bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from Pathologic Oxidation of PTPN12 Underlies ABL1 Phosphorylation in Hereditary Leiomyomatosis and Renal Cell Carcinoma
Authors: Xu Yang , Taylor Paul , Andrade Joshua , Ueberheide Beatrix , Shuch Brian , Glazer Peter M. , Bindra Ranjit S. , Moran Michael F. , Linehan W. Marston , Neel Benjamin G.
Published: April 2023

Supplementary materials, methods, and figure legends.
Supplementary Material from TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells
Authors: Li Taiwen , Fan Jingyu , Wang Binbin , Traugh Nicole , Chen Qianming , Liu Jun S. , Li Bo , Liu X. Shirley
Published: April 2023

Performance comparison between TIMER and CIBERSORT
Supplemental Figures 1-2 from Tenascin-C and Integrin α9 Mediate Interactions of Prostate Cancer with the Bone Microenvironment
Authors: San Martin Rebeca , Pathak Ravi , Jain Antrix , Jung Sung Yun , Hilsenbeck Susan G. , Piña-Barba María C. , Sikora Andrew G. , Pienta Kenneth J. , Rowley David R.
Published: April 2023

Characterization of the reactive endosteum phenotype and immune cell markers present in in prostate derived bone metastasis. Immunohistochemistry
Supplementary methods and figure legends from miR-193b–Regulated Signaling Networks Serve as Tumor Suppressors in Liposarcoma and Promote Adipogenesis in Adipose-Derived Stem Cells
Authors: Mazzu Ying Z. , Hu Yulan , Soni Rajesh K. , Mojica Kelly M. , Qin Li-Xuan , Agius Phaedra , Waxman Zachary M. , Mihailovic Aleksandra , Socci Nicholas D. , Hendrickson Ronald C. , Tuschl Thomas , Singer Samuel
Published: April 2023

Supplementary methods (plasmid construction, mass spectrometry, bioinformatics)
Supplementary Figure 7 from Helicase-Driven Activation of NFκB-COX2 Pathway Mediates the Immunosuppressive Component of dsRNA-Driven Inflammation in the Human Tumor Microenvironment
Authors: Theodoraki Marie-Nicole , Yerneni Saigopalakrishna , Sarkar Saumendra N. , Orr Brian , Muthuswamy Ravikumar , Voyten Jamie , Modugno Francesmary , Jiang Weijian , Grimm Melissa , Basse Per H. , Bartlett David L. , Edwards Robert P. , Kalinski Pawel
Published: April 2023

dsDNA selectively mobilize CXCL10 production, rather than CCL22 and suppressive component of inflammation in mouse myeloid cells.
Sypplementary materials and methods from Intratumoral Immunotherapy with XCL1 and sFlt3L Encoded in Recombinant Semliki Forest Virus–Derived Vectors Fosters Dendritic Cell–Mediated T-cell Cross-Priming
Authors: Sánchez-Paulete Alfonso R. , Teijeira Álvaro , Quetglas José I. , Rodríguez-Ruiz María E. , Sánchez-Arráez Álvaro , Labiano Sara , Etxeberria Iñaki , Azpilikueta Arantza , Bolaños Elixabet , Ballesteros-Briones María Cristina , Casares Noelia , Quezada Sergio A. , Berraondo Pedro , Sancho David , Smerdou Cristian , Melero Ignacio
Published: April 2023

Suppplementary materials and methods
Supplementary Figure 5 from Helicase-Driven Activation of NFκB-COX2 Pathway Mediates the Immunosuppressive Component of dsRNA-Driven Inflammation in the Human Tumor Microenvironment
Authors: Theodoraki Marie-Nicole , Yerneni Saigopalakrishna , Sarkar Saumendra N. , Orr Brian , Muthuswamy Ravikumar , Voyten Jamie , Modugno Francesmary , Jiang Weijian , Grimm Melissa , Basse Per H. , Bartlett David L. , Edwards Robert P. , Kalinski Pawel
Published: April 2023

Interplay between IFNÃŽÂ± and COX-2/PGE2 system in the regulation of and suppressive inflammatory mediators.
Supplementary figure 5 from Intratumoral Immunotherapy with XCL1 and sFlt3L Encoded in Recombinant Semliki Forest Virus–Derived Vectors Fosters Dendritic Cell–Mediated T-cell Cross-Priming
Authors: Sánchez-Paulete Alfonso R. , Teijeira Álvaro , Quetglas José I. , Rodríguez-Ruiz María E. , Sánchez-Arráez Álvaro , Labiano Sara , Etxeberria Iñaki , Azpilikueta Arantza , Bolaños Elixabet , Ballesteros-Briones María Cristina , Casares Noelia , Quezada Sergio A. , Berraondo Pedro , Sancho David , Smerdou Cristian , Melero Ignacio
Published: April 2023

Administration of SFV-XF into MC38 tumors shows no detectable T-cell infiltration increases.
Supplementary Tables from Twist1 Regulates Vimentin through Cul2 Circular RNA to Promote EMT in Hepatocellular Carcinoma
Authors: Meng Jing , Chen Shuang , Han Jing-Xia , Qian Baoxin , Wang Xiao-Rui , Zhong Wei-Long , Qin Yuan , Zhang Heng , Gao Wan-Feng , Lei Yue-Yang , Yang Wei , Yang Lan , Zhang Chao , Liu Hui-Juan , Liu Yan-Rong , Zhou Hong-Gang , Sun Tao , Yang Cheng
Published: April 2023

Table S1ï¼ŽThe plasmids information. Table S2ï¼ŽThe primers of overexpressed vectors and siRNA. Table S3ï¼ŽThe primers of RT-PCR. Table S4ï¼ŽClinical characteristics of the patients used for developing PDTX models. Table S5ï¼ŽThe sequences of circRNAs probe for FISH.
Table S2 from IL-6 Mediates Cross-Talk between Tumor Cells and Activated Fibroblasts in the Tumor Microenvironment
Authors: Karakasheva Tatiana A. , Lin Eric W. , Tang Qiaosi , Qiao Edmund , Waldron Todd J. , Soni Monica , Klein-Szanto Andres J. , Sahu Varun , Basu Devraj , Ohashi Shinya , Baba Kiichiro , Giaccone Zachary T. , Walker Sarah R. , Frank David A. , Wileyto E. Paul , Long Qi , Dunagin Margaret C. , Raj Arjun , Diehl J. Alan , Wong K.K. , Bass Adam J. , Rustgi Anil K.
Published: April 2023

Results of the cytokine array of conditioned media from co-cultured ESCC cells and CAFs, presented as relative fluorescence
Supplemental Figure 6 from A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity
Authors: Díaz-Carballo David , Saka Sahitya , Klein Jacqueline , Rennkamp Tobias , Acikelli Ali H. , Malak Sascha , Jastrow Holger , Wennemuth Gunther , Tempfer Clemens , Schmitz Inge , Tannapfel Andrea , Strumberg Dirk
Published: April 2023

Resistance profile and spherogenicity of SKOV3 ovarian carcinoma models.
SV-8: Asymmetric division of P1 oncogenerative cells from A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity
Authors: Díaz-Carballo David , Saka Sahitya , Klein Jacqueline , Rennkamp Tobias , Acikelli Ali H. , Malak Sascha , Jastrow Holger , Wennemuth Gunther , Tempfer Clemens , Schmitz Inge , Tannapfel Andrea , Strumberg Dirk
Published: April 2023

P1 cells seem to undergo divisions in to similar oncogenerative cells by cytoplasm separation. The process is in par orchestrated with the participation of mitochondria which delimitate boundaries of cytoplasms to be separated. After this, it is possible to observe a directional cytokinesis like separation of multinucleated cells.
SV-7: P1 cells in quiescent phase from A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity
Authors: Díaz-Carballo David , Saka Sahitya , Klein Jacqueline , Rennkamp Tobias , Acikelli Ali H. , Malak Sascha , Jastrow Holger , Wennemuth Gunther , Tempfer Clemens , Schmitz Inge , Tannapfel Andrea , Strumberg Dirk
Published: April 2023

P1 oncogenerative cells undergo long quiescent phases in which they do not appear to generate and eject G1 cells.
SV-6: P1 oncogenerative cells. Lateral division from A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity
Authors: Díaz-Carballo David , Saka Sahitya , Klein Jacqueline , Rennkamp Tobias , Acikelli Ali H. , Malak Sascha , Jastrow Holger , Wennemuth Gunther , Tempfer Clemens , Schmitz Inge , Tannapfel Andrea , Strumberg Dirk
Published: April 2023

The lateral separation of G1 from P1 cells is observed in this clip.
Figure S4 from Extracellular Matrix Protein Tenascin C Increases Phagocytosis Mediated by CD47 Loss of Function in Glioblastoma
Authors: Ma Ding , Liu Senquan , Lal Bachchu , Wei Shuang , Wang Shuyan , Zhan Daqian , Zhang Hao , Lee Richard S. , Gao Peisong , Lopez-Bertoni Hernando , Ying Mingyao , Li Jian Jian , Laterra John , Wilson Mary Ann , Xia Shuli
Published: April 2023

Figure S4 shows Sanger sequencing of GL261 clone 29.
Figure S1 from Elevated Heme Synthesis and Uptake Underpin Intensified Oxidative Metabolism and Tumorigenic Functions in Non–Small Cell Lung Cancer Cells
Authors: Sohoni Sagar , Ghosh Poorva , Wang Tianyuan , Kalainayakan Sarada Preeta , Vidal Chantal , Dey Sanchareeka , Konduri Purna Chaitanya , Zhang Li
Published: April 2023

Fig. S1 (A) The levels of the rate-limiting heme biosynthetic enzyme ALAS1 are elevated in NSCLC cells. (B) The levels of heme transporter SLC46A1 are elevated in NSCLC cells. (C) The levels of heme degradation enzyme HMOX1 are elevated in NSCLC cells. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in tumorigenic cells were compared to the levels in non-tumorigenic cells with a Welch 2-sample t-test.*, p-value ,0.05, **, p-value < 0.005.
Table S3 from NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model
Authors: Liu Yan , Li Yuyang , Liu Shengwu , Adeegbe Dennis O. , Christensen Camilla L. , Quinn Max M. , Dries Ruben , Han Shiwei , Buczkowski Kevin , Wang Xiaoen , Chen Ting , Gao Peng , Zhang Hua , Li Fei , Hammerman Peter S. , Bradner James E. , Quayle Steven N. , Wong Kwok-Kin
Published: April 2023

List of hits in the top 10% of screen hits from NCI-H69 and GLC-16 xenograft tumors
Figure S4 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Interphase FISH demonstrates copy number gain of Met and Hgf in NF1-MET, NF1-P53, and NF1 MPNSTs.
Figure S3 from Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors
Authors: Peacock Jacqueline D. , Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Bowman Megan , Madaj Zachary , Koeman Julie , Boguslawski Elissa A. , Grit Jamie , Dodd Rebecca D. , Khachaturov Vadim , Cardona Diana M. , Chen Mark , Kirsch David G. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: April 2023

Metaphase FISH analysis of R26-MET transgene.
NK cells mediate synergistic antitumor effects of combined inhibition of HDAC6 and BET in a SCLC preclinical model from NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model
Authors: Liu Yan , Li Yuyang , Liu Shengwu , Adeegbe Dennis O. , Christensen Camilla L. , Quinn Max M. , Dries Ruben , Han Shiwei , Buczkowski Kevin , Wang Xiaoen , Chen Ting , Gao Peng , Zhang Hua , Li Fei , Hammerman Peter S. , Bradner James E. , Quayle Steven N. , Wong Kwok-Kin
Published: April 2023

This section contains 10 supplemental figures and related figure legends.
Supplementary video 2 from A Novel Small-Molecule Inhibitor of MRCK Prevents Radiation-Driven Invasion in Glioblastoma
Authors: Birch Joanna L. , Strathdee Karen , Gilmour Lesley , Vallatos Antoine , McDonald Laura , Kouzeli Ariadni , Vasan Richa , Qaisi Abdulrahman Hussain , Croft Daniel R. , Crighton Diane , Gill Kathryn , Gray Christopher H. , Konczal Jennifer , Mezna Mokdad , McArthur Duncan , Schüttelkopf Alexander W. , McConnell Patricia , Sime Mairi , Holmes William M. , Bower Justin , McKinnon Heather J. , Drysdale Martin , Olson Michael F. , Chalmers Anthony J.
Published: April 2023

GFP E2 cells irradiated with 2Gy in an ex vivo brain slice motility assay
Supplementary figures from CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets
Authors: Cortazar Ana R. , Torrano Veronica , Martín-Martín Natalia , Caro-Maldonado Alfredo , Camacho Laura , Hermanova Ivana , Guruceaga Elizabeth , Lorenzo-Martín Luis F. , Caloto Ruben , Gomis Roger R. , Apaolaza Iñigo , Quesada Victor , Trka Jan , Gomez-Muñoz Antonio , Vincent Silvestre , Bustelo Xose R. , Planes Francisco J. , Aransay Ana M. , Carracedo Arkaitz
Published: April 2023

Supplementary figures
Supplementary Figure S3 from mTOR Inhibition via Displacement of Phosphatidic Acid Induces Enhanced Cytotoxicity Specifically in Cancer Cells
Authors: Nguyen Tra-Ly , Nokin Marie-Julie , Egorov Maxim , Tomé Mercedes , Bodineau Clément , Di Primo Carmelo , Minder Lætitia , Wdzieczak-Bakala Joanna , Garcia-Alvarez Maria Concepcion , Bignon Jérôme , Thoison Odile , Delpech Bernard , Surpateanu Georgiana , Frapart Yves-Michel , Peyrot Fabienne , Abbas Kahina , Terés Silvia , Evrard Serge , Khatib Abdel-Majid , Soubeyran Pierre , Iorga Bogdan I. , Durán Raúl V. , Collin Pascal
Published: April 2023

The file contains supplementary results showing that ICSN3250 antagonized with phosphatidic acid to inhibit mTORC1.
Figure S6 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

Combination of RNA splicing modulator compounds and ATR inhibition sensitizes U2AF1(S34F)-expressing cells.
Figure S1 from Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes
Authors: Nguyen Hai Dang , Leong Wan Yee , Li Weiling , Reddy Pavankumar N.G. , Sullivan Jack D. , Walter Matthew J. , Zou Lee , Graubert Timothy A.
Published: April 2023

U2AF1(S34F)-expressing cells induce R loop-associated ATR-mediated RPA32 phosphorylation.
DEGs between AD and SCC from GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma
Authors: Zhang Weiruo , Bouchard Gina , Yu Alice , Shafiq Majid , Jamali Mehran , Shrager Joseph B. , Ayers Kelsey , Bakr Shaimaa , Gentles Andrew J. , Diehn Maximilian , Quon Andrew , West Robert B. , Nair Viswam , van de Rijn Matt , Napel Sandy , Plevritis Sylvia K.
Published: April 2023

This supplement file contains the identified differentially expressed genes (DEGs) between lung adenocarcinoma (AD) and squamous cell carcinoma (SCC) patients.
Figure S4 from Plk1-Mediated Phosphorylation of TSC1 Enhances the Efficacy of Rapamycin
Authors: Li Zhiguo , Kong Yifan , Song Longzhen , Luo Qian , Liu Jinghui , Shao Chen , Hou Xianzeng , Liu Xiaoqi
Published: April 2023

Tumors derived from cells expressing myc-TSC1-2E mutant are more sensitive to rapamycin
Figure S2 from YAP1-Mediated Suppression of USP31 Enhances NFκB Activity to Promote Sarcomagenesis
Authors: Ye Shuai , Lawlor Matthew A. , Rivera-Reyes Adrian , Egolf Shaun , Chor Susan , Pak Koreana , Ciotti Gabrielle E. , Lee Avery C. , Marino Gloria E. , Shah Jennifer , Niedzwicki David , Weber Kristy , Park Paul M.C. , Alam Md. Zahidul , Grazioli Alison , Haldar Malay , Xu Mousheng , Perry Jennifer A. , Qi Jun , Eisinger-Mathason T.S. Karin
Published: April 2023

Supplemental ChIP-Seq and RNA-seq information
Figure S4 from Semaphorin 7A Promotes Macrophage-Mediated Lymphatic Remodeling during Postpartum Mammary Gland Involution and in Breast Cancer
Authors: Elder Alan M. , Tamburini Beth A.J. , Crump Lyndsey S. , Black Sarah A. , Wessells Veronica M. , Schedin Pepper J. , Borges Virginia F. , Lyons Traci R.
Published: April 2023

Additional characterization of lymphatic and macrophage interaction
Figure S3 from Semaphorin 7A Promotes Macrophage-Mediated Lymphatic Remodeling during Postpartum Mammary Gland Involution and in Breast Cancer
Authors: Elder Alan M. , Tamburini Beth A.J. , Crump Lyndsey S. , Black Sarah A. , Wessells Veronica M. , Schedin Pepper J. , Borges Virginia F. , Lyons Traci R.
Published: April 2023

SEMA7A expression in 66cl4 and E0771 cell lines with PDPN+ macrophage and LVD in those tumors
Table S1 from Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism
Authors: Lopes-Ramos Camila M. , Kuijjer Marieke L. , Ogino Shuji , Fuchs Charles S. , DeMeo Dawn L. , Glass Kimberly , Quackenbush John
Published: April 2023

Extensive clinical features for the dataset included in the study.
Supplementary Data from Inhibition of the Stromal p38MAPK/MK2 Pathway Limits Breast Cancer Metastases and Chemotherapy-Induced Bone Loss
Authors: Murali Bhavna , Ren Qihao , Luo Xianmin , Faget Douglas V. , Wang Chun , Johnson Radia Marie , Gruosso Tina , Flanagan Kevin C. , Fu Yujie , Leahy Kathleen , Alspach Elise , Su Xinming , Ross Michael H. , Burnette Barry , Weilbaecher Katherine N. , Park Morag , Mbalaviele Gabriel , Monahan Joseph B. , Stewart Sheila A.
Published: April 2023

Supplementary Data from Inhibition of the Stromal p38MAPK/MK2 Pathway Limits Breast Cancer Metastases and Chemotherapy-Induced Bone Loss
Supplementary methods from The Canonical Wnt Pathway Drives Macropinocytosis in Cancer
Authors: Redelman-Sidi Gil , Binyamin Anna , Gaeta Isabella , Palm Wilhelm , Thompson Craig B. , Romesser Paul B. , Lowe Scott W. , Bagul Mukta , Doench John G. , Root David E. , Glickman Michael S.
Published: April 2023

Supplementary methods and legends for supplementary figures
Supplementary Materials and Methods from Targeting PARP1 in XRCC1-Deficient Sporadic Invasive Breast Cancer or Preinvasive Ductal Carcinoma In Situ Induces Synthetic Lethality and Chemoprevention
Authors: Ali Reem , Al-Kawaz Abdulbaqi , Toss Michael S. , Green Andrew R. , Miligy Islam M. , Mesquita Katia A. , Seedhouse Claire , Mirza Sameer , Band Vimla , Rakha Emad A , Madhusudan Srinivasan
Published: April 2023

Supplementary materials and Methods for Compounds and reagents, Generation of XRCC1 knockouts using CRISPR/Cas-9 system, Clonogenic assays, Cell Proliferation assays, Cell synchronization and functional studies, Confocal microscopy, Invasion and migration assays, qRT-PCR analysis of epithelial-mesenchymal transition (EMT) gene expression, Generation of 3D spheroids, human Invasive breast cancers and DCIS cohorts (demographics and treatment).
Supplementary figures 1-3 from Extracorporeal Photochemotherapy Drives Monocyte-to-Dendritic Cell Maturation to Induce Anticancer Immunity
Authors: Ventura Alessandra , Vassall Aaron , Robinson Eve , Filler Renata , Hanlon Douglas , Meeth Katrina , Ezaldein Harib , Girardi Michael , Sobolev Olga , Bosenberg Marcus W. , Edelson Richard L.
Published: April 2023

Additional data for Figure 1, showing individual tumor growth curves (Figure S1), and tumor histology analysis (Figures S2-S3), for review and publication
Data File S3 from Dose and Schedule Determine Distinct Molecular Mechanisms Underlying the Efficacy of the p53–MDM2 Inhibitor HDM201
Authors: Jeay Sébastien , Ferretti Stéphane , Holzer Philipp , Fuchs Jeanette , Chapeau Emilie A. , Wartmann Markus , Sterker Dario , Romanet Vincent , Murakami Masato , Kerr Grainne , Durand Eric Y. , Gaulis Swann , Cortes-Cros Marta , Ruetz Stephan , Stachyra Therese-Marie , Kallen Joerg , Furet Pascal , Würthner Jens , Guerreiro Nelson , Halilovic Ensar , Jullion Astrid , Kauffmann Audrey , Kuriakose Emil , Wiesmann Marion , Jensen Michael R. , Hofmann Francesco , Sellers William R.
Published: April 2023

Insertional results from Arf-/- PB in vivo resistance screens. A and C, Tables listing all sequenced samples with their model number (i.e. X25272), the transplanted fragment number (i.e. P0M1-P1M5-P2M19, P for passage, and M for Mouse), tumor status (DR=drug resistant, or veh=vehicle treated) and treatment schedule (A) QD for daily or (C) 2QW for biweekly. Total number of reads and tumor pathology are labeled for each sample. Insertional landscapes are displayed on the right part of the table where the averaged normalized diversity sequencing counts are indicated for each Common insertion site gene (gCIS) and each tumor. B and D, List of the genes found differentially enriched for PB insertions in HDM201 resistant tumors compared to untreated tumors (B) continuous daily treatment or (D) biweekly intermittent treatment. The data in D were extracted from previous report (28) for intermittent 100 mg/kg biweekly dosing schedule, and reanalyzed with only 6 tumor models used out of 16 in previous report. Fold change, p-value and FDR were calculated for each gene in comparative analyses of untreated tumor samples vs. resistant tumor samples. PercentSample indicated the percentage of resistant tumors with insertion in that gene. The predicted function GOF (gain of function), LOF (loss of function) or uncertain is also indicated.
Table S2 from Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma
Authors: Luoto Suvi , Hermelo Ismaïl , Vuorinen Elisa M. , Hannus Paavo , Kesseli Juha , Nykter Matti , Granberg Kirsi J.
Published: April 2023

Table contains immune response related gene clusters identified in clustering analysis and used in other analyses.
Supp Figures S4-S6 from Lorlatinib Treatment Elicits Multiple On- and Off-Target Mechanisms of Resistance in ALK-Driven Cancer
Authors: Redaelli Sara , Ceccon Monica , Zappa Marina , Sharma Geeta G. , Mastini Cristina , Mauri Mario , Nigoghossian Marion , Massimino Luca , Cordani Nicoletta , Farina Francesca , Piazza Rocco , Gambacorti-Passerini Carlo , Mologni Luca
Published: April 2023

Localization of N1178H, Sanger sequencing, and triple combo on AS4 cells
Supplementary Figure Legends from An ATM/TRIM37/NEMO Axis Counteracts Genotoxicity by Activating Nuclear-to-Cytoplasmic NF-κB Signaling
Authors: Wu Geyan , Song Libing , Zhu Jinrong , Hu Yameng , Cao Lixue , Tan Zhanyao , Zhang Shuxia , Li Ziwen , Li Jun
Published: April 2023

Supplementary Figure Legends to support primary figures.
Figure S1 from Loss of MED12 Induces Tumor Dormancy in Human Epithelial Ovarian Cancer via Downregulation of EGFR
Authors: Luo Xiao-Lin , Deng Cheng-Cheng , Su Xiao-Dong , Wang Fang , Chen Zhen , Wu Xing-Ping , Liang Shao-Bo , Liu Ji-Hong , Fu Li-Wu
Published: April 2023

MTT assay of HO8910 and SKOV3 cells treated with DDP and Carboplatin.
Supplementary Fig S1 from Mucosal HPV E6/E7 Peptide Vaccination in Combination with Immune Checkpoint Modulation Induces Regression of HPV+ Oral Cancers
Authors: Dorta-Estremera Stephanie , Chin Renee L. , Sierra Gloria , Nicholas Courtney , Yanamandra Ananta V. , Nookala Sita M.K. , Yang Guojun , Singh Shail , Curran Michael A. , Sastry K. Jagannadha
Published: April 2023

Gating strategy to analyze TILs after immunotherapy combinations
Figure S1 from Pharmacologic Ascorbate Reduces Radiation-Induced Normal Tissue Toxicity and Enhances Tumor Radiosensitization in Pancreatic Cancer
Authors: Alexander Matthew S. , Wilkes Justin G. , Schroeder Samuel R. , Buettner Garry R. , Wagner Brett A. , Du Juan , Gibson-Corley Katherine , O’Leary Brianne R. , Spitz Douglas R. , Buatti John M. , Berg Daniel J. , Bodeker Kellie L. , Vollstedt Sandy , Brown Heather A. , Allen Bryan G. , Cullen Joseph J.
Published: April 2023

The effect of ascorbate and catalase on clonogenic cell survival in PDAC.
Table S1, Table S2, Figure S1, Table S3, Table S4, Table S5, Table S6 from Epithelial–Mesenchymal Transition in Human Prostate Cancer Demonstrates Enhanced Immune Evasion Marked by IDO1 Expression
Authors: Kolijn Kimberley , Verhoef Esther I. , Smid Marcel , Böttcher René , Jenster Guido W. , Debets Reno , van Leenders Geert J.L.H.
Published: April 2023

Supplementary Table S1: Histopathological features of clinical samples, Supplementary Table S2: Specifications on antibodies used for immune-stainings, Supplementary Figure S1: Example of microdissection of tumor regions, Supplementary Table S3: Mapping statistics of RNA sequencing, Supplementary Table S4: List of differentially expressed genes in N-cadherin positive versus negative EMT regions, Supplementary Table S5: Summary of Ingenuity Pathway Analysis, Supplementary Table S6: List of differentially expressed EMT-associated genes as identified by Ingenuity in N-cadherin negative versus positive regions
Figure S4 from Cyclophilin A Function in Mammary Epithelium Impacts Jak2/Stat5 Signaling, Morphogenesis, Differentiation, and Tumorigenesis in the Mammary Gland
Authors: Volker Sonja E. , Hedrick Shannon E. , Feeney Yvonne B. , Clevenger Charles V.
Published: April 2023

Immunohistochemistry of CypA+/+ x erbB2 and CypA-/- x erbB2
Table S3 from Reduced Expression of PROX1 Transitions Glioblastoma Cells into a Mesenchymal Gene Expression Subtype
Authors: Goudarzi Kaveh M. , Espinoza Jaime A. , Guo Min , Bartek Jiri , Nistér Monica , Lindström Mikael S. , Hägerstrand Daniel
Published: April 2023

GSEA for PROX1 correlated genes in glioblastoma cell lines
Supplementary Methodology from Paclitaxel Reduces Tumor Growth by Reprogramming Tumor-Associated Macrophages to an M1 Profile in a TLR4-Dependent Manner
Authors: Wanderley Carlos W. , Colón David F. , Luiz João Paulo M. , Oliveira Francisco F. , Viacava Paula R. , Leite Caio A. , Pereira Janaina A. , Silva Camila M. , Silva Cassia R. , Silva Rangel L. , Speck-Hernandez Cesar A. , Mota José M. , Alves-Filho José C. , Lima-Junior Roberto C. , Cunha Thiago M. , Cunha Fernando Q.
Published: April 2023

Supplementary material and methods
Figure S3 from Paclitaxel Reduces Tumor Growth by Reprogramming Tumor-Associated Macrophages to an M1 Profile in a TLR4-Dependent Manner
Authors: Wanderley Carlos W. , Colón David F. , Luiz João Paulo M. , Oliveira Francisco F. , Viacava Paula R. , Leite Caio A. , Pereira Janaina A. , Silva Camila M. , Silva Cassia R. , Silva Rangel L. , Speck-Hernandez Cesar A. , Mota José M. , Alves-Filho José C. , Lima-Junior Roberto C. , Cunha Thiago M. , Cunha Fernando Q.
Published: April 2023

PCX blocks the M2 macrophage polarization induced by IL-4
Figure S2 from Paclitaxel Reduces Tumor Growth by Reprogramming Tumor-Associated Macrophages to an M1 Profile in a TLR4-Dependent Manner
Authors: Wanderley Carlos W. , Colón David F. , Luiz João Paulo M. , Oliveira Francisco F. , Viacava Paula R. , Leite Caio A. , Pereira Janaina A. , Silva Camila M. , Silva Cassia R. , Silva Rangel L. , Speck-Hernandez Cesar A. , Mota José M. , Alves-Filho José C. , Lima-Junior Roberto C. , Cunha Thiago M. , Cunha Fernando Q.
Published: April 2023

Macrophages are resistant to cytotoxic effect of PCX
Table S4 from Loss of Pax5 Exploits Sca1-BCR-ABLp190 Susceptibility to Confer the Metabolic Shift Essential for pB-ALL
Authors: Martín-Lorenzo Alberto , Auer Franziska , Chan Lai N. , García-Ramírez Idoia , González-Herrero Inés , Rodríguez-Hernández Guillermo , Bartenhagen Christoph , Dugas Martin , Gombert Michael , Ginzel Sebastian , Blanco Oscar , Orfao Alberto , Alonso-López Diego , Rivas Javier De Las , García-Cenador Maria B. , García-Criado Francisco J. , Müschen Markus , Sánchez-García Isidro , Borkhardt Arndt , Vicente-Dueñas Carolina , Hauer Julia
Published: April 2023

Differentially expressed genes in bone marrow tumors from Sca1-BCR-ABLp190+Pax5+/- mice compared to wild-type B220+ bone marrow B cells. (17032 genes-probesets with FDR = 0.05)
Supplementary Tables S1 and S2 from Neonatal Inflammatory Markers Are Associated with Childhood B-cell Precursor Acute Lymphoblastic Leukemia
Authors: Søegaard Signe Holst , Rostgaard Klaus , Skogstrand Kristin , Wiemels Joseph Leo , Schmiegelow Kjeld , Hjalgrim Henrik
Published: April 2023

ICD-10 codes for infections and ATC codes for antimicrobials.
Supplementary Table S5 from Neonatal Inflammatory Markers Are Associated with Childhood B-cell Precursor Acute Lymphoblastic Leukemia
Authors: Søegaard Signe Holst , Rostgaard Klaus , Skogstrand Kristin , Wiemels Joseph Leo , Schmiegelow Kjeld , Hjalgrim Henrik
Published: April 2023

Variation in associations between prenatally initiated karyotypes and other kayotypes.
Tables S1 and S2 from YAP/TAZ Initiates Gastric Tumorigenesis via Upregulation of MYC
Authors: Choi Wonyoung , Kim Jeongsik , Park Jaeoh , Lee Da-Hye , Hwang Daehee , Kim Jeong-Hwan , Ashktorab Hassan , Smoot Duane , Kim Seon-Young , Choi Chan , Koh Gou Young , Lim Dae-Sik
Published: April 2023

Table S1. Pathologic diagnoses of Lats1/2iÎ"Lgr5 mice. Table S2. GSEA results for C6 Oncogenic Signatures in GSE62254 (MSS/EMT vs REST).
Fig, S7 from RIPK1 Binds MCU to Mediate Induction of Mitochondrial Ca2+ Uptake and Promotes Colorectal Oncogenesis
Authors: Zeng Fanxin , Chen Xiao , Cui Weiyi , Wen Wei , Lu Fujian , Sun Xueting , Ma Dongwei , Yuan Ye , Li Zezhong , Hou Ning , Zhao Hong , Bi Xinyu , Zhao Jianjun , Zhou Jianguo , Zhang Yan , Xiao Rui-Ping , Cai Jianqiang , Zhang Xiuqin
Published: April 2023

Figure S7. RIPK1 Ubiquitination Site Mutation does not Change the Mitochondrial Location of RIPK1. (A) Representative photomicrographs in HT29 transfected with Mito-DsRed and RIPK1-K377R-GFP. Scale bar: 5Î¼m.
Suplementary Figures with legends from Tumor-Derived TGFβ Alters the Ability of Plasmacytoid Dendritic Cells to Respond to Innate Immune Signaling
Authors: Terra Mariana , Oberkampf Marine , Fayolle Catherine , Rosenbaum Pierre , Guillerey Camille , Dadaglio Gilles , Leclerc Claude
Published: April 2023

Supplementary Figures S1 through S9. (1) Supplementary Figure S1: Phenotypical characterization of pDCs in the spleen of TC-1 and B16-OVA tumor-bearing mice. (2) Supplementary Figure S2. Purification of pDCs and gene family analysis. (3) Supplementary Figure S3. pDCs infiltrating TC-1 and B16-OVA tumors exhibit a distinct transcriptomic profile. (4) Supplementary Figure S4. Purified TA-pDCs produce cytokines and chemokines following CpG-stimulation. (5) Supplementary Figure S5. B16-OVA TCM contain TGF-β and inhibit pDC activation following CpG-stimulation. (6) Supplementary Figure S6. Lack of reversibility of the TCM inhibitory effect on pDC activation following CpG-stimulation. (7) Supplementary Figure S7. TCM from pDCs deficient mice contain TGF-β and inhibit pDC activation following CpG-stimulation. (8) Supplementary Figure S8. Depletion of NK cells by NK1.1 antibody treatment and representation of NK cell subsets in the spleen of tumor-bearing mice. (9) Supplementary Figure S9. Effect of anti-TGF-β antibody treatment on the growth of TC-1 tumor.
Figure S4 from Zika Virus Selectively Kills Aggressive Human Embryonal CNS Tumor Cells In Vitro and In Vivo
Authors: Kaid Carolini , Goulart Ernesto , Caires-Júnior Luiz C. , Araujo Bruno H.S. , Soares-Schanoski Alessandra , Bueno Heloisa M.S. , Telles-Silva Kayque A. , Astray Renato M. , Assoni Amanda F. , Júnior Antônio F.R. , Ventini Daniella C. , Puglia Ana L.P. , Gomes Roselane P. , Zatz Mayana , Okamoto Oswaldo K.
Published: April 2023

Characterization of the orthotopic metastatic model of ATRT with the USP7-ATRT cell line.
Supplementary Data from Astrocyte Elevated Gene-1 Regulates Macrophage Activation in Hepatocellular Carcinogenesis
Authors: Robertson Chadia L. , Mendoza Rachel G. , Jariwala Nidhi , Dozmorov Mikhail , Mukhopadhyay Nitai D. , Subler Mark A. , Windle Jolene J. , Lai Zhao , Fisher Paul B. , Ghosh Shobha , Sarkar Devanand
Published: April 2023

This file contains supplementary tables showing Bayesian analysis data.
Figure S2 from Zika Virus Selectively Kills Aggressive Human Embryonal CNS Tumor Cells In Vitro and In Vivo
Authors: Kaid Carolini , Goulart Ernesto , Caires-Júnior Luiz C. , Araujo Bruno H.S. , Soares-Schanoski Alessandra , Bueno Heloisa M.S. , Telles-Silva Kayque A. , Astray Renato M. , Assoni Amanda F. , Júnior Antônio F.R. , Ventini Daniella C. , Puglia Ana L.P. , Gomes Roselane P. , Zatz Mayana , Okamoto Oswaldo K.
Published: April 2023

Characterization of hiPSC and respective hiPSC-derived NPCs and neurons.
Aleksic_Supplementary Table S5 from Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage
Authors: Aleksic Tamara , Gray Nicki , Wu Xiaoning , Rieunier Guillaume , Osher Eliot , Mills Jack , Verrill Clare , Bryant Richard J. , Han Cheng , Hutchinson Kathryn , Lambert Adam G. , Kumar Rajeev , Hamdy Freddie C. , Weyer-Czernilofsky Ulrike , Sanderson Michael P. , Bogenrieder Thomas , Taylor Stephen , Macaulay Valentine M.
Published: April 2023

Table S5 Genomic locations of IGF-1R binding in DU145 prostate cancer cells.
Supplementary table 8-14 from Patient-Derived Xenograft Models Reveal Intratumor Heterogeneity and Temporal Stability in Neuroblastoma
Authors: Braekeveldt Noémie , von Stedingk Kristoffer , Fransson Susanne , Martinez-Monleon Angela , Lindgren David , Axelson Håkan , Levander Fredrik , Willforss Jakob , Hansson Karin , Øra Ingrid , Backman Torbjörn , Börjesson Anna , Beckman Siv , Esfandyari Javanshir , Berbegall Ana P. , Noguera Rosa , Karlsson Jenny , Koster Jan , Martinsson Tommy , Gisselsson David , Påhlman Sven , Bexell Daniel
Published: April 2023

Supplementary Table S8. Related to Figure 5. List of top varying peptides based on SD across all samples derived from Patient/PDOX #5. Supplementary Table S9. Related to Figure 5. List of top varying phospho-peptides based on SD across all samples derived from Patient/PDOX #5. Supplementary Table S10. Related to Figure 5. List of enriched Gene Ontology terms by cluster derived from the protein clusters defined in Suppl. Table S8. Supplementary Table S11. Related to Figure 5. List of enriched Gene Ontology terms by cluster derived from the phospho-protein clusters defined in Suppl. Table S9. Supplementary Table S12. Related to Figure 5. List of differentially expressed proteins from group 1-3 of PDOX #5. Supplementary Table S13. Related to Figure 5. List of differentially expressed phosphorylated proteins from group 1-3 of PDOX #5. Supplementary Table S14. Related to Figure 5. List of peptides measured in the targeted PRM assay.
Supplementary table 6-7 from Patient-Derived Xenograft Models Reveal Intratumor Heterogeneity and Temporal Stability in Neuroblastoma
Authors: Braekeveldt Noémie , von Stedingk Kristoffer , Fransson Susanne , Martinez-Monleon Angela , Lindgren David , Axelson Håkan , Levander Fredrik , Willforss Jakob , Hansson Karin , Øra Ingrid , Backman Torbjörn , Börjesson Anna , Beckman Siv , Esfandyari Javanshir , Berbegall Ana P. , Noguera Rosa , Karlsson Jenny , Koster Jan , Martinsson Tommy , Gisselsson David , Påhlman Sven , Bexell Daniel
Published: April 2023

Supplementary Table S6. Related to Figure 4. Top 1000 varying genes based on SD across all samples derived from Patient/PDOX #5. Supplementary Table S7. Related to Figure 4. List of enriched Gene Ontology terms by cluster derived from the gene clusters defined in Suppl. Table S6.
Supplementary Figure 8 from CRISPR/Cas9-Mediated Knockout of DGK Improves Antitumor Activities of Human T Cells
Authors: Jung In-Young , Kim Yoon-Young , Yu Ho-Sung , Lee Myoungsoo , Kim Seokjoong , Lee Jungmin
Published: April 2023

CRISPR/Cas9-mediated DGK KO improves tumor control in mouse model where PD-1 KO fails to invigorate anti-tumor activity.
Supplementary table 1-2 from Patient-Derived Xenograft Models Reveal Intratumor Heterogeneity and Temporal Stability in Neuroblastoma
Authors: Braekeveldt Noémie , von Stedingk Kristoffer , Fransson Susanne , Martinez-Monleon Angela , Lindgren David , Axelson Håkan , Levander Fredrik , Willforss Jakob , Hansson Karin , Øra Ingrid , Backman Torbjörn , Börjesson Anna , Beckman Siv , Esfandyari Javanshir , Berbegall Ana P. , Noguera Rosa , Karlsson Jenny , Koster Jan , Martinsson Tommy , Gisselsson David , Påhlman Sven , Bexell Daniel
Published: April 2023

Supplementary Table S1. Related to Figure 1. List of all somatic mutations detected in patient tumors, and in PDOXs from low and high in vivo generations. Supplementary Table S2. Related to Figure 2. List of all chromosomal copy number changes in patient tumors, and in PDOXs from low and high in vivo generations.
Supplementary Figure 3 from CRISPR/Cas9-Mediated Knockout of DGK Improves Antitumor Activities of Human T Cells
Authors: Jung In-Young , Kim Yoon-Young , Yu Ho-Sung , Lee Myoungsoo , Kim Seokjoong , Lee Jungmin
Published: April 2023

Analysis of potential off-target sites identified in silico.
Figure S7 from Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes
Authors: Bu Wen , Liu Zhenyu , Jiang Weiyu , Nagi Chandandeep , Huang Shixia , Edwards Dean P. , Jo Eunji , Mo Qianxing , Creighton Chad J. , Hilsenbeck Susan G. , Leavitt Andrew D. , Lewis Michael T. , Wong Stephen T. C. , Li Yi
Published: April 2023

The gene expression of RAS family and Vimentin.
Table S1 from Transcriptomic Differences between Primary Colorectal Adenocarcinomas and Distant Metastases Reveal Metastatic Colorectal Cancer Subtypes
Authors: Kamal Yasmin , Schmit Stephanie L. , Hoehn Hannah J. , Amos Christopher I. , Frost H. Robert
Published: April 2023

Table S1. Genes removed from the tissue sensitive analysis. All genes with a tissue specific weight for either colon, rectum, lung, or liver, of >2 were removed.
Figure S1 from Mammary Precancerous Stem and Non-Stem Cells Evolve into Cancers of Distinct Subtypes
Authors: Bu Wen , Liu Zhenyu , Jiang Weiyu , Nagi Chandandeep , Huang Shixia , Edwards Dean P. , Jo Eunji , Mo Qianxing , Creighton Chad J. , Hilsenbeck Susan G. , Leavitt Andrew D. , Lewis Michael T. , Wong Stephen T. C. , Li Yi
Published: April 2023

MMTV-Wnt1 precancerous glands contain WAP+ cells.
Figures S1-S5 from Ribosomal Lesions Promote Oncogenic Mutagenesis
Authors: Sulima Sergey O. , Kampen Kim R. , Vereecke Stijn , Pepe Daniele , Fancello Laura , Verbeeck Jelle , Dinman Jonathan D. , De Keersmaecker Kim
Published: April 2023

This file contains 5 supplementary figures containing key data that could not be fitted in the main figures.
Supplementary materials and methods from Single-Cell Analysis Reveals a Preexisting Drug-Resistant Subpopulation in the Luminal Breast Cancer Subtype
Authors: Prieto-Vila Marta , Usuba Wataru , Takahashi Ryou-u , Shimomura Iwao , Sasaki Hideo , Ochiya Takahiro , Yamamoto Yusuke
Published: April 2023

Supplementary materials and methods
Supplementary Figure S1-9 from ROCK Inhibition Induces Terminal Adipocyte Differentiation and Suppresses Tumorigenesis in Chemoresistant Osteosarcoma Cells
Authors: Takahashi Nobuhiro , Nobusue Hiroyuki , Shimizu Takatsune , Sugihara Eiji , Yamaguchi-Iwai Sayaka , Onishi Nobuyuki , Kunitomi Haruko , Kuroda Tatsuo , Saya Hideyuki
Published: April 2023

Supplementary Fig. S1 Differentiation potential of AO and AX cells. Supplementary Fig. S2 High Intrinsic efflux capacity contributes to the chemoresistance of AO cells. Fig. S3 Immunofluorescence microscopy of FABP4 and PLIN1 expression in heterogeneous osteosarcoma cells. Supplementary Fig. S4 Effect of doxorubicin on the expression of PPARG, a master regulator of adipogenesis, in human osteosarcoma cell lines. Supplementary Fig. S5 AO-like cells expressing PPARG are present in human recurrent osteosarcoma tissue but not in parosteal osteosarcoma tissue. Supplementary Fig. S6 Treatment with fasudil alone induces terminal adipocyte differentiation in AO cells but not in AX cells. Supplementary Fig. S7 Effect of fasudil treatment on terminal adipocyte differentiation in AO cells. Supplementary Fig. S8 Treatment with fasudil alone induces growth suppression in human osteosarcoma cell lines. Supplementary Fig. S9 Effects of doxorubicin or fasudil treatment in AOT cells which have lost their adipogenic potential in AO cells.
Supplementary Data File 6 from Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
Authors: Mer Arvind S. , Ba-Alawi Wail , Smirnov Petr , Wang Yi X. , Brew Ben , Ortmann Janosch , Tsao Ming-Sound , Cescon David W. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Association between drug class and pathways in PDXs. Drugs have been classified into categories according to their known target and association is computed using gene set enrichment analysis.
Figure S4 from CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms
Authors: Castillo Joseph , Wu Esther , Lowe Christopher , Srinivasan Shrividhya , McCord Ron , Wagle Marie-Claire , Jayakar Sangeeta , Edick Melissa Gonzalez , Eastham-Anderson Jeffrey , Liu Bonnie , Hutchinson Katherine E. , Jones Wendell , Stokes Matthew P. , Tarighat Somayeh S. , Holcomb Thomas , Glibicky Andrew , Romero F. Anthony , Magnuson Steven , Huang Shih-Min A. , Plaks Vicki , Giltnane Jennifer M. , Lackner Mark R. , Mounir Zineb
Published: April 2023

Supplementary figure 4 shows additional mass spectrometry analyses of CBP/p300 histone substrates along with prostacyclin measurement across cell types (naïve T cell and Treg) following treatment with CBP/p300 inhibitor GNE-781.
Supplementary Figure 7 from Loss of the BCR-FGFR1 GEF Domain Suppresses RHOA Activation and Enhances B-Lymphomagenesis in Mice
Authors: Hu Tianxiang , Chong Yating , Lu Sumin , Qin Haiyan , Ren Mingqiang , Savage Natasha M. , Chang Chang-Sheng , Cowell John K
Published: April 2023

Engraftment of BBC2 cells in which RhoA is knocked down leads to splenomegaly (A) and increased lymph node size.
Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S7, Table S1, Table S2, Table S3, Table S4 from Single-Cell Transcriptome Analyses Reveal Endothelial Cell Heterogeneity in Tumors and Changes following Antiangiogenic Treatment
Authors: Zhao Qi , Eichten Alexandra , Parveen Asma , Adler Christina , Huang Ying , Wang Wei , Ding Yueming , Adler Alexander , Nevins Thomas , Ni Min , Wei Yi , Thurston Gavin
Published: April 2023

Figure S1, Heart endothelial cell subpopulations. Figure S2, Expression of selected genes that could distinguish EC subpopulations in heart. Figure S3, Composition of COLO205 tumor stromal cells. Figure S4, Subpopulations of tumor endothelial cells. Figure S5, Gene ontology annotation and pathway enrichment analyses on differentially. expressed genes between anti-angiogenic drug vs. hFc treatment in tip-like cells. Figure S6, Subpopulations in COLO205-derived TAFs. Figure S7, Subpopulations in heart-derived stromal fibroblasts. Table S1, Top 90 genes by ANOVA test p value that have distinctive expression pattern among heart endothelial cell subpopulations. Table S2, Top 30 genes that have distinctive expression pattern in heart EC subpopulations. Table S3, Comparison between overlapping endothelial subpopulation markers identified in heart and tumor tissue. Table S4, Changes of tumor endothelial cells expressing cell cycle genes following anti-angiogenic treatment.
Supplementary Data Combined from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: April 2023

All supplementary data in one file
Supplementary Data from Targeting BCR-ABL1 in Chronic Myeloid Leukemia by PROTAC-Mediated Targeted Protein Degradation
Authors: Burslem George M. , Schultz Anna Reister , Bondeson Daniel P. , Eide Christopher A. , Savage Stevens Samantha L. , Druker Brian J. , Crews Craig M.
Published: April 2023

Table S1 - Reverse phase protein array data for K562 cells treated with GMB-475 or GMB-651.
Supplementary Data from Targeting BCR-ABL1 in Chronic Myeloid Leukemia by PROTAC-Mediated Targeted Protein Degradation
Authors: Burslem George M. , Schultz Anna Reister , Bondeson Daniel P. , Eide Christopher A. , Savage Stevens Samantha L. , Druker Brian J. , Crews Craig M.
Published: April 2023

Supplemental Figures and Tables. Figure S1 - Immunoblotting characterization of GMB-101 and GMB-475. Figure S2 - Validation of degradation and compound toxicity via comparison of GMB-475 and GMB-651. Figure S3 - Combinations of ATP competitive TKIs with PROTAC. Figure S4 - Schematic of scaffolding roles, VHL ligand and imatinib controls for VHL and pGAB2. Figure S5 - Patient sample sorting workflow and additional patient samples. Table S2 - Patient characteristics for primary samples
Figure S4 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: April 2023

Pegvorhyaluronidase alfa increased density of T-cells and NK cells and decreased the proportion of Gr1+ myeloid-derived suppressor cells in 4T1/HAS3 orthotopic breast tumors
Figure S3 from Remodeling the Tumor Microenvironment Sensitizes Breast Tumors to Anti-Programmed Death-Ligand 1 Immunotherapy
Authors: Clift Renee , Souratha Jennifer , Garrovillo Sheryl A. , Zimmerman Susan , Blouw Barbara
Published: April 2023

Pegvorhyaluronidase alfa increased density of T-cells and NK cells and decreased the proportion of Gr1+ myeloid-derived suppressor cells in 4T1/HAS3 orthotopic breast tumors
Table S1 from MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma
Authors: Hüllein Jennifer , Słabicki Mikołaj , Rosolowski Maciej , Jethwa Alexander , Habringer Stefan , Tomska Katarzyna , Kurilov Roma , Lu Junyan , Scheinost Sebastian , Wagener Rabea , Huang Zhiqin , Lukas Marina , Yavorska Olena , Helfrich Hanne , Scholtysik René , Bonneau Kyle , Tedesco Donato , Küppers Ralf , Klapper Wolfram , Pott Christiane , Stilgenbauer Stephan , Burkhardt Birgit , Löffler Markus , Trümper Lorenz H. , Hummel Michael , Brors Benedikt , Zapatka Marc , Siebert Reiner , Kreuz Markus , Keller Ulrich , Huber Wolfgang , Zenz Thorsten
Published: April 2023

Generanks for differential shRNA effects from GENE-E class comparison analysis
Supplementary Data from Positron Emission Tomography Detects In Vivo Expression of Disialoganglioside GD2 in Mouse Models of Primary and Metastatic Osteosarcoma
Authors: Butch Elizabeth R. , Mead Paul E. , Amador Diaz Victor , Tillman Heather , Stewart Elizabeth , Mishra Jitendra K. , Kim Jieun , Bahrami Armita , Dearling Jason L.J. , Packard Alan B. , Stoddard Shana V. , Vāvere Amy L. , Han Yuanyuan , Shulkin Barry L. , Snyder Scott E.
Published: April 2023

Combined Supplementary Data file containing: Figure S1-Detailed ex vivo biodistribution data for three additional PDX tumors. Only summary data included in the manuscript Table 1. Figure S2-Multimodality imaging protocol. Figure S3-Ex vivo biodistribution of 64Cu-Bn-NOTA-hu14.18K322A in mice with and without co-injection of a therapeutic dose of unmodified hu14.18K322A to verify non-target binding. Table S1-Summary of multi-modality imaging results for all 8 animals in the osteosarcoma lung metastasis model.
Supplementary Figures with Figure legends from PIN1 Maintains Redox Balance via the c-Myc/NRF2 Axis to Counteract Kras-Induced Mitochondrial Respiratory Injury in Pancreatic Cancer Cells
Authors: Liang Chen , Shi Si , Liu Mingyang , Qin Yi , Meng Qingcai , Hua Jie , Ji Shunrong , Zhang Yuqing , Yang Jingxuan , Xu Jin , Ni Quanxing , Li Min , Yu Xianjun
Published: April 2023

Supplementary Figure 1 showed PIN1 promotes the growth of pancreatic cancer cells in vitro. Supplementary Figure 2 showed PIN1 affects the expression of the expression of mitochondrial proteins. Supplementary Figure 3 showed Immunoblot analysis of anti-oxidative genes expression in pancreatic cancer cells with silencing of PIN1 expression. Supplementary Figure 4 showed c-Myc is involved in PIN1-induced malignant potential. Supplementary Figure 5 showed the percentage of NRF2-positive cells with different grades of PIN1 expression in the PDAC tissue microarray.
Video S2 from Stathmin Is Required for Normal Mouse Mammary Gland Development and Δ16HER2-Driven Tumorigenesis
Authors: Segatto Ilenia , Zompit Mara De Marco , Citron Francesca , D'Andrea Sara , Vinciguerra Gian Luca Rampioni , Perin Tiziana , Berton Stefania , Mungo Giorgia , Schiappacassi Monica , Marchini Cristina , Amici Augusto , Vecchione Andrea , Baldassarre Gustavo , Belletti Barbara
Published: April 2023

NMuMG shSTM cells