bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This file contains all the methods and material information that cannot be included in the main text due to space limitation.
Table S6 from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

Supplemental Table S6. Hallmark gene sets up in ACT-treated HCmel3 melanomas (EDT, early during treatment) versus non-treated (NT) control HCmel3 melanomas (GSEA results).
Supplementary Fig. 5 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

This figure contains data that explains how ATRi-induced DNA damage is regulated by DNA replication. It is supplementary to the main figure 5.
Supplementary Fig. 3 from APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition
Authors: Buisson Rémi , Lawrence Michael S. , Benes Cyril H. , Zou Lee
Published: March 2023

A figure contains data showing the induction of DNA by ATRi in A3A expressing cells. It is supplementary to the main figure 3.
Legends to Suppl. Figures from MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy
Authors: Reinhardt Julia , Landsberg Jennifer , Schmid-Burgk Jonathan L. , Ramis Bartomeu Bibiloni , Bald Tobias , Glodde Nicole , Lopez-Ramos Dorys , Young Arabella , Ngiow Shin Foong , Nettersheim Daniel , Schorle Hubert , Quast Thomas , Kolanus Waldemar , Schadendorf Dirk , Long Georgina V. , Madore Jason , Scolyer Richard A. , Ribas Antoni , Smyth Mark J. , Tumeh Paul C. , Tüting Thomas , Hölzel Michael
Published: March 2023

Legends to Supplemental Figures 1 to 7
Supplementary Methods and Supplementary Figure Legends from H-Ras and K-Ras Oncoproteins Induce Different Tumor Spectra When Driven by the Same Regulatory Sequences
Authors: Drosten Matthias , Simón-Carrasco Lucía , Hernández-Porras Isabel , Lechuga Carmen G. , Blasco María T. , Jacob Harrys K.C. , Fabbiano Salvatore , Potenza Nicoletta , Bustelo Xosé R. , Guerra Carmen , Barbacid Mariano
Published: March 2023

Supplementary Methods and Supplementary Figure Legends
Supplementary Figures 1 through 7 from H-Ras and K-Ras Oncoproteins Induce Different Tumor Spectra When Driven by the Same Regulatory Sequences
Authors: Drosten Matthias , Simón-Carrasco Lucía , Hernández-Porras Isabel , Lechuga Carmen G. , Blasco María T. , Jacob Harrys K.C. , Fabbiano Salvatore , Potenza Nicoletta , Bustelo Xosé R. , Guerra Carmen , Barbacid Mariano
Published: March 2023

Supplementary Figure S1. Generation of conditional knock-in mice that express the H-RasG12V oncoprotein from the K-Ras locus. Supplementary Figure S2. Flow cytometry analysis of myeloid cell expansion in spleens and BM of H-RasG12V expressing mice. Supplementary Figure S3. Characterization of the T-ALL induced by the H-RasG12V oncoprotein expressed from the K-Ras locus. Supplementary Figure S4. Pancreatic and lung lesions in mice expressing H-RasG12V and K-RasG12V oncoproteins from the K-Ras locus. Supplementary Figure S5. Lack of apoptosis or canonical OIS in lung cells expressing the H-RasG12V oncoprotein from the K-Ras locus. Supplementary Figure S6. H-RasG12V induced senescence-like arrest in lung cells is partially mediated by p53. Supplementary Figure S7. Differential effects of expressing the K-RasG12V and H-RasG12V oncoproteins driven from the K-Ras locus in MEFs.
Figure S3 from Therapeutic Effects of XPO1 Inhibition in Thymic Epithelial Tumors
Authors: Conforti Fabio , Zhang Xu , Rao Guanhua , De Pas Tommaso , Yonemori Yoko , Rodriguez Jose Antonio , McCutcheon Justine N. , Rahhal Raneen , Alberobello Anna T. , Wang Yisong , Zhang Yu-Wen , Guha Udayan , Giaccone Giuseppe
Published: March 2023

Validation and scoring of XPO1 IHC staining and association with survival of stages III & IV patients
Supplementary data 1 from Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer
Authors: Van Etten Jamie L. , Nyquist Michael , Li Yingming , Yang Rendong , Ho Yeung , Johnson Rachel , Ondigi Olivia , Voytas Daniel F. , Henzler Christine , Dehm Scott M.
Published: March 2023

This file contains supplementary data 1: Illumina HiSeq Sequencing metrics per sample.
Figure S2 from Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA
Authors: Jdey Wael , Thierry Sylvain , Popova Tatiana , Stern Marc-Henri , Dutreix Marie
Published: March 2023

Spontaneous DNA damages and sensitivity to AsiDNA in BC cell lines. A. Spontaneous DNA damages were monitored by alkaline comet assay. B. Basal PARP proteins activation was measured by Sandwich ELISA anti-Poly(ADP-Ribose) polymers. C,D,E. Spearman correlations analysis performed using GraphPadPrism5 software show no correlation.
Figure S1 from Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA
Authors: Jdey Wael , Thierry Sylvain , Popova Tatiana , Stern Marc-Henri , Dutreix Marie
Published: March 2023

Representation and formula of AsiDNA. AsiDNA is a New Chemical Entity, a 64-nucleotides (nt) oligodeoxyribonucleotide consisting of two 32-nt strands of complementary sequence connected through a 1,19-bis(phospho)-8-hydraza-2-hydroxy-4-oxa-9-oxo-nonadecane linker with a cholesterol at the 5Â'-end and three phosphorothioate internucleotide linkages at each of the 5Â' and the 3Â' ends. The sequence of AsiDNA is represented as 5''- X GsCsTs GTG CCC ACA ACC CAG CAA ACA AGC CTA GA L - CLTCT AGG CTT GTT TGC TGG GTT GTG GGC AC sAsGsC -3'', Where: A, C, G, T: Deoxynucleotides. X = Cholesteryl tetraethyleneglycol. L = Amino Linker. CL= Carboxylic (Hydroxyundecanoic) Acid Linker. s = Phosphorothioate linkage.
Supplementary Figure 2 from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

Hematoxylin and eosin stained samples of lung tissue from mice treated with DGKz-/- ACT and anti-PD-L1
Table S4 from Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers
Authors: Yau Edwin H. , Kummetha Indrasena Reddy , Lichinchi Gianluigi , Tang Rachel , Zhang Yunlin , Rana Tariq M.
Published: March 2023

Table with gene level analysis of transduction replicates in the secondary sgRNA library screen using STARS score
Supplemental Figure 2 from WEE1 Kinase Inhibitor AZD1775 Has Preclinical Efficacy in LKB1-Deficient Non–Small Cell Lung Cancer
Authors: Richer Amanda L. , Cala Jacqueline M. , O'Brien Kelley , Carson Vashti M. , Inge Landon J. , Whitsett Timothy G.
Published: March 2023

Active AMPK protein expression in H2030 isogenic cell lines treated with AZD1775 or 2DG.
Supplemental Information from Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response
Authors: Li Zhiguo , Li Jie , Kong Yifan , Yan Shan , Ahmad Nihal , Liu Xiaoqi
Published: March 2023

Supplemental methods and figure legends
Figure S3 from Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response
Authors: Li Zhiguo , Li Jie , Kong Yifan , Yan Shan , Ahmad Nihal , Liu Xiaoqi
Published: March 2023

Figure S3 shows that Mre11 is not involved in normal mitosis.
Supplementary Figure 7 from Cancer-Associated Fibroblasts Share Characteristics and Protumorigenic Activity with Mesenchymal Stromal Cells
Authors: Borriello Lucia , Nakata Rie , Sheard Michael A. , Fernandez G. Esteban , Sposto Richard , Malvar Jemily , Blavier Laurence , Shimada Hiroyuki , Asgharzadeh Shahab , Seeger Robert C. , DeClerck Yves A.
Published: March 2023

Combination of ruxolitinib and trametinib inhibits the growth of subcutaneous NB tumors, cell proliferation and STAT3 and ERK1/2 activation in vivo.
Supplementary Tables 1-4 from RGS12 Is a Novel Tumor-Suppressor Gene in African American Prostate Cancer That Represses AKT and MNX1 Expression
Authors: Wang Yongquan , Wang Jianghua , Zhang Li , Karatas Omer Faruk , Shao Longjiang , Zhang Yiqun , Castro Patricia , Creighton Chad J. , Ittmann Michael
Published: March 2023

Supplementary Table 1. Primers for Q-RT-PCR. Supplementary Table 2. Primers for cloning RGS12 isoforms. Supplementary Table 3. Cytobands lost or gained in African American prostate cancer. Supplementary Table 4. Correlation of CNA and gene expression on 4p16.3
Legends of Supplemental Figures 1-4 from NF1+/− Hematopoietic Cells Accelerate Malignant Peripheral Nerve Sheath Tumor Development without Altering Chemotherapy Response
Authors: Dodd Rebecca D. , Lee Chang-Lung , Overton Tess , Huang Wesley , Eward William C. , Luo Lixia , Ma Yan , Ingram Davis R. , Torres Keila E. , Cardona Diana M. , Lazar Alexander J. , Kirsch David G.
Published: March 2023

Supplemental Figures 1-4 legends
Supplementary Figures 1-6 from RGS12 Is a Novel Tumor-Suppressor Gene in African American Prostate Cancer That Represses AKT and MNX1 Expression
Authors: Wang Yongquan , Wang Jianghua , Zhang Li , Karatas Omer Faruk , Shao Longjiang , Zhang Yiqun , Castro Patricia , Creighton Chad J. , Ittmann Michael
Published: March 2023

Supplementary Figure 1. CNAs in PCA sorted by race. Supplementary Figure 2. RGS12 isoforms Supplementary Figure 3. Scatter plots of RGS12 expression in AA and EA PCa Supplementary Figure 4. Correlation of MNX1 and RGS12. Supplementary Figure 5. Activation of AKT by RGS12 knockdown in PNT1A cells. Supplementary Figure 6. Correlation of AKT1 and RGS12 in AA PCa.
Supplementary Figures 1 through 10 from SPINK6 Promotes Metastasis of Nasopharyngeal Carcinoma via Binding and Activation of Epithelial Growth Factor Receptor
Authors: Zheng Li-Sheng , Yang Jun-Ping , Cao Yun , Peng Li-Xia , Sun Rui , Xie Ping , Wang Meng-Yao , Meng Dong-Fang , Luo Dong-Hua , Zou Xiong , Chen Ming-Yuan , Mai Hai-Qiang , Guo Ling , Guo Xiang , Shao Jian-Yong , Huang Bi-Jun , Zhang Wei , Qian Chao-Nan
Published: March 2023

Supplementary Fig. S1. Expression of SPINK6 in condition medium of NPC cells. Supplementary Fig. S2. Cellular growth of NPC cells. Supplementary Fig. S3. Wound-healing ability of NPC cells upon SPINK6 knockdown. Supplementary Fig. S4. Migration and invasion of NPC cells upon silencing of KLKs. Supplementary Fig. S5. Promoted motility of NPC cells by recombinant SPINK6. Supplementary Fig. S6. Interaction between SPINK6 and EGFR. Supplementary Fig. S7. Phosphorylation of EGFR and downstream signaling molecules in NPC cells. Supplementary Fig. S8. Wound-healing ability of NPC cells. Supplementary Fig. S9. The expression of E-cadherin and vimentin in NPC cells. Supplementary Fig. S10. The expression of EGF, EGFR and KLKs in NPC and NP tissues.
Table S3 from S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma
Authors: Chow Kin-Hoe , Park Hee Jung , George Joshy , Yamamoto Keiko , Gallup Andrew D. , Graber Joel H. , Chen Yuanxin , Jiang Wen , Steindler Dennis A. , Neilson Eric G. , Kim Betty Y.S. , Yun Kyuson
Published: March 2023

Supplementary Table 3 summarizing IPA analyses for Top canonical pathways and Top upstream regulators, using the gene list in Table S2.
Table S2 from S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma
Authors: Chow Kin-Hoe , Park Hee Jung , George Joshy , Yamamoto Keiko , Gallup Andrew D. , Graber Joel H. , Chen Yuanxin , Jiang Wen , Steindler Dennis A. , Neilson Eric G. , Kim Betty Y.S. , Yun Kyuson
Published: March 2023

Supplementary Table 2 listing significantly (q,0.05 and FC>2) in S100A4-KD cells (common to both siRNA compared to scrambled control siRNA).
Supplementary Data CAN-17-0530R1 from miR-130a Deregulates PTEN and Stimulates Tumor Growth
Authors: Wei Huijun , Cui Ri , Bahr Julian , Zanesi Nicola , Luo Zhenghua , Meng Wei , Liang Guang , Croce Carlo M.
Published: March 2023

Figure S1. GFP-LC3 autophagosome puncta in MEF-iRas cells. Figure S2. X-gal staining for examining cell senescence. Figure S3. Comparing MEF-iRas, HOSE-iRas and MCF7-iRas cells for autophagic cell death. Figure S4. Cell proliferation and apoptosis in transformed MEFs with/without PTEN knockdown. Figure S5. The positions of PTEN sgRNAs in PTEN cDNA. Figure S6. Global somatic alterations of miR-130a/miR-130b. Figure S7. Correlation analysis between miR-130a and PTEN in breast cancer subtypes. Figure S8. The expression of miR-130a/miR-130b and PTEN in PR-positive and -negative breast cancer.
Supplementary Figure Legends from Immune Checkpoint Blockade, Immunogenic Chemotherapy or IFN-α Blockade Boost the Local and Abscopal Effects of Oncolytic Virotherapy
Authors: Fend Laetitia , Yamazaki Takahiro , Remy Christelle , Fahrner Catherine , Gantzer Murielle , Nourtier Virginie , Préville Xavier , Quéméneur Eric , Kepp Oliver , Adam Julien , Marabelle Aurélien , Pitt Jonathan M. , Kroemer Guido , Zitvogel Laurence
Published: March 2023

Supplementary Figure Legends
Figure S3 from Immune Checkpoint Blockade, Immunogenic Chemotherapy or IFN-α Blockade Boost the Local and Abscopal Effects of Oncolytic Virotherapy
Authors: Fend Laetitia , Yamazaki Takahiro , Remy Christelle , Fahrner Catherine , Gantzer Murielle , Nourtier Virginie , Préville Xavier , Quéméneur Eric , Kepp Oliver , Adam Julien , Marabelle Aurélien , Pitt Jonathan M. , Kroemer Guido , Zitvogel Laurence
Published: March 2023

The antitumor activity of WR is independent of TLR3 signaling
Supplemental Figures from Integrating Models to Quantify Environment-Mediated Drug Resistance
Authors: Picco Noemi , Sahai Erik , Maini Philip K. , Anderson Alexander R.A.
Published: March 2023

This file contains: results of the sensitivity analysis for parameter estimation shown in the main document (Figures S1-S4), results of curve fitting for mouse growth data under dual inhibition (Figure S5), examples for growth dynamics under dual inhibition, calibrated on representative mice from 2 cases identified in the Results section of the main document (Figures S6 and S7).
Supplementary Tables S7-18 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Tables of mice(S7); CIS genes(S8); insertions(S9); human HCC CIS gene alterations(S10); steatosis-enriched CIS(S11); pathways altered in HCC(S12-18)
Table S1 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

List of DEGs enriched in the resistant clones.
Movie S2 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

Accumulation of T-DM1 in live cells.
Supplementary Figures S1 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Supplementary Figure S1 shows FOXA1 and FOXA2 repression in steatotic mouse livers
Figure S4 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

TDM-1 resistant cell lines from a patient-derived HER2+ xenograft (PDX118) have a lysosomal derangement.
Supplementary Figure S8 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Supplementary Figure S8 shows transposon insertions in CIS genes predict expression changes in human HCC
Figure S2 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

Intracellular accumulation of T-DM1 in lysosomes.
Supplemental Figure Legends from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Figure legends for S1-S5; S1. Further representative sections of normal right kidney; S2. Glucose (Glu), glutamine (Gln), glutathione (GSH), and cell viability in RCC cells; S3. Apoptosis flow data; S4. Bioluminescence imaging, measurements, and animal weights; S5. Coronal PET MIP images overlaid with CT images.
Figure S4 from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Bioluminescence imaging, measurements, and animal weights
Figure S3 from Glutamine Addiction in Kidney Cancer Suppresses Oxidative Stress and Can Be Exploited for Real-Time Imaging
Authors: Abu Aboud Omran , Habib Samy L. , Trott Josephine , Stewart Benjamin , Liang Sitai , Chaudhari Abhijit J. , Sutcliffe Julie , Weiss Robert H.
Published: March 2023

Apoptosis flow data
Supplementary Table 1 from Transcriptional Selectivity of Epigenetic Therapy in Cancer
Authors: Sato Takahiro , Cesaroni Matteo , Chung Woonbok , Panjarian Shoghag , Tran Anthony , Madzo Jozef , Okamoto Yasuyuki , Zhang Hanghang , Chen Xiaowei , Jelinek Jaroslav , Issa Jean-Pierre J.
Published: March 2023

Supplemental Table 1: An excel file containing pathway analysis on the epigenetic inhibitors using Ingenuity Pathway Analysis (IPA) on "Diseases and Biofunctions" listing the top 10 terms for each inhibitor.
Supplementary Figures 1 through 9 and Supplementary Information from Transcriptional Selectivity of Epigenetic Therapy in Cancer
Authors: Sato Takahiro , Cesaroni Matteo , Chung Woonbok , Panjarian Shoghag , Tran Anthony , Madzo Jozef , Okamoto Yasuyuki , Zhang Hanghang , Chen Xiaowei , Jelinek Jaroslav , Issa Jean-Pierre J.
Published: March 2023

Contains Supplemental figures and information
Supplementary Table 4 from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
Authors: Davies Helen , Morganella Sandro , Purdie Colin A. , Jang Se Jin , Borgen Elin , Russnes Hege , Glodzik Dominik , Zou Xueqing , Viari Alain , Richardson Andrea L. , Børresen-Dale Anne-Lise , Thompson Alastair , Eyfjord Jorunn E. , Kong Gu , Stratton Michael R. , Nik-Zainal Serena
Published: March 2023

Detection of MMR deficient breast cancers in whole exome sequencing data (WES)
Supplementary Figure legends from Anti-Jagged Immunotherapy Inhibits MDSCs and Overcomes Tumor-Induced Tolerance
Authors: Sierra Rosa A. , Trillo-Tinoco Jimena , Mohamed Eslam , Yu Lolie , Achyut Bhagelu R. , Arbab Ali , Bradford Jennifer W. , Osborne Barbara A. , Miele Lucio , Rodriguez Paulo C.
Published: March 2023

This file contains a detailed experimental description for the Supplementary Figure legends. Briefly, Supplementary Figure 1 describes the effects of the anti-Jagged therapy in the distribution of CD31+ cells in tumors. Supplementary Figure 2 summarizes the sorting strategy by flow cytometry to identify cancer cells and myeloid cells. Supplementary Figure 3 defines the effects of the anti-Gr-1 therapy on MDSCs and MDSC-LC in tumors. Supplementary Figure 4 illustrates the effect of anti-Jagged on immunogenic antigen-presenting cells. Supplementary Figure 5 shows that anti-Jagged increases the function of antigen-specific T-cells. Supplementary Figure 6 defines the effects of the tumor-derived factors on the expression of Jagged molecules on MDSCs.
Supplementary Figure 2 from Anti-Jagged Immunotherapy Inhibits MDSCs and Overcomes Tumor-Induced Tolerance
Authors: Sierra Rosa A. , Trillo-Tinoco Jimena , Mohamed Eslam , Yu Lolie , Achyut Bhagelu R. , Arbab Ali , Bradford Jennifer W. , Osborne Barbara A. , Miele Lucio , Rodriguez Paulo C.
Published: March 2023

This figure shows the strategy for sorting of cancer cells and myeloid cells by flow cytometry. This was achieved based on the expression of CD49f and CD11b
Supplemental Table 3: predicted gene targets of differentially expressed miRNAs in the upper and bottom crypt and GO term analysis from An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia
Authors: Viswanathan Vignesh , Damle Shirish , Zhang Tao , Opdenaker Lynn , Modarai Shirin , Accerbi Monica , Schmidt Skye , Green Pamela , Galileo Deni , Palazzo Juan , Fields Jeremy , Haghighat Sepehr , Rigoutsos Isidore , Gonye Greg , Boman Bruce M.
Published: March 2023

Lists of predicted gene targets of miRNAs in the upper crypt. List of predicted gene targets in the crypt bottom. GO term analysis of the top 200 predicted gene targets for both the lists.
Whole Exome sequencing data from Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen
Authors: Probst Philipp , Kopp Janine , Oxenius Annette , Colombo Mario P. , Ritz Danilo , Fugmann Tim , Neri Dario
Published: March 2023

Whole Exome sequencing results of the WEHI164 cell line
Supplemental tables from Identification of Interacting Stromal Axes in Triple-Negative Breast Cancer
Authors: Saleh Sadiq M.I. , Bertos Nicholas , Gruosso Tina , Gigoux Mathieu , Souleimanova Margarita , Zhao Hong , Omeroglu Atilla , Hallett Michael T. , Park Morag
Published: March 2023

Supplemental Table 1: TNBCType calls match between ROI95 and the online webtool Supplemental Table 2: Summary of patient characteristics for LCM cohort Supplemental table 3: List of differentially expressed genes for each axis Supplemental Table 4: Representative pathways and genes used to label the stromal axes Supplemental Table 5: Agreement between classifications in LCM dataset and matched bulk expression profiles. Supplemental Table 6: Observed frequencies of the states for each stromal axis score across the whole cohort of TNBC patients (n=1,098). Supplemental Table 7: Enrichment and depletion of some stromal subtypes List of all stromal axis score-baed assignments as well as values entered for binomial test and resultant p-value
Figure S2 from Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen
Authors: Probst Philipp , Kopp Janine , Oxenius Annette , Colombo Mario P. , Ritz Danilo , Fugmann Tim , Neri Dario
Published: March 2023

FACS analysis of AH1-specific CD8+ T cells
Figure S1 from Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8+ T-cell Recognition of a Retroviral Antigen
Authors: Probst Philipp , Kopp Janine , Oxenius Annette , Colombo Mario P. , Ritz Danilo , Fugmann Tim , Neri Dario
Published: March 2023

Immunofluorescence analysis with MHC I tetramers on spleen and tumor sections
Supplemental Figure 5 from Cyclin D1 Restrains Oncogene-Induced Autophagy by Regulating the AMPK–LKB1 Signaling Axis
Authors: Casimiro Mathew C. , Di Sante Gabriele , Di Rocco Agnese , Loro Emanuele , Pupo Claudia , Pestell Timothy G. , Bisetto Sara , Velasco-Velázquez Marco A. , Jiao Xuanmao , Li Zhiping , Kusminski Christine M. , Seifert Erin L. , Wang Chenguang , Ly Daniel , Zheng Bin , Shen Che-Hung , Scherer Philipp E. , Pestell Richard G.
Published: March 2023

Schematic representation for cyclin D1 Cdk4/6 inhibition of LKB1 to restrain autophagy.
Supplementary tables S1-S5, S8 and S9 from Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma
Authors: Marchan Rosemarie , Büttner Bettina , Lambert Jörg , Edlund Karolina , Glaeser Iris , Blaszkewicz Meinolf , Leonhardt Gregor , Marienhoff Lisa , Kaszta Darius , Anft Moritz , Watzl Carsten , Madjar Katrin , Grinberg Marianna , Rempel Eugen , Hergenröder Roland , Selinski Silvia , Rahnenführer Jörg , Lesjak Michaela S. , Stewart Joanna D. , Cadenas Cristina , Hengstler Jan G.
Published: March 2023

Supplementary table 1 - Full list of all siRNA and shRNA used with catalog numbers. Supplementary table 2 - List on names and catalog numbers of Qiagen primer assays used in study Supplementary table 3 - Mass spectrometry settings and the fragment m/z data. Supplementary table 4 - Table of clinicopathological characteristics for all datasets of (A) ovarian (B) breast (C) colon and (D) lung cancer patients. Supplementary table 5 - Concentration of metabolites in MCF7 cells transfected with scrambled siRNA, EDI3, GPAM and CHKA siRNA and measured with NMR Supplementary table 8 - List of overlapping up- and down-regulated genes after silencing GPAM and EDI3 in MCF7 ranked according to adjusted p values (adj. p<0.01). Supplementary table 9 - Association of GPAM mRNA expression with metastasis-free survival (MFS), disease-free survival (DFS) or overall survival (OS) in different cancer types.
Supplemental Figure 3 from Cyclin D1 Restrains Oncogene-Induced Autophagy by Regulating the AMPK–LKB1 Signaling Axis
Authors: Casimiro Mathew C. , Di Sante Gabriele , Di Rocco Agnese , Loro Emanuele , Pupo Claudia , Pestell Timothy G. , Bisetto Sara , Velasco-Velázquez Marco A. , Jiao Xuanmao , Li Zhiping , Kusminski Christine M. , Seifert Erin L. , Wang Chenguang , Ly Daniel , Zheng Bin , Shen Che-Hung , Scherer Philipp E. , Pestell Richard G.
Published: March 2023

Mitochondrial fluorescence after photobleaching.
Supplemental Figure 2 from Cyclin D1 Restrains Oncogene-Induced Autophagy by Regulating the AMPK–LKB1 Signaling Axis
Authors: Casimiro Mathew C. , Di Sante Gabriele , Di Rocco Agnese , Loro Emanuele , Pupo Claudia , Pestell Timothy G. , Bisetto Sara , Velasco-Velázquez Marco A. , Jiao Xuanmao , Li Zhiping , Kusminski Christine M. , Seifert Erin L. , Wang Chenguang , Ly Daniel , Zheng Bin , Shen Che-Hung , Scherer Philipp E. , Pestell Richard G.
Published: March 2023

Chloroquine induction of autophagy in MCF10A-NeuT.
Supplemental Experimental Procedures from NFκB Promotes Ovarian Tumorigenesis via Classical Pathways That Support Proliferative Cancer Cells and Alternative Pathways That Support ALDH+ Cancer Stem–like Cells
Authors: House Carrie D. , Jordan Elizabeth , Hernandez Lidia , Ozaki Michelle , James Jana M. , Kim Marianne , Kruhlak Michael J. , Batchelor Eric , Elloumi Fathi , Cam Margaret C. , Annunziata Christina M.
Published: March 2023

Immunofluorescence image acquisition and analysis procedures
Supplementary Figures S1-S7 from Human Pluripotent Stem Cell–Derived TSC2-Haploinsufficient Smooth Muscle Cells Recapitulate Features of Lymphangioleiomyomatosis
Authors: Julian Lisa M. , Delaney Sean P. , Wang Ying , Goldberg Alexander A. , Doré Carole , Yockell-Lelièvre Julien , Tam Roger Y. , Giannikou Krinio , McMurray Fiona , Shoichet Molly S. , Harper Mary-Ellen , Henske Elizabeth P. , Kwiatkowski David J. , Darling Thomas N. , Moss Joel , Kristof Arnold S. , Stanford William L.
Published: March 2023

This file provides supplementary data pertaining to TSC2 mutation and protein expression analysis in human fibroblast cell lines (Figure S1); as well as Karyotypes (Figure S2), in vitro and in vivo pluripotency and differentiation potential (Figure S3), and genotyping mutation analysis (Figure S4) of human iPSC lines used in this study. Supplementary data regarding human-derived SMC lines, with and without TSC2 mRNA knock-down, specifically cell size analysis (Figure S5), gp100 and ER- expression (Figure S6) and cell death analysis (Figure S7), is also shown.
Supplementary Figure Legends from Human Pluripotent Stem Cell–Derived TSC2-Haploinsufficient Smooth Muscle Cells Recapitulate Features of Lymphangioleiomyomatosis
Authors: Julian Lisa M. , Delaney Sean P. , Wang Ying , Goldberg Alexander A. , Doré Carole , Yockell-Lelièvre Julien , Tam Roger Y. , Giannikou Krinio , McMurray Fiona , Shoichet Molly S. , Harper Mary-Ellen , Henske Elizabeth P. , Kwiatkowski David J. , Darling Thomas N. , Moss Joel , Kristof Arnold S. , Stanford William L.
Published: March 2023

This file contains the full descriptive legends for Supplementary Figures S1-S7.
Supplementary Table 1 from Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer
Authors: Jaeger Samira , Igea Ana , Arroyo Rodrigo , Alcalde Victor , Canovas Begoña , Orozco Modesto , Nebreda Angel R. , Aloy Patrick
Published: March 2023

Complete list of breast cancer drugs (Excel table).
Supplementary Figure Legends from SOCS1 Gene Therapy Improves Radiosensitivity and Enhances Irradiation-Induced DNA Damage in Esophageal Squamous Cell Carcinoma
Authors: Sugase Takahito , Takahashi Tsuyoshi , Serada Satoshi , Fujimoto Minoru , Hiramatsu Kosuke , Ohkawara Tomoharu , Tanaka Koji , Miyazaki Yasuhiro , Makino Tomoki , Kurokawa Yukinori , Yamasaki Makoto , Nakajima Kiyokazu , Kishimoto Tadamitsu , Mori Masaki , Doki Yuichiro , Naka Tetsuji
Published: March 2023

This text is Figure Legends of Supplementary Figure S1 and S2.
Supplementary Figure S4 from NEMO, a Transcriptional Target of Estrogen and Progesterone, Is Linked to Tumor Suppressor PML in Breast Cancer
Authors: Elsarraj Hanan S. , Valdez Kelli E. , Hong Yan , Grimm Sandra L. , Ricci Lawrence R. , Fan Fang , Tawfik Ossama , May Lisa , Cusick Therese , Inciardi Marc , Redick Mark , Gatewood Jason , Winblad Onalisa , Hilsenbeck Susan , Edwards Dean P. , Hagan Christy R. , Godwin Andrew K. , Fabian Carol , Behbod Fariba
Published: March 2023

NEMO KD results in decreased IL-6, p-serine STAT3 and PML in vivo.
Supplementary Tables S1 and S2 from Early Effector T Lymphocytes Coexpress Multiple Inhibitory Receptors in Primary Non–Small Cell Lung Cancer
Authors: Tassi Elena , Grazia Giulia , Vegetti Claudia , Bersani Ilaria , Bertolini Giulia , Molla Alessandra , Baldassari Paola , Andriani Francesca , Roz Luca , Sozzi Gabriella , Pastorino Ugo , Mortarini Roberta , Anichini Andrea
Published: March 2023

This file contains two Supplementary Tables. Table S1 lists antibodies used in flow cytometry experiments and Table S2 shows demographic and clinical parameters of the patients.
Supplementary Figure S1. from NEMO, a Transcriptional Target of Estrogen and Progesterone, Is Linked to Tumor Suppressor PML in Breast Cancer
Authors: Elsarraj Hanan S. , Valdez Kelli E. , Hong Yan , Grimm Sandra L. , Ricci Lawrence R. , Fan Fang , Tawfik Ossama , May Lisa , Cusick Therese , Inciardi Marc , Redick Mark , Gatewood Jason , Winblad Onalisa , Hilsenbeck Susan , Edwards Dean P. , Hagan Christy R. , Godwin Andrew K. , Fabian Carol , Behbod Fariba
Published: March 2023

Five ER+/PR+ DCIS patient samples were cultured under non adherent conditions and treated with E+P, E, P, and vehicle control. Only a subset of patient-derived ER+/PR+ DCIS cells responded to hormone treatment in vitro by increasing mammosphere formation efficiency.
Figure S1 from Plk1 Phosphorylation of Mre11 Antagonizes the DNA Damage Response
Authors: Li Zhiguo , Li Jie , Kong Yifan , Yan Shan , Ahmad Nihal , Liu Xiaoqi
Published: March 2023

Figure S1 shows that Plk1 suppresses DDR by inactivation of the ATM-Chk2 pathway.
Table S3 from A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220
Authors: Hou Panpan , Wu Chao , Wang Yuchen , Qi Rui , Bhavanasi Dheeraj , Zuo Zhixiang , Dos Santos Cedric , Chen Shuliang , Chen Yu , Zheng Hong , Wang Hong , Perl Alexander , Guo Deyin , Huang Jian
Published: March 2023

Supplementary Table 3. List of primers used in this study
Supplementary Figure Legends from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Legends for supplemental figures
Supplemental Table S1 from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Supplementary Table S1. A, Patient characteristics included in the study (Fig. 7, A and B). B, Patient characteristics included in the study (Fig. 7, C and D).
Supplemental Figure S7 from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Supplementary Figure S7: Recapitulated schema.
Figure S2 from A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220
Authors: Hou Panpan , Wu Chao , Wang Yuchen , Qi Rui , Bhavanasi Dheeraj , Zuo Zhixiang , Dos Santos Cedric , Chen Shuliang , Chen Yu , Zheng Hong , Wang Hong , Perl Alexander , Guo Deyin , Huang Jian
Published: March 2023

Supplementary Figure 2. sgRNAs target SPRY3 specifically delete SPRY3 gene in AML cells and SPRY3 deletion confers the resistance to Crenolanib and SPRY1 or 2 knockouts are resistant to AC220. (A) Western analysis was performed with 6 SPRY3 knockout mutants AML cells and SPRY1-3, ERK1/2 and GSK3 protein level has been examined. (B) Western analysis was performed with 6 SPRY3 knockout mutants AML cells and SPRY4 protein level has been examined with GAPDH as the loading control. (C) Cell growth curve of Wild type and SPRY3 knockout AML cells following the treatment with Crenolanib. 0.4 X 106 cells were plated in 12-well plate and treated with indicated amounts of Crenolanib for 6 days and cell numbers were counted. (D) Top: Cell growth curve of SPRY1 and SPRY2 knockout AML cells following the treatment with AC220. 0.4 X 106 cells were plated in 12-well plate and treated with indicated amounts of AC220 for 6 days and cell numbers were counted. Bottom: T7EN1 assay analysis of specific sgRNA-mediated indels at SPRY1 or SPRY2 locus in MV4-11 cells. The MV4-11 cells were transduced with lentivirus carrying sgRNA targeted SPRY1 or SPRY2. The genomic DNA from the cells was extracted and PCR amplified to test efficiency of gene disruptions by T7 endonuclease I assay using a 1.5% agarose gel. The lower migrating bands in lanes indicate the disrupted gene alleles.
Supplemental Figure S6 from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Supplementary Figure S6. Overexpression of VEGFC correlated with reduced overall survival of RCC patients. A, Kaplan-Meier survival curves of metastatic (M1) RCC patients with high or low VEGFC mRNA expression. These results are in whole or in part based upon data generated by the TCGA Research Network. B, Proportion of groups of patients with VEGFC low or high and its correlation with metastatic stage (M1). Statistical significance (Khi2 test) is indicated. C, Multivariate analysis for VEGFC, stage 3/4, metastatic stage (M1) and lymph node metastatic stage (N1). Statistical significance (p values) and the risk ratio are indicated.
Figure S1 from A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220
Authors: Hou Panpan , Wu Chao , Wang Yuchen , Qi Rui , Bhavanasi Dheeraj , Zuo Zhixiang , Dos Santos Cedric , Chen Shuliang , Chen Yu , Zheng Hong , Wang Hong , Perl Alexander , Guo Deyin , Huang Jian
Published: March 2023

Supplementary Figure 1. GO/GSEA/pathway analyses with our top candidates identified in the screen revealed that genes regulate cell adhesion are highly enriched. DAVID (the Database for Annotation, Visualization and Integrated Discovery) pathway analysis program was used to perform GO/GSEA/pathway enrichment analysis. The genes with sgRNA enrichment score above 5 were selected as the input for DAVID.
Supplementary Figure 1-8 from Calcium Promotes Human Gastric Cancer via a Novel Coupling of Calcium-Sensing Receptor and TRPV4 Channel
Authors: Xie Rui , Xu Jingyu , Xiao Yufeng , Wu Jilin , Wan Hanxing , Tang Bo , Liu Jingjing , Fan Yahan , Wang Suming , Wu Yuyun , Dong Tobias Xiao , Zhu Michael X. , Carethers John M. , Dong Hui , Yang Shiming
Published: March 2023

Supplementray Figure 1. Effect of CaCl2 on PCNA protein expression in GC cells and xenografed gastric tumors. Supplementray Figure 2. The efficiencies of CaSR shRNA transient transfection into MKN45 cells and CaSR shRNA lentiviruses transfection into SGC-7901 cells. Supplementray Figure 3. Comparisons of serum calcium concentrations in nude mice without or with an intravenous injection of CaCl2 into the tail veins. Supplementary Figure 4. CaSR-mediated Ca2+o entry through the ROC in GC cells. Supplementary Figure 5. CaSR-induced phosphorylation of β-caternin and PI3K/AKT signaling pathways in cancer cells. Supplementary Figure 6. CaSR-mediated ERK1/2, JNK signaling pathways in human normal gastric cells and cancer cells. Supplementary Figure 7. CaSR-induced phosphorylation of ERK and JUK signaling pathways and proliferation, migration and invasion of cancer cells. Supplementary Figure 8. Effect of TRPV4 agonist or antagonist on p-AKT and p-β-caternin and CaCl2-induced migration of cancer cells.
Supplemental Figure S4 from Sunitinib Stimulates Expression of VEGFC by Tumor Cells and Promotes Lymphangiogenesis in Clear Cell Renal Cell Carcinomas
Authors: Dufies Maeva , Giuliano Sandy , Ambrosetti Damien , Claren Audrey , Ndiaye Papa Diogop , Mastri Michalis , Moghrabi Walid , Cooley Lindsay S. , Ettaiche Marc , Chamorey Emmanuel , Parola Julien , Vial Valerie , Lupu-Plesu Marilena , Bernhard Jean Christophe , Ravaud Alain , Borchiellini Delphine , Ferrero Jean-Marc , Bikfalvi Andréas , Ebos John M. , Khabar Khalid Saad , Grépin Renaud , Pagès Gilles
Published: March 2023

Supplementary Figure S4. Sunitinib does not modified blood vessels. Blood vessels in experimental and patients' tumors are not normalized by sunitinib (equal coverage of CD31 labeled cells by alpha SMA labeled cells).
Supplementary Tables from STK33 Promotes Growth and Progression of Pancreatic Cancer as a Critical Downstream Mediator of HIF1α
Authors: Kong Fanyang , Kong Xiangyu , Du Yiqi , Chen Ying , Deng Xuan , Zhu Jianwei , Du Jiawei , Li Lei , Jia Zhiliang , Xie Dacheng , Li Zhaoshen , Xie Keping
Published: March 2023

One file contains 3 Supplementary Tables: Supplementary Table S1. Clinicopathologic characteristics of the PDAC patients from whom the TMA specimens were obtained; Supplementary Table S2. STK33 protein expression in PDAC TMA specimens and its relationship with patient clinicopathologic characteristics; Supplementary Table S3. The sequences of the gene-specific primers used in real-time PCR analysis, vector constructs, and ChIP analysis
Supplementary Figures and Legends from STK33 Promotes Growth and Progression of Pancreatic Cancer as a Critical Downstream Mediator of HIF1α
Authors: Kong Fanyang , Kong Xiangyu , Du Yiqi , Chen Ying , Deng Xuan , Zhu Jianwei , Du Jiawei , Li Lei , Jia Zhiliang , Xie Dacheng , Li Zhaoshen , Xie Keping
Published: March 2023

One file contains 8 Supplementary Figures and legends Supplementary Figure S1. STK33 expression patterns in human PDAC and adjacent normal pancreatic tissue specimens; Supplementary Figure S2. STK33 expression patterns in human PDAC cells; Supplementary Figure S3. Subcellular expression of STK33 and impact on patient OS; Supplementary Figure S4. Impacts of altered STK33 expression on cell proliferation; Supplementary Figure S5. STK33-promoted PDAC cell metastasis in vivo; Supplementary Figure S6. STK33 promoted PDAC lung metastasis in vivo; Supplementary Figure S7. Co-expression of STK33 and HIF-1α in PDAC tissue; Supplementary Figure S8. Impact of STK33 and HIF-1α expression on PDAC patient survival
Table S2 from Spi-B–Mediated Silencing of Claudin-2 Promotes Early Dissemination of Lung Cancer Cells from Primary Tumors
Authors: Du Wei , Xu Xing , Niu Qing , Zhang Xuexi , Wei Yiliang , Wang Ziqiao , Zhang Wei , Yan Jun , Ru Yongxin , Fu Zheng , Li Xiaobo , Jiang Yuan , Ma Zhenyi , Zhang Zhenfa , Yao Zhi , Liu Zhe
Published: March 2023

Table S2, related to Figure 4: Genes downregulated/upregulated >2-fold by Spi-B transient expression in A549 cells
Supplementary Materials and Methods, Supplementary Tables 1 through 5 and Supplementary Figures 1 through 3 from NR4A3 Suppresses Lymphomagenesis through Induction of Proapoptotic Genes
Authors: Deutsch Alexander J.A. , Rinner Beate , Pichler Martin , Prochazka Katharina , Pansy Katrin , Bischof Marco , Fechter Karoline , Hatzl Stefan , Feichtinger Julia , Wenzl Kerstin , Frisch Marie-Therese , Stiegelbauer Verena , Prokesch Andreas , Krogsdam Anne , Sill Heinz , Thallinger Gerhard G. , Greinix Hildegard T. , Wang Chenguang , Beham-Schmid Christine , Neumeister Peter
Published: March 2023

Supplementary methods. Supplementary table S1: STR analysis of cell lines. Supplementary Table S2: Oligonucleotid sequences of primers. Supplementary Table S3: Mutational analyses of NR4A1 and NR4A3. Supplementary Table S4: Correlation between NR4A1 and pro-apoptotic genes in human cancer. Supplementary Table S5: Correlation between NR4A3 and pro-apoptotic genes in human cancer. Supplementary Figure S1: NR4A1 mRNA expression analysis in Karpas-422, SuDHL4, RI-1 and U2392 after treatment with 10microM TG or DMSO. Supplementary Figure S2: NR4A1 mRNA expression analysis in Karpas-422, RI-1 and U2392 after treatment with 10microM BF175 or DMSO. Supplementary Figure S3: Positive correlation in mRNA expression of NR4A1 and NR4A3 and pro-apoptotic genes in patients with aggressive lymphomas.
Table S1 from Spi-B–Mediated Silencing of Claudin-2 Promotes Early Dissemination of Lung Cancer Cells from Primary Tumors
Authors: Du Wei , Xu Xing , Niu Qing , Zhang Xuexi , Wei Yiliang , Wang Ziqiao , Zhang Wei , Yan Jun , Ru Yongxin , Fu Zheng , Li Xiaobo , Jiang Yuan , Ma Zhenyi , Zhang Zhenfa , Yao Zhi , Liu Zhe
Published: March 2023

Table S1. Oligonucleotide sequences used for RT-PCR, ChIP, 3C assays and luciferase reporters
Detailed overview 510(k) cleared imaging devices from Regulatory Aspects of Optical Methods and Exogenous Targets for Cancer Detection
Authors: Tummers Willemieke S. , Warram Jason M. , Tipirneni Kiranya E. , Fengler John , Jacobs Paula , Shankar Lalitha , Henderson Lori , Ballard Betsy , Pfefer T. Joshua , Pogue Brian W. , Weichert Jamey P. , Bouvet Michael , Sorger Jonathan , Contag Christopher H. , Frangioni John V. , Tweedle Michael F. , Basilion James P. , Gambhir Sanjiv S. , Rosenthal Eben L.
Published: March 2023

Detailed overview of 510(k) cleared imaging devices by the FDA.
Table S3 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Table S3 contains the correlation data for TBK1 inhibitor (BX795 and Compound II) toxicity vs. mRNA expression in NSCLC lines.
Supplementary Data from ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer
Authors: Owczarek Tomasz B. , Kobayashi Takashi , Ramirez Ricardo , Rong Lijie , Puzio-Kuter Anna M. , Iyer Gopa , Teo Min Yuen , Sánchez-Vega Francisco , Wang Jingqiang , Schultz Nikolaus , Zheng Tian , Solit David B. , Al-Ahmadie Hikmat A. , Abate-Shen Cory
Published: March 2023

Supplementary Data from ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer
Figure S3 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Figure S3 shows supporting data for the identification of a TBK1-dependent molecular subtype of NSCLC cells
Figure S2 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Figure S2 contains the TBK1 adaptor-focused screen assessing the relative requirement of TBK1 first- and second-degree interactors for amino acid activation of mTORC1
Figure S1 from TBK1 Provides Context-Selective Support of the Activated AKT/mTOR Pathway in Lung Cancer
Authors: Cooper Jonathan M. , Ou Yi-Hung , McMillan Elizabeth A. , Vaden Rachel M. , Zaman Aubhishek , Bodemann Brian O. , Makkar Gurbani , Posner Bruce A. , White Michael A.
Published: March 2023

Figure S1 shows that TBK1 supports AKT/mTORC1 activation during an amino acid starved-to-fed state transition