bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 3 from ATR Is a Therapeutic Target in Synovial Sarcoma
Authors: Jones Samuel E. , Fleuren Emmy D.G. , Frankum Jessica , Konde Asha , Williamson Chris T. , Krastev Dragomir B. , Pemberton Helen N. , Campbell James , Gulati Aditi , Elliott Richard , Menon Malini , Selfe Joanna L. , Brough Rachel , Pettitt Stephen J. , Niedzwiedz Wojciech , van der Graaf Winette T.A. , Shipley Janet , Ashworth Alan , Lord Christopher J.
Published: April 2023

This file contains the details of all the primary and secondary antibodies used in this paper.
Supplementary Materials and Methods from The Natural Diterpenoid Isoforretin A Inhibits Thioredoxin-1 and Triggers Potent ROS-Mediated Antitumor Effects
Authors: Sun Xiaoyan , Wang Weiguang , Chen Jiao , Cai Xueting , Yang Jie , Yang Yang , Yan Huaijiang , Cheng Xiaolan , Ye Juan , Lu Wuguang , Hu Chunping , Sun Handong , Pu Jianxin , Cao Peng
Published: April 2023

This doctment contains supplementary methods and results of the following contents: Firstly, the isolation and conformational analysis of IsoA. Secondly, IsoA inhibited the cologenic formation in a panel of cell lines. Thirdly, IsoA induced ROS in HepG2 cells, and mitochondria should not be the main contribution to IsoA-induced ROS generation. Fourthly, IsoA showed little inhibitory effects on a series of thiol-containing enzymes, including TrxR, PDI, GR, and GST. Fifthly, we showed that Trx1 was overexpressed in cancer cells in parallel with the normal cells lines, and we found that IsoA activated ASK1/JNK signaling pathway. Finally, treatment with IsoA (15 mg/kg/day) displays no obvious toxicity to main organs (liver, kidney, and spleen) in mice by H&E staining.
Figure S4 from Cathepsin B Is Dispensable for Cellular Processing of Cathepsin B-Cleavable Antibody–Drug Conjugates
Authors: Caculitan Niña G. , dela Cruz Chuh Josefa , Ma Yong , Zhang Donglu , Kozak Katherine R. , Liu Yichin , Pillow Thomas H. , Sadowsky Jack , Cheung Tommy K. , Phung Qui , Haley Benjamin , Lee Byoung-Chul , Akita Robert W. , Sliwkowski Mark X. , Polson Andrew G.
Published: April 2023

Supplementary Figure 4: Relative quantitation via mass spectrometry of cathepsin distribution in lysosomal fractions of various cell lines. Methods are detailed under "Isolation of lysosomes and proteomic analysis" in Supplementary Methods.
Table S2 from Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation
Authors: Malakar Pushkar , Shilo Asaf , Mogilevsky Adi , Stein Ilan , Pikarsky Eli , Nevo Yuval , Benyamini Hadar , Elgavish Sharona , Zong Xinying , Prasanth Kannanganattu V. , Karni Rotem
Published: April 2023

Table S2. Full list of Up- and Down regulated genes in the RNA seq analysis
Figure S1 from miR-590-3p Promotes Ovarian Cancer Growth and Metastasis via a Novel FOXA2–Versican Pathway
Authors: Salem Mohamed , O'Brien Jacob A. , Bernaudo Stefanie , Shawer Heba , Ye Gang , Brkić Jelena , Amleh Asma , Vanderhyden Barbara C. , Refky Basel , Yang Burton B. , Krylov Sergey N. , Peng Chun
Published: April 2023

miR-590-3p promotes cell proliferation, migration, and invasion in multiple EOC cell lines.
Figure S5 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

PTPN12 regulates ABL1 phosphorylation.
Figure S4 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

PTPN12 binds tyrosine-phosphorylated ABL1 independent of PSTPIP1 and PSTPIP2.
Supplemental Fig. Legends from Familial and Somatic BAP1 Mutations Inactivate ASXL1/2-Mediated Allosteric Regulation of BAP1 Deubiquitinase by Targeting Multiple Independent Domains
Authors: Peng Hongzhuang , Prokop Jeremy , Karar Jayashree , Park Kyewon , Cao Li , Harbour J. William , Bowcock Anne M. , Malkowicz S. Bruce , Cheung Mitchell , Testa Joseph R. , Rauscher Frank J.
Published: April 2023

Supplemental figure legends
Figure S3 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

Profile of PTP substrate-trapping mutants in HEK293 cells.
Supplemental Fig. 2 from Familial and Somatic BAP1 Mutations Inactivate ASXL1/2-Mediated Allosteric Regulation of BAP1 Deubiquitinase by Targeting Multiple Independent Domains
Authors: Peng Hongzhuang , Prokop Jeremy , Karar Jayashree , Park Kyewon , Cao Li , Harbour J. William , Bowcock Anne M. , Malkowicz S. Bruce , Cheung Mitchell , Testa Joseph R. , Rauscher Frank J.
Published: April 2023

BAP1-UCH, BAP1-ULD, and ASXL2-AB form a ternary stable protein complex in vitro. Gel filtration analysis of highly purified recombinant BAP1-UCH, BAP1-ULD and ASXL2-AB, and a pre-formed UCH-ULD-AB complex. The proteins were resolved on a Superdex 200 column. The fractions were collected, and the proteins were analyzed by NuPAGE. The fraction numbers are labeled at the top of the figure. The migration of protein standards is indicated above the gels. The protein standards were in a parallel gel filtration experiment under identical conditions: (I) the elution profile of for a pre-formed UCH-ULD-AB complex; (II) the elution profile of UCH; (III) the elution profile of the AB box; and (IV) the elution profile of ULD.
Figure S6 from Syntaphilin Ubiquitination Regulates Mitochondrial Dynamics and Tumor Cell Movements
Authors: Seo Jae Ho , Agarwal Ekta , Bryant Kelly G. , Caino M. Cecilia , Kim Eui Tae , Kossenkov Andrew V. , Tang Hsin-Yao , Languino Lucia R. , Gabrilovich Dmitry I. , Cohen Andrew R. , Speicher David W. , Altieri Dario C.
Published: April 2023

Schematic model for SNPH regulation of mitochondrial trafficking in tumor cells
Figure S5 from Syntaphilin Ubiquitination Regulates Mitochondrial Dynamics and Tumor Cell Movements
Authors: Seo Jae Ho , Agarwal Ekta , Bryant Kelly G. , Caino M. Cecilia , Kim Eui Tae , Kossenkov Andrew V. , Tang Hsin-Yao , Languino Lucia R. , Gabrilovich Dmitry I. , Cohen Andrew R. , Speicher David W. , Altieri Dario C.
Published: April 2023

Requirement of Drp1 for mitochondrial trafficking
Supplemental Experimental procedures 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

In depth description of tissue arrays, cell lines, in-vitro cell culture on trabecular bone scaffolds, stroma-metastatic cell line organoid culture, histology, immunohistochemistry, immunocytochemistry, immunofluorescence, MTT assay, siRNA mediated knock down,primer design, semi quantitative PCR, qPCR, multispectral imaging and Two-dimensional RP/LC-MS
Supplementary Figure 6 from CDK1 Interacts with Sox2 and Promotes Tumor Initiation in Human Melanoma
Authors: Ravindran Menon Dinoop , Luo Yuchun , Arcaroli John J. , Liu Sucai , KrishnanKutty Lekha Nair , Osborne Douglas G. , Li Yang , Samson Jenny Mae , Bagby Stacey , Tan Aik-Choon , Robinson William A. , Messersmith Wells A. , Fujita Mayumi
Published: April 2023

Kaplan-Meier survival plots for CDK1 expression in melanoma, colon and pancreatic cancer patients. Related to Figure 7
Supplementary Figure 2 from CDK1 Interacts with Sox2 and Promotes Tumor Initiation in Human Melanoma
Authors: Ravindran Menon Dinoop , Luo Yuchun , Arcaroli John J. , Liu Sucai , KrishnanKutty Lekha Nair , Osborne Douglas G. , Li Yang , Samson Jenny Mae , Bagby Stacey , Tan Aik-Choon , Robinson William A. , Messersmith Wells A. , Fujita Mayumi
Published: April 2023

MHC I expression in human melanoma tumors and cell lines. Related to Figure 2
Supplementary figure 7 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

FACS Gating strategies to analyze tumor-infiltrating and lymph node cell suspensions
Supplementary Figure 1 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

Ex vivo tumor tissue explant culture system
Table S3 and S4 from Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC
Authors: Sun Haoyu , Xu Jing , Huang Qiang , Huang Mei , Li Kun , Qu Kun , Wen Hao , Lin Renyong , Zheng Meijuan , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: April 2023

Summary and details of HCC patients in cohort 1 and 2.
Table S2 from Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC
Authors: Sun Haoyu , Xu Jing , Huang Qiang , Huang Mei , Li Kun , Qu Kun , Wen Hao , Lin Renyong , Zheng Meijuan , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: April 2023

Univariate analysis of DFS and OS among patients with liver cancer according to clinical or immune parameters.
Figure S4 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

Figure S4. Gene expression profile analysis by GSEA and GO established the differential expression under circ-10720 overexpression. (A) GSEA plots for gene sets in PLC-PRF-5 cells overexpressing circ-10720 or control vectors. (B) Statistical analysis of up-regulated biological processes, molecular function, and cellular component of PLC-PRF-5 cells after circ-10720 overexpression. (C) Up-regulated genes associated with growth factor activity and wound healing in circ-10720 overexpressed PLC-PRF-5 cells were analyzed.
Figure S3 from Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC
Authors: Sun Haoyu , Xu Jing , Huang Qiang , Huang Mei , Li Kun , Qu Kun , Wen Hao , Lin Renyong , Zheng Meijuan , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: April 2023

Figure S3 shows (A) Cumulative percentage of IFN-γ on sorted CD160- or CD160+ NK cells of peripheral blood; (B) Scatterplot of global gene expression profiles of CD160+ and CD160- NK subsets; (C) Distribution by functional category of up- or down-regulated genes in CD160+ NK cells compared to CD160- NK cells; (D) Overview of functional pathway analysis; (E) Chemokine- or (F) cytokine- related profiles of CD160+ and CD160- NK cells; and (G) GSEA of genes up-regulated in CD160+ NK cells overlapping with gene sets from IL-2-stimulated NK cells, IL-15-stimulated NK cells and CD57- NK cells.
Figure S2 from Reduced CD160 Expression Contributes to Impaired NK-cell Function and Poor Clinical Outcomes in Patients with HCC
Authors: Sun Haoyu , Xu Jing , Huang Qiang , Huang Mei , Li Kun , Qu Kun , Wen Hao , Lin Renyong , Zheng Meijuan , Wei Haiming , Xiao Weihua , Sun Rui , Tian Zhigang , Sun Cheng
Published: April 2023

Figure S2 shows (A) Correlation between the percentage of CD160+ NK cells and the percentage of TIM3+, CD96+, NKG2A+, LAG3+, TIGIT+, or CD226+ NK cells in the tissue; and (B) Correlation between the percentage of CD160+ NK cells in the tissue and the intracellular IFN-γ, CD107a, granzyme B or perforin production.
Supplemental Figure 7 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

: Expression of CSC markers in multinucleated cells at protein and RNA levels.
Supplemental Figure 5 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

Expression of CSC markers and morphology of P1 oncogenerative and G1-Gn cells as detected by ICC and IHC.
Table S1 from Tethering IL2 to Its Receptor IL2Rβ Enhances Antitumor Activity and Expansion of Natural Killer NK92 Cells
Authors: Jounaidi Youssef , Cotten Joseph F. , Miller Keith W. , Forman Stuart A.
Published: April 2023

Primers used for Expression profiles of cytotoxicity effectors in NK92, NK92IL2 and NK92CIRB.
SV-5: P1 oncogenerative cells. Parturient events 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 formation of the crevices is observed with the subsequent detachment of G1-Gn cells from mother cytoplasm.
SV-1: P1 oncogenerative in parturient events 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

Oncogenerative P1 cells are giant cells with a syncytium-like morphology. This distinctive cell type complete cell life cycles which resemble lysogenic viral cycles. The mode of cellularization of the intracytoplasmically generated G1 cells (generation 1) is unique and takes place in different ways: a) in a lateral form which means that the G1 cells abandon the maternal P1 cells by trans cytoplasmic budding, b) through crevices formed with the participation of mitochondria around G1s until expulsion. After cellularization, the resulted aperture is filled by fusogenic HERV proteins, c) using a kind of funiculus or bridge connected to P1 maternal cells. An interesting process conducted by P1 cells is the horizontal transmission of G1 inoculating these cells into proximal receptor cells.
Figure S4 from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

PD-L1 Attenuates Anti-tumor effect of RORC in Bladder cancer
Figure S2 from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

RORC Regulates Proliferation and Apoptosis via inhibiting Glycolysis in Bladder Cancer Cells
Figure S1 from Retinoic Acid–Related Orphan Receptor C Regulates Proliferation, Glycolysis, and Chemoresistance via the PD-L1/ITGB6/STAT3 Signaling Axis in Bladder Cancer
Authors: Cao Dalong , Qi Zihao , Pang Yangyang , Li Haoran , Xie Huyang , Wu Junlong , Huang Yongqiang , Zhu Yao , Shen Yijun , Zhu Yiping , Dai Bo , Hu Xin , Ye Dingwei , Wang Ziliang
Published: April 2023

The associations between the expression of RORC and the survival of Bladder Urothelial Cancer Patients
Table S1 from CDK8 Selectively Promotes the Growth of Colon Cancer Metastases in the Liver by Regulating Gene Expression of TIMP3 and Matrix Metalloproteinases
Authors: Liang Jiaxin , Chen Mengqian , Hughes Daniel , Chumanevich Alexander A. , Altilia Serena , Kaza Vimala , Lim Chang-Uk , Kiaris Hippokratis , Mythreye Karthikeyan , Pena Maria Marjorette , Broude Eugenia V. , Roninson Igor B.
Published: April 2023

List of key resources and reagents
Figure S4 from CDK8 Selectively Promotes the Growth of Colon Cancer Metastases in the Liver by Regulating Gene Expression of TIMP3 and Matrix Metalloproteinases
Authors: Liang Jiaxin , Chen Mengqian , Hughes Daniel , Chumanevich Alexander A. , Altilia Serena , Kaza Vimala , Lim Chang-Uk , Kiaris Hippokratis , Mythreye Karthikeyan , Pena Maria Marjorette , Broude Eugenia V. , Roninson Igor B.
Published: April 2023

Supplemental data for SMAD4, CTNNB1 and STAT1 knockdown and microRNA analysis
Figure S3 from CDK8 Selectively Promotes the Growth of Colon Cancer Metastases in the Liver by Regulating Gene Expression of TIMP3 and Matrix Metalloproteinases
Authors: Liang Jiaxin , Chen Mengqian , Hughes Daniel , Chumanevich Alexander A. , Altilia Serena , Kaza Vimala , Lim Chang-Uk , Kiaris Hippokratis , Mythreye Karthikeyan , Pena Maria Marjorette , Broude Eugenia V. , Roninson Igor B.
Published: April 2023

TIMP3 and MMP3 immunofluorescence in hepatic metastases and analysis of MMP3 knockdown and TIMP3 overexpression.
Figure S2 from CDK8 Selectively Promotes the Growth of Colon Cancer Metastases in the Liver by Regulating Gene Expression of TIMP3 and Matrix Metalloproteinases
Authors: Liang Jiaxin , Chen Mengqian , Hughes Daniel , Chumanevich Alexander A. , Altilia Serena , Kaza Vimala , Lim Chang-Uk , Kiaris Hippokratis , Mythreye Karthikeyan , Pena Maria Marjorette , Broude Eugenia V. , Roninson Igor B.
Published: April 2023

Supplemental data for TIMP3 and MMPs expression analysis.
Supplementary Tables S1-S4 from Nuclear Receptor LRH-1 Functions to Promote Castration-Resistant Growth of Prostate Cancer via Its Promotion of Intratumoral Androgen Biosynthesis
Authors: Xiao Lijia , Wang Yuliang , Xu Kexin , Hu Hao , Xu Zhenyu , Wu Dinglan , Wang Zhu , You Wenxing , Ng Chi-Fai , Yu Shan , Chan Franky Leung
Published: April 2023

Supplementary Tables S1-S4
Video 1 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
Authors: Newton Yulia , Novak Adam M. , Swatloski Teresa , McColl Duncan C. , Chopra Sahil , Graim Kiley , Weinstein Alana S. , Baertsch Robert , Salama Sofie R. , Ellrott Kyle , Chopra Manu , Goldstein Theodore C. , Haussler David , Morozova Olena , Stuart Joshua M.
Published: April 2023

Video showing basic functionality of the TumorMap for the first-time user.
Table S4 from SWI/SNF-Compromised Cancers Are Susceptible to Bromodomain Inhibitors
Authors: Shorstova Tatiana , Marques Maud , Su Jie , Johnston Jake , Kleinman Claudia L. , Hamel Nancy , Huang Sidong , Alaoui-Jamali Moulay A. , Foulkes William D. , Witcher Michael
Published: April 2023

RNAseq data for SCCOHT1 and OVCAR8 cell lines
Supplemental Figure 5 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
Authors: Newton Yulia , Novak Adam M. , Swatloski Teresa , McColl Duncan C. , Chopra Sahil , Graim Kiley , Weinstein Alana S. , Baertsch Robert , Salama Sofie R. , Ellrott Kyle , Chopra Manu , Goldstein Theodore C. , Haussler David , Morozova Olena , Stuart Joshua M.
Published: April 2023

Supplemental Figure 5: (A) Overview of the method to compute differential expression for samples in the integrated pan-cancer group vs. other samples in the TCGA cohort. Tissue composition imbalance was corrected for by performing t-tests within each tissue. For each gene, t-statistics were computed within each tumor type separately and then summarized per-gene t-statistics were calculated as an arithmetic mean, weighted by the inverse variance of the all the tissue-specific t-statistics values. (B) The distribution of log-transformed TPM values estimated from the mRNA-Seq data showing a normal-like distribution. (C) Comparing the log-transformed TPM values of the mRNA-Seq data to a normal distribution shows a reasonable agreement with the tumor data having slightly heavier tails. (D) Venn diagram representing the innate and adaptive immune systems and different levels of evidence supporting higher activity of each of the components of those systems in the pan-cancer cluster when compared to the rest of the TCGA cohort. We found evidence of both innate and adaptive immune system signaling with a number of different analyses. (E) Detailed version of the immune-related pathway characterizing the integrated pan-cancer cluster. This version of the pathway shows additional genes and their connections that are not shown in the summarized version of the immune signaling pathway of Figure 1D of the main text.
Figure S2 from SWI/SNF-Compromised Cancers Are Susceptible to Bromodomain Inhibitors
Authors: Shorstova Tatiana , Marques Maud , Su Jie , Johnston Jake , Kleinman Claudia L. , Hamel Nancy , Huang Sidong , Alaoui-Jamali Moulay A. , Foulkes William D. , Witcher Michael
Published: April 2023

Response of sensitive and resistant cells to BETi
Supplemental Figure 1 from TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
Authors: Newton Yulia , Novak Adam M. , Swatloski Teresa , McColl Duncan C. , Chopra Sahil , Graim Kiley , Weinstein Alana S. , Baertsch Robert , Salama Sofie R. , Ellrott Kyle , Chopra Manu , Goldstein Theodore C. , Haussler David , Morozova Olena , Stuart Joshua M.
Published: April 2023

Supplemental Figure 1: RSS transformed correlations correct for platform-specific inflation biases. Maps produced from different molecular data types. Samples in the maps are colored by tissue of origin. (A) Similarity score distributions for every pair of samples for each individual data platform. Spearman Rho was computed for mRNA, miRNA, RPPA, SCNV, and methylation platforms. HOCUS score was used for mutation data. (B) RSS-standardized similarity scores for every pair of samples for each individual data platform. The density curves demonstrate that RSS transformation corrects for platform-specific inflation biases. (C) (i)-(vi) Maps produced from each of the six molecular data types using OpenOrd layout. (vii) mRNA expression map produced using Principal Component Analysis method. Principal components 1 and 2 are used to represent the mRNA expression space. (viii) mRNA expression map produced using tSNE method. Dimensions 1 and 2 are used to represent the mRNA expression space. (D) Maps produced from inferred gene activities using the PARADIGM and SPIA methods. (E) Maps integrating more than one molecular data type.
Supplementary Fig 1 from YAP Suppresses Lung Squamous Cell Carcinoma Progression via Deregulation of the DNp63–GPX2 Axis and ROS Accumulation
Authors: Huang Hsinyi , Zhang Wenjing , Pan Yafang , Gao Yijun , Deng Lei , Li Fuming , Li Fei , Ma Xueyan , Hou Shenda , Xu Jing , Li Peixue , Li Xiaoxun , Hu Guohong , Li Cheng , Chen Haiquan , Zhang Lei , Ji Hongbin
Published: April 2023

YAP activation inhibits SCC cell growth by disturbing ROS homeostasis.
Table S2 from Exosomes from Glioma-Associated Mesenchymal Stem Cells Increase the Tumorigenicity of Glioma Stem-like Cells via Transfer of miR-1587
Authors: Figueroa Javier , Phillips Lynette M. , Shahar Tal , Hossain Anwar , Gumin Joy , Kim Hoon , Bean Andrew J. , Calin George A. , Fueyo Juan , Walters Edgar T. , Kalluri Raghu , Verhaak Roel G. , Lang Frederick F.
Published: April 2023

MSC-derived exosomes contain highly expressed and highly enriched miRNA.
Figure S5 from KDM4 Inhibition Targets Breast Cancer Stem–like Cells
Authors: Metzger Eric , Stepputtis Stella S. , Strietz Juliane , Preca Bogdan-Tiberius , Urban Sylvia , Willmann Dominica , Allen Anita , Zenk Fides , Iovino Nicola , Bronsert Peter , Proske Amelie , Follo Marie , Boerries Melanie , Stickeler Elmar , Xu Jiangchun , Wallace Michael B. , Stafford Jeffrey A. , Kanouni Toufike , Maurer Jochen , Schüle Roland
Published: April 2023

H3K9me3 levels increase upon treatment with QC6352. Changes in H3K9me3 levels are depicted according to genomic location.
Figure S2 from Exosomes from Glioma-Associated Mesenchymal Stem Cells Increase the Tumorigenicity of Glioma Stem-like Cells via Transfer of miR-1587
Authors: Figueroa Javier , Phillips Lynette M. , Shahar Tal , Hossain Anwar , Gumin Joy , Kim Hoon , Bean Andrew J. , Calin George A. , Fueyo Juan , Walters Edgar T. , Kalluri Raghu , Verhaak Roel G. , Lang Frederick F.
Published: April 2023

GA-hMSC-derived exosomes increase GSC proliferation and clonogenicity.
Figure S2 from KDM4 Inhibition Targets Breast Cancer Stem–like Cells
Authors: Metzger Eric , Stepputtis Stella S. , Strietz Juliane , Preca Bogdan-Tiberius , Urban Sylvia , Willmann Dominica , Allen Anita , Zenk Fides , Iovino Nicola , Bronsert Peter , Proske Amelie , Follo Marie , Boerries Melanie , Stickeler Elmar , Xu Jiangchun , Wallace Michael B. , Stafford Jeffrey A. , Kanouni Toufike , Maurer Jochen , Schüle Roland
Published: April 2023

KDM4B, C, or D do not control proliferation and xenograft tumor growth of BCSC1.
Table S1 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

Table S1: Primers.
Supplementary Data from MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma
Authors: Kim Edward , Zucconi Beth E. , Wu Muzhou , Nocco Sarah E. , Meyers David J. , McGee Jean S. , Venkatesh Samantha , Cohen Daniel L. , Gonzalez Estela C. , Ryu Byungwoo , Cole Philip A. , Alani Rhoda M.
Published: April 2023

Figures S1-S5 and Table S1. Supplementary Figure S1. p300 depletion and phenotype analysis in melanoma cell lines. Supplementary Figure S2. Molecular pathways associated with p300 in melanoma. Supplementary Figure S3. MITF is essential for melanoma survival. Supplementary Figure S4. Characterization of p300/CBP HAT inhibitor A-485*. Supplementary Figure S5. Schematic procedure of A-485* synthesis. Table S1. ChIPâ€�PCR primer sequences for the characterization of MITF gene upstream regulatory region
Supplementary Data from MITF Expression Predicts Therapeutic Vulnerability to p300 Inhibition in Human Melanoma
Authors: Kim Edward , Zucconi Beth E. , Wu Muzhou , Nocco Sarah E. , Meyers David J. , McGee Jean S. , Venkatesh Samantha , Cohen Daniel L. , Gonzalez Estela C. , Ryu Byungwoo , Cole Philip A. , Alani Rhoda M.
Published: April 2023

Supplementary figure descriptions
SI legends from A Convolutional Neural Network Uses Microscopic Images to Differentiate between Mouse and Human Cell Lines and Their Radioresistant Clones
Authors: Toratani Masayasu , Konno Masamitsu , Asai Ayumu , Koseki Jun , Kawamoto Koichi , Tamari Keisuke , Li Zhihao , Sakai Daisuke , Kudo Toshihiro , Satoh Taroh , Sato Katsutoshi , Motooka Daisuke , Okuzaki Daisuke , Doki Yuichiro , Mori Masaki , Ogawa Kazuhiko , Ishii Hideshi
Published: April 2023

SI legends
Supplementary figure legends from Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer
Authors: D'Costa Zenobia , Jones Keaton , Azad Abul , van Stiphout Ruud , Lim Su Y. , Gomes Ana L. , Kinchesh Paul , Smart Sean C. , Gillies McKenna W. , Buffa Francesca M. , Sansom Owen J. , Muschel Ruth J. , O'Neill Eric , Fokas Emmanouil
Published: April 2023

Supplementary figure legends for Supplementary Figures 1 (Survival of PDAC cells in-vitro and in-vivo), 2 (ELISA, Western blot and Immunostaining), 3 (RTqPCR), 4 (Migration assay) and 5 (Flow cytometry).
Supplementary Figure 5 from Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer
Authors: D'Costa Zenobia , Jones Keaton , Azad Abul , van Stiphout Ruud , Lim Su Y. , Gomes Ana L. , Kinchesh Paul , Smart Sean C. , Gillies McKenna W. , Buffa Francesca M. , Sansom Owen J. , Muschel Ruth J. , O'Neill Eric , Fokas Emmanouil
Published: April 2023

Supplementary Figure describing the impact of TIMP-1 on immune cell populations in the in-vivo experiments.
Supplemental Figure (2) from Upregulation of Cystathionine-β-Synthase in Colonic Epithelia Reprograms Metabolism and Promotes Carcinogenesis
Authors: Phillips Ches'Nique M. , Zatarain John R. , Nicholls Michael E. , Porter Craig , Widen Steve G. , Thanki Ketan , Johnson Paul , Jawad Muhammad U. , Moyer Mary P. , Randall James W. , Hellmich Judith L. , Maskey Manjit , Qiu Suimin , Wood Thomas G. , Druzhyna Nadiya , Szczesny Bartosz , Módis Katalin , Szabo Csaba , Chao Celia , Hellmich Mark R.
Published: April 2023

Cysteine metabolites in NCM356 CBS cells.
Supplemental Figure (1) from Upregulation of Cystathionine-β-Synthase in Colonic Epithelia Reprograms Metabolism and Promotes Carcinogenesis
Authors: Phillips Ches'Nique M. , Zatarain John R. , Nicholls Michael E. , Porter Craig , Widen Steve G. , Thanki Ketan , Johnson Paul , Jawad Muhammad U. , Moyer Mary P. , Randall James W. , Hellmich Judith L. , Maskey Manjit , Qiu Suimin , Wood Thomas G. , Druzhyna Nadiya , Szczesny Bartosz , Módis Katalin , Szabo Csaba , Chao Celia , Hellmich Mark R.
Published: April 2023

Comparison of metabolite levels in CBS2 vs. vector control NCM356 cells.
Video 3 from Optical Coherence Tomography Detects Necrotic Regions and Volumetrically Quantifies Multicellular Tumor Spheroids
Authors: Huang Yongyang , Wang Shunqiang , Guo Qiongyu , Kessel Sarah , Rubinoff Ian , Chan Leo Li-Ying , Li Peter , Liu Yaling , Qiu Jean , Zhou Chao
Published: April 2023

Distribution of necrotic tissue in a HCT 116 tumor spheroid over time.
Supplementary Data from Combined c-Met/Trk Inhibition Overcomes Resistance to CDK4/6 Inhibitors in Glioblastoma
Authors: Olmez Inan , Zhang Ying , Manigat Laryssa , Benamar Mouadh , Brenneman Breanna , Nakano Ichiro , Godlewski Jakub , Bronisz Agnieszka , Lee Jeongwu , Abbas Tarek , Abounader Roger , Purow Benjamin
Published: April 2023

This file contains supplementary figures, primer sequences for PCR, and supplementary references
Figure S5 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. S5 (A) The quantified luminescence signals representing tumor volumes from mice bearing orthotopic H1299 tumor xenografts treated with saline (control), and SA (50 mg/kg, I.V.) every 3 days (n = 6/group). Treatments started 4 days after cell implantation. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in treated tumors were compared to the levels in untreated tumors with a Welch 2-sample t-test. The difference between control and SA was not statistically significant. (B) The sequences of Y. pestis HasA and HSPs. The changed amino acid residues are indicated. (C) HSP1 and HSP2 bind to heme beads. CA (carbonic anhydrase) serves as the negative control while BSA serves as the positive control. These were used and described previously by Lal et al, 2018, Nucleic Acids Res, 46: 215-228. (D) HSP2 remains in the medium even after prolonged incubation with NSCLC cells. H1299 NSCLC cells were incubated with 40 μM HSP2 in the medium for the indicated time periods. Then, the proteins in 5 μl medium was analyzed on SDS-PAGE gels. Medium and HSP2 are usually refreshed after 3 days. Shown in the same gel are samples from RPMI medium (RPMI), RPMI medium with HSP2, and RPMI medium + serum. (E) Quantified levels of HSP2 in the medium relative to the major serum protein albumin. For statistical analysis, the levels in 1-72 hours of incubation were compared to the levels in 0 hour of incubation with a Welch 2-sample t-test. The variations are not statistically significant. (F) The DIC and fluorescent images of cells incubated with ZnPP or ZnPP+HSP2. H1299 NSCLC cells were incubated with 40 μM ZnPP or 40 μM ZnPP+HSP2 for 12 hours. Cells were washed to reduce background fluorescence from the medium before imaging. DIC and fluorescent (from ZnPP) images of the cells were taken and shown here. ZnPP bound with HSP2 did not enter the cells. (G) ZnPP in the absence of HSP2 entered NSCLC cells and co-localized with mitotracker green.
Figure S4 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. S4. Proteins and enzymes relating to heme and mitochondrial functions are upregulated in human NSCLC tissues relative to control normal tissues. The examined proteins and enzymes include the rate-limiting heme synthetic enzyme ALAS1 (A), the heme transporter SLC48A1 (B), the hemoprotein OXPHOS subunit cytochrome c (CYCS) (C), hemoprotein PTGS2 (D), and the regulator promoting mitochondrial biogenesis TFAM (E). Shown are the representative Montages and 10X images of control and NSCLC tumor tissue sections stained with DAPI or antibodies against the indicated proteins. The yellow rectangles in Montages denote the regions shown in 10X images. Scale bar: montage, 1 mm; 10X, 20 μm. Protein levels were quantified with cellSens dimension software (Olympus). The values shown in the graphs are averages of signals quantified from six control and NSCLC independent tissue slides, respectively. Signals were calculated as described in Methods. Data are plotted as mean {plus minus} SD. For statistical analysis, the levels in treated tumors were compared to the levels in untreated tumors with a Welch 2-sample t-test. **, p-value < 0.005.
Figure S3 from Downregulation of Membrane Trafficking Proteins and Lactate Conditioning Determine Loss of Dendritic Cell Function in Lung Cancer
Authors: Caronni Nicoletta , Simoncello Francesca , Stafetta Francesca , Guarnaccia Corrado , Ruiz-Moreno Juan Sebastian , Opitz Bastian , Galli Thierry , Proux-Gillardeaux Veronique , Benvenuti Federica
Published: April 2023

Identification of lactic acid in the TCM, effect on DCs vitality and maturation
Figure S2 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. S2 The levels of heme in subcellular organelles in NSCLC cell lines. (A) Heme levels in cytoplasm. (B) Heme levels in nucleus. (C) Heme levels in endoplasmic reticulum. (D) Heme levels in Golgi. (E) Heme levels in plasma membrane. (F) The levels of OXPHOS complex subunit cytochrome c (CYCS) are elevated in NSCLC cells. (G) The levels of OXPHOS complex subunit COX4I1 are elevated in NSCLC cells. (H) The levels of heme-containing enzyme cyclooxygenase (PTGS2) 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 S4 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 GOrilla synergistic upregulated hits
Table S1 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 epigenetic genes and related shRNAs
Figure S2 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

Genome-wide B allele frequency (BAF) (ring 1) and predicted subclonal clusters (ring 2) as determined by the TITAN software program for A) Plexiform neurofibroma, B) Pre-Treatment, C) Post-Treatment D) Recurrent tumor samples.
Supplementary Text from Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures
Authors: Tasdemir Nilgun , Bossart Emily A. , Li Zheqi , Zhu Li , Sikora Matthew J. , Levine Kevin M. , Jacobsen Britta M. , Tseng George C. , Davidson Nancy E. , Oesterreich Steffi
Published: April 2023

Supplementary Text
Supplementary Table S3 from Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures
Authors: Tasdemir Nilgun , Bossart Emily A. , Li Zheqi , Zhu Li , Sikora Matthew J. , Levine Kevin M. , Jacobsen Britta M. , Tseng George C. , Davidson Nancy E. , Oesterreich Steffi
Published: April 2023

Lists of upregulated and downregulated pathways in ILC versus IDC cell lines.
Supplementary video 1 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

untreated GFP E2 cells in an ex vivo brain slice motility assay
Figure S1 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

Increased GBM cell invasion in vivo is confirmed by a human specific antibody against HLA and measurement of tumour volume by multi-slice T2 MR imaging
Figure S2 from TRPM2 Mediates Neutrophil Killing of Disseminated Tumor Cells
Authors: Gershkovitz Maya , Caspi Yaki , Fainsod-Levi Tanya , Katz Ben , Michaeli Janna , Khawaled Saleh , Lev Shaya , Polyansky Lola , Shaul Merav E. , Sionov Ronit V. , Cohen-Daniel Leonor , Aqeilan Rami I. , Shaul Yoav D. , Mori Yasuo , Karni Rotem , Fridlender Zvi G. , Binshtok Alexander M. , Granot Zvi
Published: April 2023

Supplemental Figure S2. TRPM2kd AT3 and LLC cells resistant to H2O2 and neutrophil cytotoxicity. A. Relative expression of TRPM2 in control TRPM2+ cells TRPM2kd AT3 and LLC cells. B. TRPM2kd AT3 and LLC cells are resistant to H2O2 cytotoxicity. C. TRPM2kd AT3 and LLC cells are resistant to neutrophil cytotoxicity. **p<0.01
Supplementary Material 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 material and methods, as well as the legends for Supplementary Figures 1-7.
Suppl Table 1 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

Suppl Table 1
Supplementary Figure S2 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 did not act through mechanisms previously described for other mTOR inhibitors.
Figure S1-S12 from Adoptive Immunotherapy Using PRAME-Specific T Cells in Medulloblastoma
Authors: Orlando Domenico , Miele Evelina , De Angelis Biagio , Guercio Marika , Boffa Iolanda , Sinibaldi Matilde , Po Agnese , Caruana Ignazio , Abballe Luana , Carai Andrea , Caruso Simona , Camera Antonio , Moseley Annemarie , Hagedoorn Renate S. , Heemskerk Mirjam H.M. , Giangaspero Felice , Mastronuzzi Angela , Ferretti Elisabetta , Locatelli Franco , Quintarelli Concetta
Published: April 2023

Supplemental Figures and Legends
Supplement Materials and Methods from Long Noncoding RNA CRYBG3 Blocks Cytokinesis by Directly Binding G-Actin
Authors: Pei Hailong , Hu Wentao , Guo Ziyang , Chen Huaiyuan , Ma Ji , Mao Weidong , Li Bingyan , Wang Aiqing , Wan Jianmei , Zhang Jian , Nie Jing , Zhou Guangming , Hei Tom K.
Published: April 2023

Supplement Materials and Methods
Supplement Figure Legend from Long Noncoding RNA CRYBG3 Blocks Cytokinesis by Directly Binding G-Actin
Authors: Pei Hailong , Hu Wentao , Guo Ziyang , Chen Huaiyuan , Ma Ji , Mao Weidong , Li Bingyan , Wang Aiqing , Wan Jianmei , Zhang Jian , Nie Jing , Zhou Guangming , Hei Tom K.
Published: April 2023

Supplement Figure Legends
Data Supplement 2 from Differential Burden of Rare and Common Variants on Tumor Characteristics, Survival, and Mode of Detection in Breast Cancer
Authors: Li Jingmei , Ugalde-Morales Emilio , Wen Wei Xiong , Decker Brennan , Eriksson Mikael , Torstensson Astrid , Christensen Helene Nordahl , Dunning Alison M. , Allen Jamie , Luccarini Craig , Pooley Karen A. , Simard Jacques , Dorling Leila , Easton Douglas F. , Teo Soo Hwang , Hall Per , Czene Kamila
Published: April 2023

Table S1 describes primer sequences and amplicon details. Table S2 summarizes percent callable bases and depth summary for the dataset. Table S3 lists the criteria for the hard filtering of variant calls. Table S4 shows a list of common variants used in the construction of the breast cancer polygenic risk scores. Table S5 shows a summary of 649 protein-truncating variants by gene in 597 unique samples. Table S6 tabulates protein-truncating variants and carrier counts.
Supplementary Table 1 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

Supplementary Table 1 showing additional FACS analysis results for Figure 7A of the manuscript, for review and publication
Supplementary Figure 9 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 relevant to Figure 6, showing ability of TI-derived monocytes to stimulate CD4 T cells in a culture assay, for review and publication
Data File S1 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

List of individual shRNA scores. File containing raw data of individual shRNAs quantified by barcode sequencing of DMSO- and HDM201- treated samples. Log fold changes of individual shRNAs compared to plasmid library and of HDM201-treated samples compared to DMSO-control are also listed.
Table S6 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 copy number variation of genes adjacent to CDK4 (AGAP2, MARCH9, TSPAN31) in samples with CDK4 amplification.
Table S5 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

Tables contain statistically significant associations between cluster activities and mutations or copy number variations in genes.
Table S1 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

Tables contain GEO sample accession numbers for reference cells, genes for which mutation and copy number variation data was downloaded and primer sequences used for qRT-PCR analysis.