatinib/pembrolizumab and MSK-IMPACT cohorts.
Supplementary Figure 5 from Identification and Characterization of Cancer Cells That Initiate Metastases to the Brain and Other Organs
Authors: Berghoff Anna. S. , Liao Yunxiang , Karreman Matthia A. , Ilhan-Mutlu Ayseguel , Gunkel Katharina , Sprick Martin R. , Eisen Christian , Kessler Tobias , Osswald Matthias , Wünsche Susanne , Feinauer Manuel , Gril Brunhilde , Marmé Frederic , Michel Laura L. , Bago-Horvath Zuszanna , Sahm Felix , Becker Natalia , Breckwoldt Michael O. , Solecki Gergely , Gömmel Miriam , Huang Lulu , Rübmann Petra , Thome Carina M. , Ratliff Miriam , Trumpp Andreas , Steeg Patricia S. , Preusser Matthias , Wick Wolfgang , Winkler Frank
Published: April 2023

Supplementary Figure 5 shows cell cycle analysis.
Figure S2 from Qa-1b Modulates Resistance to Anti–PD-1 Immune Checkpoint Blockade in Tumors with Defects in Antigen Processing
Authors: Zhang Xiao , Sabio Erich , Krishna Chirag , Ma Xiaoxiao , Wang Jingming , Jiang Hui , Havel Jonathan J. , Chan Timothy A.
Published: April 2023

Figure S2. All anti-PD-1, IgG treated tumors plotted in one frame.
Figure S4 from Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7–APEH–Proteasome Axis in High-grade Serous Ovarian Carcinoma
Authors: Tangri Apoorva , Lighty Kinzie , Loganathan Jagadish , Mesmar Fahmi , Podicheti Ram , Zhang Chi , Iwanicki Marcin , Drapkin Ronny , Nakshatri Harikrishna , Mitra Sumegha
Published: April 2023

Figure S4 shows the relationship between UCHL1, PSMA7, and APEH.
Figure S3 from Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7–APEH–Proteasome Axis in High-grade Serous Ovarian Carcinoma
Authors: Tangri Apoorva , Lighty Kinzie , Loganathan Jagadish , Mesmar Fahmi , Podicheti Ram , Zhang Chi , Iwanicki Marcin , Drapkin Ronny , Nakshatri Harikrishna , Mitra Sumegha
Published: April 2023

Figure S3 shows the effect of UCHL1 inhibitor, LDN57444 in vivo and in vitro.
Supplementary Table 2 from CHK2 Inhibition Provides a Strategy to Suppress Hematologic Toxicity from PARP Inhibitors
Authors: Xu Zhen , Vandenberg Cassandra J. , Lieschke Elizabeth , Di Rago Ladina , Scott Clare L. , Majewski Ian J.
Published: April 2023

Count table and fold enrichment for screens performed with the CRISPR/Cas9 DNA repair gene library. Read counts and analysis of guide enrichment or depletion in cells treated with olaparib (40 nM or 2 µM) or an untreated control. We present guide counts in each condition, normalised counts and log fold changes.
Supplemental Figure 1 from Autophagy-Dependent Sensitization of Triple-Negative Breast Cancer Models to Topoisomerase II Poisons by Inhibition of the Nucleosome Remodeling Factor
Authors: Tyutyunyk-Massey Liliya , Sun Yilun , Dao Nga , Ngo Hannah , Dammalapati Mallika , Vaidyanathan Ashish , Singh Manjulata , Haqqani Syed , Haueis Joshua , Finnegan Ryan , Deng Xiaoyan , Kirberger Steve E. , Bos Paula D. , Bandyopadhyay Dipankar , Pomerantz William C.K. , Pommier Yves , Gewirtz David A. , Landry Joseph W.
Published: April 2023

Supplemental Figure 1. BPTF Suppresses Sensitivity to Select Chemotherapies Independently of Efflux Pump Activity.
Table S1 from mDKN-01, a Novel Anti-DKK1 mAb, Enhances Innate Immune Responses in the Tumor Microenvironment
Authors: Haas Michael S. , Kagey Michael H. , Heath Heidi , Schuerpf Franziska , Rottman James B. , Newman Walter
Published: April 2023

mDKN-01 has Additive Activity with an Anti-PD-1 Antibody
Figure S7 from mDKN-01, a Novel Anti-DKK1 mAb, Enhances Innate Immune Responses in the Tumor Microenvironment
Authors: Haas Michael S. , Kagey Michael H. , Heath Heidi , Schuerpf Franziska , Rottman James B. , Newman Walter
Published: April 2023

Flow Cytometry Gating Strategy
Figure S6 from mDKN-01, a Novel Anti-DKK1 mAb, Enhances Innate Immune Responses in the Tumor Microenvironment
Authors: Haas Michael S. , Kagey Michael H. , Heath Heidi , Schuerpf Franziska , Rottman James B. , Newman Walter
Published: April 2023

Effect of Anti-NK1.1 Antibody Depletion on Various Circulating and Splenic Immune Cells
Figure S5 from mDKN-01, a Novel Anti-DKK1 mAb, Enhances Innate Immune Responses in the Tumor Microenvironment
Authors: Haas Michael S. , Kagey Michael H. , Heath Heidi , Schuerpf Franziska , Rottman James B. , Newman Walter
Published: April 2023

mDKN-01 Treatment Does Not Activate b-Catenin Dependent Wnt Signaling
Figure S3 from mDKN-01, a Novel Anti-DKK1 mAb, Enhances Innate Immune Responses in the Tumor Microenvironment
Authors: Haas Michael S. , Kagey Michael H. , Heath Heidi , Schuerpf Franziska , Rottman James B. , Newman Walter
Published: April 2023

mDKN-01 Does Not Affect B16 Cell Proliferation
Supplementary Table S1 from Neoadjuvant Chemotherapy Induces IL34 Signaling and Promotes Chemoresistance via Tumor-Associated Macrophage Polarization in Esophageal Squamous Cell Carcinoma
Authors: Nakajima Shotaro , Mimura Kosaku , Saito Katsuharu , Thar Min Aung Kyi , Endo Eisei , Yamada Leo , Kase Koji , Yamauchi Naoto , Matsumoto Takuro , Nakano Hiroshi , Kanke Yasuyuki , Okayama Hirokazu , Saito Motonobu , Neupane Prajwal , Saze Zenichiro , Watanabe Yohei , Hanayama Hiroyuki , Hayase Suguru , Kaneta Akinao , Momma Tomoyuki , Ohki Shinji , Ohira Hiromasa , Kono Koji
Published: April 2023

Univariate and multivariate analyses of risk factors for OS and RFS after NAC in patients with ESCC
Supplementary Figure from Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma
Authors: Tokarsky E. John , Crow Jesse C. , Guenther Lillian M. , Sherman John , Taslim Cenny , Alexe Gabriela , Pishas Kathleen I. , Rask Galen , Justis Blake S. , Kasumova Ana , Stegmaier Kimberly , Lessnick Stephen L. , Theisen Emily R.
Published: April 2023

Supplementary Figure from Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma
Supplementary Figure from MYC Promotes Tyrosine Kinase Inhibitor Resistance in ROS1-Fusion-Positive Lung Cancer
Authors: Iyer Sudarshan R. , Odintsov Igor , Schoenfeld Adam J. , Siau Evan , Mattar Marissa S. , de Stanchina Elisa , Khodos Inna , Drilon Alexander , Riely Gregory J. , Ladanyi Marc , Somwar Romel , Davare Monika A.
Published: April 2023

Supplementary Figure from MYC Promotes Tyrosine Kinase Inhibitor Resistance in ROS1-Fusion-Positive Lung Cancer
Supplementary Data from MYC Promotes Tyrosine Kinase Inhibitor Resistance in ROS1-Fusion-Positive Lung Cancer
Authors: Iyer Sudarshan R. , Odintsov Igor , Schoenfeld Adam J. , Siau Evan , Mattar Marissa S. , de Stanchina Elisa , Khodos Inna , Drilon Alexander , Riely Gregory J. , Ladanyi Marc , Somwar Romel , Davare Monika A.
Published: April 2023

Supplementary Data from MYC Promotes Tyrosine Kinase Inhibitor Resistance in ROS1-Fusion-Positive Lung Cancer
Supplementary Figure from MUC16 Promotes Liver Metastasis of Pancreatic Ductal Adenocarcinoma by Upregulating NRP2-Associated Cell Adhesion
Authors: Marimuthu Saravanakumar , Lakshmanan Imayavaramban , Muniyan Sakthivel , Gautam Shailendra K. , Nimmakayala Rama Krishna , Rauth Sanchita , Atri Pranita , Shah Ashu , Bhyravbhatla Namita , Mallya Kavita , Grandgenett Paul M. , Hollingsworth Michael A. , Datta Kaustubh , Jain Maneesh , Ponnusamy Moorthy P. , Batra Surinder K.
Published: April 2023

Supplementary Figure from MUC16 Promotes Liver Metastasis of Pancreatic Ductal Adenocarcinoma by Upregulating NRP2-Associated Cell Adhesion
Supplementary Data from Enhanced Vulnerability of LKB1-Deficient NSCLC to Disruption of ATP Pools and Redox Homeostasis by 8-Cl-Ado
Authors: Galan-Cobo Ana , Stellrecht Christine M. , Yilmaz Emrullah , Yang Chao , Qian Yu , Qu Xiao , Akhter Ishita , Ayres Mary L. , Fan Youhong , Tong Pan , Diao Lixia , Ding Jie , Giri Uma , Gudikote Jayanthi , Nilsson Monique , Wierda William G. , Wang Jing , Skoulidis Ferdinandos , Minna John D. , Gandhi Varsha , Heymach John V.
Published: April 2023

Supplementary Data from Enhanced Vulnerability of LKB1-Deficient NSCLC to Disruption of ATP Pools and Redox Homeostasis by 8-Cl-Ado
Supplementary Data from Stromal p53 Regulates Breast Cancer Development, the Immune Landscape, and Survival in an Oncogene-Specific Manner
Authors: Wu Jinghai , Liu Xin , Reeser Julie A. Wallace , Trimboli Anthony J. , Pécot Thierry , Sizemore Gina M. , Naidu Shan K. , Fernandez Soledad A. , Yu Lianbo , Hallett Michael , Park Morag , Leone Gustavo W. , Hildreth Blake E. , Ostrowski Michael C.
Published: April 2023

Supplementary Data from Stromal p53 Regulates Breast Cancer Development, the Immune Landscape, and Survival in an Oncogene-Specific Manner
Supplementary Figure from Multi-omics Profiling Shows BAP1 Loss Is Associated with Upregulated Cell Adhesion Molecules in Uveal Melanoma
Authors: Baqai Usman , Purwin Timothy J. , Bechtel Nelisa , Chua Vivian , Han Anna , Hartsough Edward J. , Kuznetsoff Jeffim N. , Harbour J. William , Aplin Andrew E.
Published: April 2023

Supplementary Figure from Multi-omics Profiling Shows BAP1 Loss Is Associated with Upregulated Cell Adhesion Molecules in Uveal Melanoma
Supplementary Data from Intratumoral Electroporation of Plasmid Encoded IL12 and Membrane-Anchored Anti-CD3 Increases Systemic Tumor Immunity
Authors: Han Mia , Nguyen Bianca , Lee Jack Y. , Browning Erica , Zhang Jun , Mukhopadhyay Anandaroop , Gujar Ravindra , Salazar Jon , Hermiz Reneta , Svenson Lauren , Rolig Annah S. , Redmond William L. , Algazi Alain P. , Daud Adil I. , Canton David A. , Twitty Christopher G.
Published: April 2023

Supplementary Data from Intratumoral Electroporation of Plasmid Encoded IL12 and Membrane-Anchored Anti-CD3 Increases Systemic Tumor Immunity
Supplementary Table from TRAF4 Inhibits Bladder Cancer Progression by Promoting BMP/SMAD Signaling
Authors: Iyengar Prasanna Vasudevan , Marvin Dieuwke Louise , Lama Dilraj , Tan Tuan Zea , Suriyamurthy Sudha , Xie Feng , van Dinther Maarten , Mei Hailiang , Verma Chandra Shekhar , Zhang Long , Ritsma Laila , ten Dijke Peter
Published: April 2023

Supplementary Table from TRAF4 Inhibits Bladder Cancer Progression by Promoting BMP/SMAD Signaling
Supplementary Figure from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Authors: Majumder Anurima , Hosseinian Sina , Stroud Mia , Adhikari Emma , Saller James J. , Smith Matthew A. , Zhang Guolin , Agarwal Shruti , Creixell Marc , Meyer Benjamin S. , Kinose Fumi , Bowers Kiah , Fang Bin , Stewart Paul A. , Welsh Eric A. , Boyle Theresa A. , Meyer Aaron S. , Koomen John M. , Haura Eric B.
Published: April 2023

Supplementary Figure from Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration
Supplementary Figure from TRAF4 Inhibits Bladder Cancer Progression by Promoting BMP/SMAD Signaling
Authors: Iyengar Prasanna Vasudevan , Marvin Dieuwke Louise , Lama Dilraj , Tan Tuan Zea , Suriyamurthy Sudha , Xie Feng , van Dinther Maarten , Mei Hailiang , Verma Chandra Shekhar , Zhang Long , Ritsma Laila , ten Dijke Peter
Published: April 2023

Supplementary Figure from TRAF4 Inhibits Bladder Cancer Progression by Promoting BMP/SMAD Signaling
Supplementary Figure S4 from Sox2 Is an Oncogenic Driver of Small-Cell Lung Cancer and Promotes the Classic Neuroendocrine Subtype
Authors: Voigt Ellen , Wallenburg Madeline , Wollenzien Hannah , Thompson Ethan , Kumar Kirtana , Feiner Joshua , McNally Moira , Friesen Hunter , Mukherjee Malini , Afeworki Yohannes , Kareta Michael S.
Published: April 2023

Gaussian mixed modeling of SOX2 target gene expression
Supplementary Figure from MUC1-C Dictates JUN and BAF-Mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells
Authors: Bhattacharya Atrayee , Fushimi Atsushi , Yamashita Nami , Hagiwara Masayuki , Morimoto Yoshihiro , Rajabi Hasan , Long Mark D. , Abdulla Maha , Ahmad Rehan , Street Kelly , Liu Song , Liu Tao , Kufe Donald
Published: April 2023

Supplementary Figure from MUC1-C Dictates JUN and BAF-Mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells
Supplementary Figures 1-3 from GATM-Mediated Creatine Biosynthesis Enables Maintenance of FLT3-ITD–Mutant Acute Myeloid Leukemia
Authors: Zhang Yuan , Newsom Kimberly J. , Zhang Mei , Kelley Jeffry S. , Starostik Petr
Published: April 2023

S1. Analysis of differential gene expression in MV4-11 cells with or without FLT3 TKIs. S2.Expression of GAMT, SLC7A1 and SLC6A9 in AML cells (n=173) from TCGA LAML dataset and normal bone marrow (BM) cells (n=70) from GTEx database. S3. FLT3-ITD N51sequence and K562 cells lentiviral vector FLT3 transductions.
Supplementary Figure from Therapeutic Targeting of Stromal-Tumor HGF-MET Signaling in an Organotypic Triple-Negative Breast Tumor Model
Authors: Singh Sunil , Lamichhane Astha , Rafsanjani Nejad Pouria , Heiss Jacob , Baumann Hannah , Gudneppanavar Ravindra , Leipzig Nic D. , Konopka Michael , Luker Gary D. , Tavana Hossein
Published: April 2023

Supplementary Figure from Therapeutic Targeting of Stromal-Tumor HGF-MET Signaling in an Organotypic Triple-Negative Breast Tumor Model
Supplementary Data from EPAC Regulates Melanoma Growth by Stimulating mTORC1 Signaling and Loss of EPAC Signaling Dependence Correlates with Melanoma Progression
Authors: Krishnan Aishwarya , Bhasker Aishwarya I. , Singh Mithalesh K. , Rodriguez Carlos. I. , Pérez Edgardo Castro , Altameemi Sarah , Lares Marcos , Khan Hamidullah , Ndiaye Mary , Ahmad Nihal , Schieke Stefan M. , Setaluri Vijayasaradhi
Published: April 2023

Supplementary Data from EPAC Regulates Melanoma Growth by Stimulating mTORC1 Signaling and Loss of EPAC Signaling Dependence Correlates with Melanoma Progression
Supplementary Figure from TGF-β-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast–Mediated Epithelial–Mesenchymal Transition in Colorectal Cancer
Authors: Yang Mengdi , Li Dan , Jiang Zhiyuan , Li Changcan , Ji Suyuan , Sun Jing , Chang Yujie , Ruan Shunyi , Wang Zhiyu , Liang Rui , Dai Xueyu , Li Bin , Zhao Hui
Published: April 2023

Supplementary Figure from TGF-β-Induced FLRT3 Attenuation Is Essential for Cancer-Associated Fibroblast–Mediated Epithelial–Mesenchymal Transition in Colorectal Cancer
Supplementary Figure from T-cell Dysfunction upon Expression of MYC with Altered Phosphorylation at Threonine 58 and Serine 62
Authors: Daniel Colin J. , Pelz Carl , Wang Xiaoyan , Munks Michael W. , Ko Aaron , Murugan Dhaarini , Byers Sarah A. , Juarez Eleonora , Taylor Karyn L. , Fan Guang , Coussens Lisa M. , Link Jason M. , Sears Rosalie C.
Published: April 2023

Supplementary Figure from T-cell Dysfunction upon Expression of MYC with Altered Phosphorylation at Threonine 58 and Serine 62
Supplementary Data from Origins and Timing of Emerging Lesions in Advanced Renal Cell Carcinoma
Authors: Wallace Andrew , Porten Sima P. , Lo Amy A. , Oreper Daniel , Lounsbury Nicolas , Havnar Charles , Pechuan-Jorge Ximo , Zill Oliver A. , Meng Maxwell V.
Published: April 2023

Supplementary Data from Origins and Timing of Emerging Lesions in Advanced Renal Cell Carcinoma
Supplementary Tables 1-7 from Heritable Variants in the Chromosome 1q22 Locus Increase Gastric Cancer Risk via Altered Chromatin Looping and Increased UBAP2L Expression
Authors: Guan Wei , Yang Nan , Zuo Xianglin , Wang Xuchun , Cao Pingping , Chu Ying , Qin Zhongyong , Cheng He , Shi Xiao , Ma Tingzheng , Xu Zekuan , Sun Yujie
Published: April 2023

Supplementary Table S1. Clinicopathological characteristics of 44 patients. Supplementary Table S2. The primers sequences for q-PCR. Supplementary Table S3. The shRNA sequences of SCR and sh-U. Supplementary Table S4. The primer sequences for UBAP2L Expression Plasmid (ex-U). Supplementary Table S5. The primer sequences for construction of Enhancer Plasmids. Supplementary Table S6. The primer sequences for amplification of DNA fragments including risk SNPs. Supplementary Table S7. The primers used in 3C assays.
Supplementary Data from Glioblastoma–Astrocyte Connexin 43 Gap Junctions Promote Tumor Invasion
Authors: McCutcheon Sean , Spray David C.
Published: April 2023

Supplementary Data from Glioblastoma–Astrocyte Connexin 43 Gap Junctions Promote Tumor Invasion
Supplementary Figure 1 from Heritable Variants in the Chromosome 1q22 Locus Increase Gastric Cancer Risk via Altered Chromatin Looping and Increased UBAP2L Expression
Authors: Guan Wei , Yang Nan , Zuo Xianglin , Wang Xuchun , Cao Pingping , Chu Ying , Qin Zhongyong , Cheng He , Shi Xiao , Ma Tingzheng , Xu Zekuan , Sun Yujie
Published: April 2023

The eQTL analysis, expression and Kaplan-Meier analysis of several other genes within the LD block of the risk SNP rs2075570.