bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S1 from Aromatase Acetylation Patterns and Altered Activity in Response to Sirtuin Inhibition
Authors: Molehin Deborah , Castro-Piedras Isabel , Sharma Monica , Sennoune Souad R. , Arena Daphne , Manna Pulak R. , Pruitt Kevin
Published: April 2023

Expression of endogenous aromatase protein and exogenous aromatase constructs in different cell lines and their effect on estradiol levels
Supplementary Data from Autophagy, Cell Viability, and Chemoresistance Are Regulated By miR-489 in Breast Cancer
Authors: Soni Mithil , Patel Yogin , Markoutsa Eleni , Jie Chunfa , Liu Shou , Xu Peisheng , Chen Hexin
Published: April 2023

Figure S1. miR-489 modulates autophagy. Figure S2. Western blot analysis of autophagy flux in breast cancers. Figure S3. Validation of microarray using real-time RT-PCR analysis. Figure S4. miR-489 restoration in HCC1954 and T47D cells under starvation. Figure S5. Endogenous expression level of miR-489 in different classes of breast cancer cell lines. Figure S6. Drug sensitivity assay with cisplatin and doxorubicin. Figure S7. ULK1 restoration rescues MDA-MB-231 cells from cytotoxic effect of miR-489. Figure S8. Characterization and validation of nanoparticles in vitro and in vivo. Figure S9. Correlation of miR-489 and ULK1 mRNA expression in breast cancers. Supplemental Experimental Procedures Supplementary Table 1: Primer list and sequences. Supplementary Table 2: Demographic and histopathology data of the patient samples.
Supplementary Figure 3 from Inhibition of the ATR–CHK1 Pathway in Ewing Sarcoma Cells Causes DNA Damage and Apoptosis via the CDK2-Mediated Degradation of RRM2
Authors: Koppenhafer Stacia L. , Goss Kelli L. , Terry William W. , Gordon David J.
Published: April 2023

Supplementary Figure 3 shows the effects of a CHK1 inhibitor on the shRRM1 and shRRM2 cells.
All Supplementary Data from Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance
Authors: Hoff Fieke W. , Hu Chenyue W. , Qiu Yihua , Ligeralde Andrew , Yoo Suk-Young , Scheurer Michael E. , de Bont Eveline S.J.M. , Qutub Amina A. , Kornblau Steven M. , Horton Terzah M.
Published: April 2023

This file contains all supplementary tables and figures. Supplemental Table S1. COG treatment protocols pediatric ALL patients. Supplementary Table S2. This table contains the "Rosetta Stone" for the antibody and protein nomenclature (HUGO, MiMI, GeneCards) together with the RPPA staining details. Supplementary Table S3. Protein membership for the 31 defined protein functional groups. Supplementary Table S4. ALL protein constellation membership for the 114 protein clusters. Supplementary Table S5. T-ALL protein constellation membership for the 114 protein clusters. Supplementary Table S6. B-ALL protein constellation membership for the 114 protein clusters. Supplementary Table S7. This table shows the univariate and multivariate Cox Proportional Hazard Model Supplementary Table S8. Protein cluster membership for the leukemic cell lines. Supplementary Fig. S1. Computational work flow. Supplementary Fig. S2. The co-occurrence probability matrices are shown for the PFG ''FLI1'' and ''Apoptosis Occurring''. Supplementary Fig. S3. Principal component analysis for the year of collection and for the processing time of the leukemic samples. Supplementary Fig. S4. (A) Unsupervised hierarchical clustering and (B) principal component analysis plot for the CD34+ cells (black) and the pediatric ALL patient samples (red). Supplementary Fig. S5. Unsupervised hierarchical clustering and k-means for all proteins and ALL patients. Supplementary Fig. S6. Optimization calculation meta-galaxy pediatric ALL. Supplementary Fig. S7. Meta-galaxy analysis restricted to B-ALL cases. Supplementary Fig. S8. Significantly changed protein targets identified for each signature and each constellation. Supplementary Fig. S9. A minimal set of 30 antibodies that could predict classification of patients into signatures. Supplementary Fig. S10. (A) Unsupervised hierarchical clustering of pediatric ALL patient samples and leukemic cell lines (N=95)
Legends for Supplementary Figures from Inhibition of Discoidin Domain Receptor 1 Prevents Stroma-Induced Peritoneal Metastasis in Gastric Carcinoma
Authors: Jin Hyejin , Ham In-Hye , Oh Hye Jeong , Bae Cheong A , Lee Dakeun , Kim Young-Bae , Son Sang-Yong , Chwae Yong-Joon , Han Sang-Uk , Brekken Rolf A. , Hur Hoon
Published: April 2023

Legends for Supplementary Figures
Supplementary Table S3 from ABCC1-Exported Sphingosine-1-phosphate, Produced by Sphingosine Kinase 1, Shortens Survival of Mice and Patients with Breast Cancer
Authors: Yamada Akimitsu , Nagahashi Masayuki , Aoyagi Tomoyoshi , Huang Wei-Ching , Lima Santiago , Hait Nitai C. , Maiti Aparna , Kida Kumiko , Terracina Krista P. , Miyazaki Hiroshi , Ishikawa Takashi , Endo Itaru , Waters Michael R. , Qi Qianya , Yan Li , Milstien Sheldon , Spiegel Sarah , Takabe Kazuaki
Published: April 2023

Expression of activated SphK1 in breast cancer.
Figure S4 from Inhibition of Discoidin Domain Receptor 1 Prevents Stroma-Induced Peritoneal Metastasis in Gastric Carcinoma
Authors: Jin Hyejin , Ham In-Hye , Oh Hye Jeong , Bae Cheong A , Lee Dakeun , Kim Young-Bae , Son Sang-Yong , Chwae Yong-Joon , Han Sang-Uk , Brekken Rolf A. , Hur Hoon
Published: April 2023

A, Collagen was expressed at a higher level in fibroblasts than in gastric cancer cell lines. B, Western blotting analysis showed that low-dose 7rh can reduce the phosphorylation of DDR1 as well as upregulate DDR1 levels.
Supplementary Table S2 from ABCC1-Exported Sphingosine-1-phosphate, Produced by Sphingosine Kinase 1, Shortens Survival of Mice and Patients with Breast Cancer
Authors: Yamada Akimitsu , Nagahashi Masayuki , Aoyagi Tomoyoshi , Huang Wei-Ching , Lima Santiago , Hait Nitai C. , Maiti Aparna , Kida Kumiko , Terracina Krista P. , Miyazaki Hiroshi , Ishikawa Takashi , Endo Itaru , Waters Michael R. , Qi Qianya , Yan Li , Milstien Sheldon , Spiegel Sarah , Takabe Kazuaki
Published: April 2023

Expressions of ABCB1 and ABCC1 in breast cancer.
Supplementary Figure S4 from ABCC1-Exported Sphingosine-1-phosphate, Produced by Sphingosine Kinase 1, Shortens Survival of Mice and Patients with Breast Cancer
Authors: Yamada Akimitsu , Nagahashi Masayuki , Aoyagi Tomoyoshi , Huang Wei-Ching , Lima Santiago , Hait Nitai C. , Maiti Aparna , Kida Kumiko , Terracina Krista P. , Miyazaki Hiroshi , Ishikawa Takashi , Endo Itaru , Waters Michael R. , Qi Qianya , Yan Li , Milstien Sheldon , Spiegel Sarah , Takabe Kazuaki
Published: April 2023

SphK1 expression in MCF7 cells transfected with vector, ABCB1 or ABCC1.
Supplementary Tables and Figures from Efficacy of a Covalent ERK1/2 Inhibitor, CC-90003, in KRAS-Mutant Cancer Models Reveals Novel Mechanisms of Response and Resistance
Authors: Aronchik Ida , Dai Yumin , Labenski Matt , Barnes Carmen , Jones Terri , Qiao Lixin , Beebe Lisa , Malek Mehnaz , Elis Winfried , Shi Tao , Mavrommatis Konstantinos , Bray Gordon L. , Filvaroff Ellen H.
Published: April 2023

Table S1. Summary of CC-90003 specificity data resulting from cellular and biochemical assays. Table S2. Response of BRAF mutant cell lines to CC-90003 ERK 1/2 inhibition. Table S3. Summary of dose finding efficacy study in HCT-116 xenograft model. Figure S1. CC-90003 Mass spectrometry analysis of CC-90003 covalent ERK1/2 binding. Figure S2. CC-90003 Inhibits proliferation and induces apoptosis in a panel of KRAS mutant Lung, Pancreatic and Colorectal cancer cell lines. Figure S3. Assessment of ERK inhibitor PD markers in BRAF and KRAS mutant Cancer Models. Figure S4. CC-90003 inhibits proliferation of a subset of BRAF and KRAS mutant cell lung cancer lines and induces cell death more robustly, compared to published inhibitors. Figure S5. CC-90003 inhibits colony formation in a set of KRAS mutant PDX models ex vivo. Figure S6. CC-90003 does not reduce body weights of animals bearing KRAS mutant PDX derived tumors. Figure S7. Genes differentially expressed in CXF-243 PDX model compared to other models used in the study. Figure S8. Genes differentially expressed in CXF-243, CXF-975 and CXF-1034 PDX models compared to other models used in the study. Figure S9. Combination of CC-90003 with EGFR inhibitor Afatinib and NK inhibitor JNK-IN-8. Figure S10. Quantification of Western Blot data in Figure 4. Figure S11. CC-90003 does not reduce body weights of animals bearing LXFA-1674 KRAS mutant lung cancer PDX derived tumors. Figure S12. Regrowth of LXFA-1674 KRAS mutant lung cancer PDX derived tumors following discontinuation of treatment by Docetaxel and CC-90003 combination with Docetaxel. Figure S13. CC-90003 alone and in combination with Docetaxel modulates stemness program in ex vivo serial passaging Mammocult assay.
Table S2 from MCL1 and DEDD Promote Urothelial Carcinoma Progression
Authors: Hong Andrew L. , Guerriero Jennifer L. , Doshi Mihir B. , Kynnap Bryan D. , Kim Won Jun , Schinzel Anna C. , Modiste Rebecca , Schlauch Amy J. , Adam Rosalyn M. , Kwiatkowski David J. , Beroukhim Rameen , Letai Anthony , Rosenberg Jonathan E. , Hahn William C.
Published: April 2023

Correlation of mRNA-seq and CNV
Supplementary Tables 1-5 from Cancer Stem Cell Phenotypes in ER+ Breast Cancer Models Are Promoted by PELP1/AIB1 Complexes
Authors: Truong Thu H. , Hu Hsiangyu , Temiz Nuri A. , Hagen Kyla M. , Girard Brian J. , Brady Nicholas J. , Schwertfeger Kathryn L. , Lange Carol A. , Ostrander Julie H.
Published: April 2023

Supplementary Tables 1-5 containing gene lists and pathway analyses from Mass spectrometry and RNA-seq.
Supplementary figure legends from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

Supplementary figure legends
Supplementary Table 2 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

Synergy of TAK-228 in combination with TAK-117 determined by combination index
Supplementary Table 1 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

Mutation status of bladder cancer cell lines
Supplementary Figure S6 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

Effects of TAK-228 in combination with paclitaxel on bladder cancer models.
Supplementary Figure S5 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

Effects of TAK-228 in combination with TAK-117 in RT4 cells.
Supplementary Figure S3 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models
Authors: Hernández-Prat Anna , Rodriguez-Vida Alejo , Juanpere-Rodero Nuria , Arpi Oriol , Menéndez Silvia , Soria-Jiménez Luis , Martínez Alejandro , Iarchouk Natalia , Rojo Federico , Albanell Joan , Brake Rachael , Rovira Ana , Bellmunt Joaquim
Published: April 2023

In vivo effects of TAK-228 on the T24 xenograft model.
Table S1 from Pattern-Specific Transcriptomics Identifies ASGR2 as a Predictor of Hematogenous Recurrence of Gastric Cancer
Authors: Tanaka Haruyoshi , Kanda Mitsuro , Miwa Takashi , Tanaka Chie , Kobayashi Daisuke , Umeda Shinichi , Shibata Masahiro , Suenaga Masaya , Hattori Norifumi , Hayashi Masamichi , Iwata Naoki , Yamada Suguru , Nakayama Goro , Fujiwara Michitaka , Kodera Yasuhiro
Published: April 2023

Specific primers for PCR and small interfering RNA
Supplementary Figures 1-9, Supplementary Tables 1-3 from An Integrated Stress Response Agent that Modulates DR5-Dependent TRAIL Synergy Reduces Patient-Derived Glioma Stem Cell Viability
Authors: Sheikh Saad , Saxena Deeksha , Tian Xiaobing , Amirshaghaghi Ahmad , Tsourkas Andrew , Brem Steven , Dorsey Jay F.
Published: April 2023

S1: Raw bioluminescence data obtained from screens of kinase, protease, and redox inhibitors. S2: Bioluminescent and viability data from U251 DR5 Luciferase cells treated with an NH125 dilution series. S3: Representative images of T4213 neurospheres taken under 40X magnification demonstrate that T4213 enrich for CD133 (red) SOX2 (orange) and Nestin (green) (scale bar = 25 microns). S4: Representative phase contrast images of TMZ, and NH125 treated GSC taken under 10X magnification (scale bar = 100 microns). S5: Caspase 3/7 activity increases in NH125 treated GSC. GSC were incubated with either 0 M NH125 (0.1% DMSO) or 5 M NH125 for twenty-four hours followed by addition of Caspase 3/7 Glo. S6: NH125 leads to a dose dependent increase in markers of apoptosis. S7: GSC that acquire a differentiated morphology are less sensitive to NH125. S8: The ten most significant canonical pathways from analysis of the transcriptional data of NH125 treated U251 and NHA. S9: PEG-PCL-NH125 treatment of U251 leads to an increase in CHOP and DR5 expression in vitro. Table S1: Knockout of CHOP leads to an abrogation of NH125 mediated TRAIL synergy. Table S2: IC50 values from a panel of NH125 treated cells. Table S3: Addition of low dose TRAIL leads to increased synergy in glioma stem cells.
Supplementary multimedia file 1 from Radiation-Induced Malignant Transformation of Preneoplastic and Normal Breast Primary Epithelial Cells
Authors: Repullés Joan , Anglada Teresa , Soler David , Ramírez Juan Carlos , Genescà Anna , Terradas Mariona
Published: April 2023

Video containing time-lapse images acquired during the first 9 hours after seeding.
Supplementary methods from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer
Authors: Stover Elizabeth H. , Baco Maria B. , Cohen Ofir , Li Yvonne Y. , Christie Elizabeth L. , Bagul Mukta , Goodale Amy , Lee Yenarae , Pantel Sasha , Rees Matthew G. , Wei Guo , Presser Adam G. , Gelbard Maya K. , Zhang Weiqun , Zervantonakis Ioannis K. , Bhola Patrick D. , Ryan Jeremy , Guerriero Jennifer L. , Montero Joan , Liang Felice J. , Cherniack Andrew D. , Piccioni Federica , Matulonis Ursula A. , Bowtell David D.L. , Sarosiek Kristopher A. , Letai Anthony , Garraway Levi A. , Johannessen Cory M. , Meyerson Matthew
Published: April 2023

Supplementary detailed methods
Supplementary Figure 7 from Radiation-Induced Malignant Transformation of Preneoplastic and Normal Breast Primary Epithelial Cells
Authors: Repullés Joan , Anglada Teresa , Soler David , Ramírez Juan Carlos , Genescà Anna , Terradas Mariona
Published: April 2023

Acini
Supplementary Table S6 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer
Authors: Stover Elizabeth H. , Baco Maria B. , Cohen Ofir , Li Yvonne Y. , Christie Elizabeth L. , Bagul Mukta , Goodale Amy , Lee Yenarae , Pantel Sasha , Rees Matthew G. , Wei Guo , Presser Adam G. , Gelbard Maya K. , Zhang Weiqun , Zervantonakis Ioannis K. , Bhola Patrick D. , Ryan Jeremy , Guerriero Jennifer L. , Montero Joan , Liang Felice J. , Cherniack Andrew D. , Piccioni Federica , Matulonis Ursula A. , Bowtell David D.L. , Sarosiek Kristopher A. , Letai Anthony , Garraway Levi A. , Johannessen Cory M. , Meyerson Matthew
Published: April 2023

CRISPR-Cas9 screen enrichment analysis
Supplementary Table S5 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer
Authors: Stover Elizabeth H. , Baco Maria B. , Cohen Ofir , Li Yvonne Y. , Christie Elizabeth L. , Bagul Mukta , Goodale Amy , Lee Yenarae , Pantel Sasha , Rees Matthew G. , Wei Guo , Presser Adam G. , Gelbard Maya K. , Zhang Weiqun , Zervantonakis Ioannis K. , Bhola Patrick D. , Ryan Jeremy , Guerriero Jennifer L. , Montero Joan , Liang Felice J. , Cherniack Andrew D. , Piccioni Federica , Matulonis Ursula A. , Bowtell David D.L. , Sarosiek Kristopher A. , Letai Anthony , Garraway Levi A. , Johannessen Cory M. , Meyerson Matthew
Published: April 2023

CRISPR-Cas9 screen data
Supplementary Table S3 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer
Authors: Stover Elizabeth H. , Baco Maria B. , Cohen Ofir , Li Yvonne Y. , Christie Elizabeth L. , Bagul Mukta , Goodale Amy , Lee Yenarae , Pantel Sasha , Rees Matthew G. , Wei Guo , Presser Adam G. , Gelbard Maya K. , Zhang Weiqun , Zervantonakis Ioannis K. , Bhola Patrick D. , Ryan Jeremy , Guerriero Jennifer L. , Montero Joan , Liang Felice J. , Cherniack Andrew D. , Piccioni Federica , Matulonis Ursula A. , Bowtell David D.L. , Sarosiek Kristopher A. , Letai Anthony , Garraway Levi A. , Johannessen Cory M. , Meyerson Matthew
Published: April 2023

ORF constructs in secondary mini-pool overexpression screen
Supp. Figure 3 from Targeted AKT Inhibition in Prostate Cancer Cells and Spheroids Reduces Aerobic Glycolysis and Generation of Hyperpolarized [1-13C] Lactate
Authors: Tee Sui Seng , Suster Izabela , Truong Steven , Jeong Sangmoo , Eskandari Roozbeh , DiGialleonardo Valentina , Alvarez Julio A. , Aldeborgh Hannah N. , Keshari Kayvan R.
Published: April 2023

Co-localization analysis of HKII and CoxIV. LnCAP cells were grown on coverslips, fixed and permeablized for detection of HKII and CoxIV, coupled to Alexa488 and Alexa594 secondary antibodies respectively. Co-localization analysis was performed by the MSKCC Molecular Cytology Core using the ImageJ software. Scale bar = 100μm
Figure S6 from Epigenetic Silencing of THY1 Tracks the Acquisition of the Notch1–EGFR Signaling in a Xenograft Model of CD44+/CD24low/CD90+ Myoepithelial Cells
Authors: Montanari Micaela , Carbone Maria Rita , Coppola Luigi , Giuliano Mario , Arpino Grazia , Lauria Rossella , Nardone Agostina , Leccia Felicia , Trivedi Meghana V. , Garbi Corrado , Bianco Roberto , Avvedimento Enrico V. , De Placido Sabino , Veneziani Bianca Maria
Published: April 2023

Thy1 and EGFR expression in breast cancer cell lines
Supplementary Figures S1 - S4 from Growth Factor–Independent 1 Is a Tumor Suppressor Gene in Colorectal Cancer
Authors: Chen Min-Shan , Lo Yuan-Hung , Chen Xi , Williams Christopher S. , Donnelly Jessica M. , Criss Zachary K. , Patel Shreena , Butkus Joann M. , Dubrulle Julien , Finegold Milton J. , Shroyer Noah F.
Published: April 2023

Supplementary Figure 1. Specificity of GFI1 antibody. Supplementary Figure 2. Cell cycle and apoptosis analysis of GFI1-expressing CRC cancer cell lines in vitro. Supplementary Figure 3. Expression of CDX2 in the intestine. Supplementary Figure 4. Loss of Gfi1 affects secretory cell lineages.
Supplemental Methods from YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity
Authors: Sugihara Takaaki , Werneburg Nathan W. , Hernandez Matthew C. , Yang Lin , Kabashima Ayano , Hirsova Petra , Yohanathan Lavanya , Sosa Carlos , Truty Mark J. , Vasmatzis George , Gores Gregory J. , Smoot Rory L.
Published: April 2023

Supplemental methods section
Supplementary Materials and Methods from Integration of Distinct ShcA Signaling Complexes Promotes Breast Tumor Growth and Tyrosine Kinase Inhibitor Resistance
Authors: Ha Jacqueline R. , Ahn Ryuhjin , Smith Harvey W. , Sabourin Valerie , Hébert Steven , Cepeda Cañedo Eduardo , Im Young Kyuen , Kleinman Claudia L. , Muller William J. , Ursini-Siegel Josie
Published: April 2023

Experimental methods for Crispr/Cas9 genomic editing, BioID, immunoblot analysis, immunoprecipitation analysis, immunohistochemistry and bioinformatics.
Table S1 from Combinations of Tyrosine Kinase Inhibitor and ERAD Inhibitor Promote Oxidative Stress–Induced Apoptosis through ATF4 and KLF9 in Medullary Thyroid Cancer
Authors: Bagheri-Yarmand Rozita , Sinha Krishna M. , Li Ling , Lu Yue , Cote Gilbert J. , Sherman Steven I. , Gagel Robert F.
Published: April 2023

CI analysis of sunitinib (SU) or vandetanib (Van) combined with eeyarestatin in TT cells.
Figure S1 from Combinations of Tyrosine Kinase Inhibitor and ERAD Inhibitor Promote Oxidative Stress–Induced Apoptosis through ATF4 and KLF9 in Medullary Thyroid Cancer
Authors: Bagheri-Yarmand Rozita , Sinha Krishna M. , Li Ling , Lu Yue , Cote Gilbert J. , Sherman Steven I. , Gagel Robert F.
Published: April 2023

Synergistic cytotoxic effects of combination of eeyarestatin with sunitinib in MZCRC1 cells.
Figure S5. from Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing
Authors: Maag Jesper L.V. , Fisher Oliver M. , Levert-Mignon Angelique , Kaczorowski Dominik C. , Thomas Melissa L. , Hussey Damian J. , Watson David I. , Wettstein Antony , Bobryshev Yuri V. , Edwards Melanie , Dinger Marcel E. , Lord Reginald V.
Published: April 2023

Supplementary figure 5. LncRNAs and mutational signatures. IGV coverage plot of two previously characterised lncRNAs (a) AFAP1-AS1, (b) HNF1A-AS1 upregulated in EAC. Coverage is normalised as counts per million reads. (c) TCGA RNA-seq EAC data was utilised to validate neighbor lncRNA-mRNA pair correlation. Through TCGA alignment of Refseq only 15 of our differentially expressed lncRNAs-gene pairs were available in the TCGA data and then subsequently correlated using the same methods as presented in the main article. (d) SNPs in normal samples were removed from this analysis. All NDBE, LGD and EAC patients were investigated for mutational signatures as described. Only mutations covered by {greater than or equal to}20 reads were used to determine the presence of transcriptional mutation signatures (a) Five signatures were identified, which was used to (e) cluster the patients based on each signatures contribution to the patients mutations.
Figure S3 from Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing
Authors: Maag Jesper L.V. , Fisher Oliver M. , Levert-Mignon Angelique , Kaczorowski Dominik C. , Thomas Melissa L. , Hussey Damian J. , Watson David I. , Wettstein Antony , Bobryshev Yuri V. , Edwards Melanie , Dinger Marcel E. , Lord Reginald V.
Published: April 2023

Supplementary figure 3. Work flow and filtering steps for gene selection following machine learning to discover EAC driver genes. (a) For cross validation we used all normalised reads from EdgeR as cpm. These were put through the R package CMA using four cross-validation methods to find driver genes between EAC and NDBE. Loodat (leave-one-out), Bootstrap, Monte Carlo, Five-cross validation was used. All four methods were compared and genes present in {greater than or equal to}2 methods were kept (n=52). These 52 genes were then investigated for differential expression in EAC vs NDBE (n=39). Gene ontology enrichment was run on this filtered set. Furthermore, genes from all 4 cross validations methods were used as a gene panel and validated in 2 independent micro array data sets comparing EAC vs NDBE (GSE37203 and GSE26886). Random forest analysis was conducted to identify the most important genes of the 12-gene panel using the combined microarray datasets, and subsequently tested on two separate, public microarrays of benign and malignant gastric and colonic tissues. (b) The RNA-seq expression of the selected 12-gene panel of MSMO1, ACAA1, COL17A1, CXCL2, MKNK2, AQP9, E2F3, DHCR24, CTSL, KLF4, PM20D2, CREB5 for EAC and NDBE. Y-axis is log2(cpm 1). (c) AUROC curves for the 4-gene signature on RNA-seq data (left) the two individual microarray data sets (right, bottom left) comparing EAC and NDBE that were used to identify the 4-gene signature. (bottom right) Independent microarray data set used to validate the 4-gene signature on (d) Decision tree of the 12-gene signature on colonic (left) and gastric (right) normal and tumor tissues identifying E2F3 and KLF4 as main classification drivers.
Figure S2 from Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing
Authors: Maag Jesper L.V. , Fisher Oliver M. , Levert-Mignon Angelique , Kaczorowski Dominik C. , Thomas Melissa L. , Hussey Damian J. , Watson David I. , Wettstein Antony , Bobryshev Yuri V. , Edwards Melanie , Dinger Marcel E. , Lord Reginald V.
Published: April 2023

Supplementary figure 2. Differentially expressed transcriptions factors between LGD and NDBE, and examples of EAC specific genes and eigen-modules from WGCNA. (a) Box plots of the top transcription factors (FOSB, FOSB, EGR1, EGR3, NR4A1, ATF3) differentially expressed between LGD and BE and the corresponding expression in Nsq and EAC. y-axis is log2(cpm 1). (b) Boxplot (top) and IGV coverage plot (bottom) of two examples of highly connected, and also differentially expressed gens between both EAC and NDBE/LGD in the brown eigenmodule. (c, d ) (left) Heatmap (top), median eigenexpression (bottom), (right) protein-protein-interaction network (top), and network gene ontology enrichment (bottom) of eigenmodules found to be either over- (c) or underexpressed (d) in EAC. Genes are coloured based on differential expression, of either EAC and NDBE/LGD (red), EAC vs NDBE (blue), EAC vs LGD (green).
Supplementary Figure Legends from Diffuse Intrinsic Pontine Glioma Cells Are Vulnerable to Mitotic Abnormalities Associated with BMI-1 Modulation
Authors: Senthil Kumar Shiva , Sengupta Satarupa , Zhu Xiaoting , Mishra Deepak Kumar , Phoenix Timothy , Dyer Lisa , Fuller Christine , Stevenson Charles B. , DeWire Mariko , Fouladi Maryam , Drissi Rachid
Published: April 2023

Supplementary Figure Legends
Figure S4 from Diffuse Intrinsic Pontine Glioma Cells Are Vulnerable to Mitotic Abnormalities Associated with BMI-1 Modulation
Authors: Senthil Kumar Shiva , Sengupta Satarupa , Zhu Xiaoting , Mishra Deepak Kumar , Phoenix Timothy , Dyer Lisa , Fuller Christine , Stevenson Charles B. , DeWire Mariko , Fouladi Maryam , Drissi Rachid
Published: April 2023

Immunoblot analysis of BMI-1 and H2AK119Ub after treatment of DIPG cells with PTC596 and EPZ011989 at Days 6 and 8 as represented in figure 5D.
Figure S3 from Diffuse Intrinsic Pontine Glioma Cells Are Vulnerable to Mitotic Abnormalities Associated with BMI-1 Modulation
Authors: Senthil Kumar Shiva , Sengupta Satarupa , Zhu Xiaoting , Mishra Deepak Kumar , Phoenix Timothy , Dyer Lisa , Fuller Christine , Stevenson Charles B. , DeWire Mariko , Fouladi Maryam , Drissi Rachid
Published: April 2023

A, Soft agar assay of an additional cell line, CCHMC-DIPG-1, to assess sensitization to IR when treated with PTC596 and its respective quantification. Error bars represent the SD from two independent experiments run in triplicate. B, Relative cell growth calculated by WST-1 assay at Day 7 used to calculate the CI values in figure 4C. Three independent experiments were performed and data from one experiment is shown as a representative result. Error bars represent the SD from triplicates.
Supplementary Figure 4 from Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma
Authors: Arend Rebecca C. , Londoño Angelina I. , Montgomery Allison M. , Smith Haller J. , Dobbin Zachary C. , Katre Ashwini A. , Martinez Alba , Yang Eddy S. , Alvarez Ronald D. , Huh Warner K. , Bevis Kerri S. , Straughn J. Michael , Estes Jacob M. , Novak Lea , Crossman David K. , Cooper Sara J. , Landen Charles N. , Leath Charles A.
Published: April 2023

Pathway and network analysis.
Supplementary Figure 3 from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models
Authors: Khandelwal Garima , Girotti María Romina , Smowton Christopher , Taylor Sam , Wirth Christopher , Dynowski Marek , Frese Kristopher K. , Brady Ged , Dive Caroline , Marais Richard , Miller Crispin
Published: April 2023

Differences in fold change between primary tumour and CDXF1 before and after processing using Xenome.
Supplementary Figure 1 from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models
Authors: Khandelwal Garima , Girotti María Romina , Smowton Christopher , Taylor Sam , Wirth Christopher , Dynowski Marek , Frese Kristopher K. , Brady Ged , Dive Caroline , Marais Richard , Miller Crispin
Published: April 2023

Overview of data processing pipeline.
Supplemental Figure Legend from NME1 Drives Expansion of Melanoma Cells with Enhanced Tumor Growth and Metastatic Properties
Authors: Wang Ying , Leonard M. Kathryn , Snyder Devin E. , Fisher Matthew L. , Eckert Richard L. , Kaetzel David M.
Published: April 2023

Supplemental Figure 1
Figures S1,2,4-8 from Genomic Alterations Associated with Recurrence and TNBC Subtype in High-Risk Early Breast Cancers
Authors: Wilson Timothy R. , Udyavar Akshata R. , Chang Ching-Wei , Spoerke Jill M. , Aimi Junko , Savage Heidi M. , Daemen Anneleen , O'Shaughnessy Joyce A. , Bourgon Richard , Lackner Mark R.
Published: April 2023

Supplemental figures 1,2,4-8 as supporting figures to the manuscript.
Figure S2 from UNC-45A Is a Novel Microtubule-Associated Protein and Regulator of Paclitaxel Sensitivity in Ovarian Cancer Cells
Authors: Mooneyham Ashley , Iizuka Yoshie , Yang Qing , Coombes Courtney , McClellan Mark , Shridhar Vijayalakshmi , Emmings Edith , Shetty Mihir , Chen Liqiang , Ai Teng , Meints Joyce , Lee Michael K. , Gardner Melissa , Bazzaro Martina
Published: April 2023

Polyclonal and clones of paclitaxel-resistant ovarian cancer cells overcome cell death on multipolar spindles
Supplementary Figure Legends Legends from Synthetic Lethality of PARP Inhibition and Ionizing Radiation is p53-dependent
Authors: Sizemore Steven T. , Mohammad Rahman , Sizemore Gina M. , Nowsheen Somaira , Yu Hao , Ostrowski Michael C. , Chakravarti Arnab , Xia Fen
Published: April 2023

Figure legends for Supplemental Figures 1 through 3.
Supplementary Figure 5. (A-B) from Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk
Authors: Petitalot Ambre , Dardillac Elodie , Jacquet Eric , Nhiri Naima , Guirouilh-Barbat Josée , Julien Patrick , Bouazzaoui Isslam , Bonte Dorine , Feunteun Jean , Schnell Jeff A. , Lafitte Philippe , Aude Jean-Christophe , Noguès Catherine , Rouleau Etienne , Lidereau Rosette , Lopez Bernard S. , Zinn-Justin Sophie , Caputo Sandrine M.
Published: April 2023

Size Exclusion Chromatography profiles obtained on BRCA1 BRCT domains free (red curve) or in complex with BACH1-P (purple), AB-1P (green), AB-2P (blue). The experiment was performed using a Superdex-75 10/300 GL column (GE Healthcare) pre-equilibrated with 50mM Tris-HCl pH 7.5, 150 mM NaCl, 10 mM β-mercaptoethanol and protease inhibitors (Roche).
Table S2 from The Tissue-Reconstructing Ability of Colon CSCs Is Enhanced by FK506 and Suppressed by GSK3 Inhibition
Authors: Ishida Ryo , Koyanagi-Aoi Michiyo , Oshima Nobu , Kakeji Yoshihiro , Aoi Takashi
Published: April 2023

Primer List
Figure S6 from The Tissue-Reconstructing Ability of Colon CSCs Is Enhanced by FK506 and Suppressed by GSK3 Inhibition
Authors: Ishida Ryo , Koyanagi-Aoi Michiyo , Oshima Nobu , Kakeji Yoshihiro , Aoi Takashi
Published: April 2023

Effects of knock down of RCAN2 by siRNA on 2nd V50 cells.
Supplementary Figure 1 (A). from Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk
Authors: Petitalot Ambre , Dardillac Elodie , Jacquet Eric , Nhiri Naima , Guirouilh-Barbat Josée , Julien Patrick , Bouazzaoui Isslam , Bonte Dorine , Feunteun Jean , Schnell Jeff A. , Lafitte Philippe , Aude Jean-Christophe , Noguès Catherine , Rouleau Etienne , Lidereau Rosette , Lopez Bernard S. , Zinn-Justin Sophie , Caputo Sandrine M.
Published: April 2023

Western blot analysis of the expression of BRCA1 and I-SceI measured after expression of either WT BRCA1 or VUS in the HR assays. BRCA1 was revealed using an anti-BRCA1 (mouse, ab16780, Abcam) and I-SceI with an anti-HA (mouse, sc-7392, Santa Cruz Biotechnology Inc.).
Figure S3 from The Tissue-Reconstructing Ability of Colon CSCs Is Enhanced by FK506 and Suppressed by GSK3 Inhibition
Authors: Ishida Ryo , Koyanagi-Aoi Michiyo , Oshima Nobu , Kakeji Yoshihiro , Aoi Takashi
Published: April 2023

Forced expression of SEMA6A, FAM105A and RCAN2.
Supp tables from Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk
Authors: Petitalot Ambre , Dardillac Elodie , Jacquet Eric , Nhiri Naima , Guirouilh-Barbat Josée , Julien Patrick , Bouazzaoui Isslam , Bonte Dorine , Feunteun Jean , Schnell Jeff A. , Lafitte Philippe , Aude Jean-Christophe , Noguès Catherine , Rouleau Etienne , Lidereau Rosette , Lopez Bernard S. , Zinn-Justin Sophie , Caputo Sandrine M.
Published: April 2023

Supplementary table I: List of 78 BRCA1 BRCT missense VUS from the UMD-BRCA1 database. Bioinformatics in silico protein and 3D prediction scores, classification from BRCAShare (ex-UMD-BRCA1), BIC, kConfab and ClinVar databases. Supplementary table II: Classification of the BRCA1 VUS C1697R on the basis of multifactorial information Supplementary table III: Quantification of the percentage of fluorescence corresponding to nuclear BRCA1. The yes/no results extracted from this quantification to obtain Figure 3B were deduced from a statistical analysis using a t-test calculation.
Supplemental Figure 3 from A Role for Tryptophan-2,3-dioxygenase in CD8 T-cell Suppression and Evidence of Tryptophan Catabolism in Breast Cancer Patient Plasma
Authors: Greene Lisa I. , Bruno Tullia C. , Christenson Jessica L. , D'Alessandro Angelo , Culp-Hill Rachel , Torkko Kathleen , Borges Virginia F. , Slansky Jill E. , Richer Jennifer K.
Published: April 2023

Alterations in tryptophan catabolites in breast cancer and pregnancy-associated breast cancer.
Supplementary Table 3 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
Authors: Mulder Celine , Prust Nadine , van Doorn Sander , Reinecke Maria , Kuster Bernhard , van Bergen en Henegouwen Paul , Lemeer Simone
Published: April 2023

Processed Proteins
Supplemental Figure 2 from A Role for Tryptophan-2,3-dioxygenase in CD8 T-cell Suppression and Evidence of Tryptophan Catabolism in Breast Cancer Patient Plasma
Authors: Greene Lisa I. , Bruno Tullia C. , Christenson Jessica L. , D'Alessandro Angelo , Culp-Hill Rachel , Torkko Kathleen , Borges Virginia F. , Slansky Jill E. , Richer Jennifer K.
Published: April 2023

Alterations in tryptophan catabolites in breast cancer subtypes.
Supplementary Table 1 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
Authors: Mulder Celine , Prust Nadine , van Doorn Sander , Reinecke Maria , Kuster Bernhard , van Bergen en Henegouwen Paul , Lemeer Simone
Published: April 2023

Raw Peptides
Supplementary Methods from Mitochondrial DNA Mutations are Associated with Ulcerative Colitis Preneoplasia but Tend to be Negatively Selected in Cancer
Authors: Baker Kathryn T. , Nachmanson Daniela , Kumar Shilpa , Emond Mary J. , Ussakli Cigdem , Brentnall Teresa A. , Kennedy Scott R. , Risques Rosa Ana
Published: April 2023

Supplementary Methods
Supplemental microarray data from Senescent Carcinoma-Associated Fibroblasts Upregulate IL8 to Enhance Prometastatic Phenotypes
Authors: Wang Tao , Notta Faiyaz , Navab Roya , Joseph Joella , Ibrahimov Emin , Xu Jing , Zhu Chang-Qi , Borgida Ayelet , Gallinger Steven , Tsao Ming-Sound
Published: April 2023

Supplemental Microarray Data
Supplemental Materials and Methods from Senescent Carcinoma-Associated Fibroblasts Upregulate IL8 to Enhance Prometastatic Phenotypes
Authors: Wang Tao , Notta Faiyaz , Navab Roya , Joseph Joella , Ibrahimov Emin , Xu Jing , Zhu Chang-Qi , Borgida Ayelet , Gallinger Steven , Tsao Ming-Sound
Published: April 2023

Supplemental Materials and Methods
Supplementary Methods from Establishment of the First Well-differentiated Human Pancreatic Neuroendocrine Tumor Model
Authors: Benten Daniel , Behrang Yasmin , Unrau Ludmilla , Weissmann Victoria , Wolters-Eisfeld Gerrit , Burdak-Rothkamm Susanne , Stahl Felix R. , Anlauf Martin , Grabowski Patricia , Möbs Markus , Dieckhoff Jan , Sipos Bence , Fahl Martina , Eggers Corinna , Perez Daniel , Bockhorn Maximillian , Izbicki Jakob R. , Lohse Ansgar W. , Schrader Jörg
Published: April 2023

Supplementary Methods
Supplementary Figure Legends 1-5 from The Activation of MEK/ERK Signaling Pathway by Bone Morphogenetic Protein 4 to Increase Hepatocellular Carcinoma Cell Proliferation and Migration
Authors: Chiu Chiang-Yen , Kuo Kung-Kai , Kuo Tzu-Lei , Lee King-The , Cheng Kuang-Hung
Published: April 2023

PDF file - 40K
Supplementary Figure 1 from The Activation of MEK/ERK Signaling Pathway by Bone Morphogenetic Protein 4 to Increase Hepatocellular Carcinoma Cell Proliferation and Migration
Authors: Chiu Chiang-Yen , Kuo Kung-Kai , Kuo Tzu-Lei , Lee King-The , Cheng Kuang-Hung
Published: April 2023

PDF file - 61K
Supplementary Figures 1-4 from CDK4/6 Therapeutic Intervention and Viable Alternative to Taxanes in CRPC
Authors: Stice James P. , Wardell Suzanne E. , Norris John D. , Yllanes Alexander P. , Alley Holly M. , Haney Victoria O. , White Hannah S. , Safi Rachid , Winter Peter S. , Cocce Kimberly J. , Kishton Rigel J. , Lawrence Scott A. , Strum Jay C. , McDonnell Donald P.
Published: April 2023

Supplemental Figure 1. The effects of G1T28 are due to CDK4/6 inhibition. Supplemental Figure 2. Analysis of pharmacodynamics endpoints indicates on-target activity in 22Rv1 tumors. A. Supplemental Figure 3. G1T38 and G128 have similar in vitro efficacy. Supplemental Figure 4. G1T28 inhibits anti-androgen stimulated prostate cancer cell growth.
Supplementary Data from Activation of Epidermal Growth Factor Receptor and Its Downstream Signaling Pathway by Nitric Oxide in Response to Ionizing Radiation
Authors: Lee Hyung-Chahn , An Sungkwan , Lee Hansoo , Woo Sang-Hyeok , Jin Hyeon-Ok , Seo Sung-Keum , Choe Tae-Boo , Yoo Doo-Hyun , Lee Su-Jae , Hong Young-Joon , Park Myung-Jin , Rhee Chang-Hun , Park In-Chul , Hong Seok-Il
Published: April 2023

Supplementary Data from Activation of Epidermal Growth Factor Receptor and Its Downstream Signaling Pathway by Nitric Oxide in Response to Ionizing Radiation
Supplementary Figures S1-S5 from Induction of Antiproliferative Connective Tissue Growth Factor Expression in Wilms' Tumor Cells by Sphingosine-1-Phosphate Receptor 2
Authors: Li Mei-Hong , Sanchez Teresa , Pappalardo Anna , Lynch Kevin R. , Hla Timothy , Ferrer Fernando
Published: April 2023

Supplementary Figures S1-S5 from Induction of Antiproliferative Connective Tissue Growth Factor Expression in Wilms' Tumor Cells by Sphingosine-1-Phosphate Receptor 2
Supplementary Table 2 from The Lymphotactin Receptor Is Expressed in Epithelial Ovarian Carcinoma and Contributes to Cell Migration and Proliferation
Authors: Kim Mijung , Rooper Lisa , Xie Jia , Rayahin Jamie , Burdette Joanna E. , Kajdacsy-Balla Andre A. , Barbolina Maria V.
Published: April 2023

PDF file - 65K, Expression of XCR1 RNA in samples of ovarian carcinoma and non-malignant ovary
Table S2 from Metastasis-Specific Gene Expression in Autochthonous and Allograft Mouse Mammary Tumor Models: Stratification and Identification of Targetable Signatures
Authors: Ross Christina , Szczepanek Karol , Lee Maxwell , Yang Howard , Peer Cody J. , Kindrick Jessica , Shankarappa Priya , Lin Zhi-Wei , Sanford Jack D. , Figg William D. , Hunter Kent W.
Published: April 2023

GSEA and IPA analysis results
Supplementary Methods from The Lymphotactin Receptor Is Expressed in Epithelial Ovarian Carcinoma and Contributes to Cell Migration and Proliferation
Authors: Kim Mijung , Rooper Lisa , Xie Jia , Rayahin Jamie , Burdette Joanna E. , Kajdacsy-Balla Andre A. , Barbolina Maria V.
Published: April 2023

PDF file - 127K, Detailed description of some of the routine procedures used to generate the data
Figure S4 from Metastasis-Specific Gene Expression in Autochthonous and Allograft Mouse Mammary Tumor Models: Stratification and Identification of Targetable Signatures
Authors: Ross Christina , Szczepanek Karol , Lee Maxwell , Yang Howard , Peer Cody J. , Kindrick Jessica , Shankarappa Priya , Lin Zhi-Wei , Sanford Jack D. , Figg William D. , Hunter Kent W.
Published: April 2023

Nicotine and Cotinine serum levels
Supplementary Figures 1-7 from TLE1 Is an Anoikis Regulator and Is Downregulated by Bit1 in Breast Cancer Cells
Authors: Brunquell Chris , Biliran Hector , Jennings Scott , Ireland Shubha Kale , Chen Renwei , Ruoslahti Erkki
Published: April 2023

PDF file - 817K, S1. Expression of exogenous GFP-TLE1 in stable MCF10A derived GFP-TLE1 and control overexpressing cells was confirmed by SDSPAGE and immunoblotting using the total cell lysates derived from control and TLE1 overexpressing pools against specific antibodies to TLE1 and B-actin. S2 Knockdown of TLE1 has no impact on the morphology and anchorage-dependent growth of breast cancer cells. S3 The increased anoikis sensitivity induced by TLE1 downregulation is attenuated by forced TLE1 expression. S4 Knockdown of TLE1 attenuates the anchorage independent growth of breast cancer cells S5 Overexpression of TLE1 enhances the anchorage independent growth of breast cancer cells. S6 TLE1 suppresses apoptosis induced by Bit1. S7 Anoikis induction in HEK 293T cells.
Supplementary Tables 1 - 2 from The Signal Peptide of Mouse Mammary Tumor Virus-Env: A Phosphoprotein Tumor Modulator
Authors: Feldman Dafna , Roniger Maayan , Bar-Sinai Allan , Braitbard Ori , Natan Carmit , Love Dona C. , Hanover John A. , Hochman Jacob
Published: April 2023

PDF file - 69K, Supplemental Table 1 Primers used to construct plasmids expressing point mutations in the p14 sequence Supplemental Table 2 Primers used to construct plasmids expressing deletions in the p14 sequence
Supplementary Figure 2 from Cancer-Associated Fibroblasts Induce Matrix Metalloproteinase–Mediated Cetuximab Resistance in Head and Neck Squamous Cell Carcinoma Cells
Authors: Johansson Ann-Charlotte , Ansell Anna , Jerhammar Fredrik , Lindh Maja Bradic , Grénman Reidar , Munck-Wikland Eva , Östman Arne , Roberg Karin
Published: April 2023

PDF file - 170K, Protection from cetuximab treatment is provided by cancer-associated fibroblast-derived soluble factors
Supplementary Table 3 from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity
Authors: Stangl Christina , Post Jasmin B. , van Roosmalen Markus J. , Hami Nizar , Verlaan-Klink Ingrid , Vos Harmjan R. , van Es Robert M. , Koudijs Marco J. , Voest Emile E. , Snippert Hugo J.G. , Kloosterman W.P.
Published: April 2023

Supplementary Table 3. Z-scores of significantly differential expressed genes (provided separately due to size)
Supplementary Materials and Methods from Diverse BRAF Gene Fusions Confer Resistance to EGFR-Targeted Therapy via Differential Modulation of BRAF Activity
Authors: Stangl Christina , Post Jasmin B. , van Roosmalen Markus J. , Hami Nizar , Verlaan-Klink Ingrid , Vos Harmjan R. , van Es Robert M. , Koudijs Marco J. , Voest Emile E. , Snippert Hugo J.G. , Kloosterman W.P.
Published: April 2023

Supplementary Materials and Methods
Supplementary Figure 1 - 6, Table 1 from Exosomes Promote Ovarian Cancer Cell Invasion through Transfer of CD44 to Peritoneal Mesothelial Cells
Authors: Nakamura Koji , Sawada Kenjiro , Kinose Yasuto , Yoshimura Akihiko , Toda Aska , Nakatsuka Erika , Hashimoto Kae , Mabuchi Seiji , Morishige Ken-ichirou , Kurachi Hirohisa , Lengyel Ernst , Kimura Tadashi
Published: April 2023

Supplementary Figure 1. MMP-9 activity is involved in EOC invasion through HPMC. Supplementary Figure 2. Inhibition of exosome secretion attenuates CD44 uptake by HPMCs and suppresses TYK-nu cell invasion. Supplementary Figure 3. Inhibition of exosome uptake attenuates CD44 expression in HPMCs. Supplementary Figure 4. Immunofluorescent analyses. Supplementary Figure 5. Not only CD44 but MMP-9 are strongly expressed in peritoneal mesothelial cells interacting with ovarian cancer cells. Supplementary Figure 6. Acquisition of CD44 of mouse omental tissues from ovarian cancer cells is dose-dependent. Supplementary Table 1. Clinical characteristics of ovarian cancer patients with stage III-IV consecutively treated at Osaka University Hospital between 2011 and 2015.
Supplementary Table 3 from Suppression of G-protein–Coupled Receptor Kinase 3 Expression Is a Feature of Classical GBM That Is Required for Maximal Growth
Authors: Woerner B. Mark , Luo Jingqin , Brown Kristin R. , Jackson Erin , Dahiya Sonika M. , Mischel Paul , Benovic Jeffrey L. , Piwnica-Worms David , Rubin Joshua B.
Published: April 2023

PDF file - 63KB
Supplementary Table 1 from Suppression of G-protein–Coupled Receptor Kinase 3 Expression Is a Feature of Classical GBM That Is Required for Maximal Growth
Authors: Woerner B. Mark , Luo Jingqin , Brown Kristin R. , Jackson Erin , Dahiya Sonika M. , Mischel Paul , Benovic Jeffrey L. , Piwnica-Worms David , Rubin Joshua B.
Published: April 2023

PDF file - 66KB
Supplementary Figure 3 from Suppression of G-protein–Coupled Receptor Kinase 3 Expression Is a Feature of Classical GBM That Is Required for Maximal Growth
Authors: Woerner B. Mark , Luo Jingqin , Brown Kristin R. , Jackson Erin , Dahiya Sonika M. , Mischel Paul , Benovic Jeffrey L. , Piwnica-Worms David , Rubin Joshua B.
Published: April 2023

PDF file - 1979KB
Video 3 from Complex Rab4-Mediated Regulation of Endosomal Size and EGFR Activation
Authors: Tubbesing Kate , Ward Jamie , Abini-Agbomson Raymond , Malhotra Aditi , Rudkouskaya Alena , Warren Janine , Lamar John , Martino Nina , Adam Alejandro P. , Barroso Margarida
Published: April 2023

Video S3. Live-cell Fast Airyscan Microscopy of EGF, LDL and Tf uptake and early trafficking steps in MCF10A and MDAMB231, corresponds to Figure 3D.
Supplementary Figures 1-10 from Multiple Isoforms of CDC25 Oppose ATM Activity to Maintain Cell Proliferation during Vertebrate Development
Authors: Verduzco Daniel , Dovey Jennifer Shepard , Shukla Abhay A. , Kodym Elisabeth , Skaug Brian A. , Amatruda James F.
Published: April 2023

PDF file - 2.3MB, Supplementary Figures and Legends S1. Standstill mutants exhibit persistent growth defects and eventual embryonic death. S2. In situ hybridization of cdc25a in 36 hpf zebrafish embryos. S3. Knockdown of cdc25a by a translation-blocking morpholino phenocopies the standstill phenotype. S4. Zebrafish exhibit a robust cell-cycle arrest following treatment with ionizing radiation, as evaluated by anti-pH3 immunohistochemistry. S5. Inhibition of ATM with the ATM inhibitor KU55933 leads to radiosensitivity in zebrafish. S6. Inhibition of DNA damage response pathways with caffeine leads to increased cell proliferation in cdc25a-/- embryos. S7. The G1/S checkpoint is not activated in cdc25a-deficient embryos. S8. Loss of proliferation precedes the appearance of �H2AX. S9. Overexpression of Cdc25A does not lead to decreased ATM function. S10. Deleterious effects of ATM knockdown.