bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S8 from ID1 Is Critical for Tumorigenesis and Regulates Chemoresistance in Glioblastoma
Authors: Sachdeva Rohit , Wu Megan , Smiljanic Sandra , Kaskun Oleksandra , Ghannad-Zadeh Kimia , Celebre Angela , Isaev Keren , Morrissy A. Sorana , Guan Jennifer , Tong Jiefei , Chan Jeffrey , Wilson Taylor M. , Al-Omaishi Sayf , Munoz David G. , Dirks Peter B. , Moran Michael F. , Taylor Michael D. , Reimand Jüri , Das Sunit
Published: April 2023

(A) TMZ IC50 curves for U251 control and U251.TR cells. (B) U251 and U251.TR cells colony forming assay at different concentrations of TMZ. (C) Western blot analysis for EGFR and p-EGFR-1068 from lysates of U251and U251.TR cells.
Figure S4 from ID1 Is Critical for Tumorigenesis and Regulates Chemoresistance in Glioblastoma
Authors: Sachdeva Rohit , Wu Megan , Smiljanic Sandra , Kaskun Oleksandra , Ghannad-Zadeh Kimia , Celebre Angela , Isaev Keren , Morrissy A. Sorana , Guan Jennifer , Tong Jiefei , Chan Jeffrey , Wilson Taylor M. , Al-Omaishi Sayf , Munoz David G. , Dirks Peter B. , Moran Michael F. , Taylor Michael D. , Reimand Jüri , Das Sunit
Published: April 2023

(A) Flow chart of RNA-seq analysis. (B) RT-qPCR validation confirmed a reduction in EGF transcript, with similar trends to RNA-seq data. ****P<0.0001
Supplementary Data from Direct Targeting of MYCN Gene Amplification by Site-Specific DNA Alkylation in Neuroblastoma
Authors: Yoda Hiroyuki , Inoue Takahiro , Shinozaki Yoshinao , Lin Jason , Watanabe Takayoshi , Koshikawa Nobuko , Takatori Atsushi , Nagase Hiroki
Published: April 2023

Table S1. IC50 values of MYCN-A3-treated 27 cancer cell lines. Table S2. List of Kyoto Encyclopedia Genes and Genome (KEGG) pathways and their relative group-wise expression differences between MYCN-A3 and MYCNcr-a.
Supplementary Methods from Syndecan-Mediated Ligation of ECM Proteins Triggers Proliferative Arrest of Disseminated Tumor Cells
Authors: Shibue Tsukasa , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Extended descriptions on experimental strategy
Supplementary Figures (S1-S18) from Syndecan-Mediated Ligation of ECM Proteins Triggers Proliferative Arrest of Disseminated Tumor Cells
Authors: Shibue Tsukasa , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Supplementary Figure S1. Involvement of integrin:FAK-signaling in driving ERK activation and proliferation in vivo, related to Figure 1; Supplementary Figure S2. In vitro and in vivo behaviors of various mammary carcinoma cell types, related to Figure 1; Supplementary Figure S3. MoT culture as an in vitro model system to study signaling in DTCs, related to Figures 1 and 2; Supplementary Figure S4. ECM proteins in the lungs that surround recently-extravasated solitary DTCs, related to Figures 1 and 2; Supplementary Figure S5. KSR phosphorylation in nonaggressive/aggressive cancer cell types, related to Figure 2; Supplementary Figure S6. Restoration of ERK activation and proliferation by genetic depletion of Par-1, related to Figure 3; Supplementary Figure S7. Par-1:KSR:Ras/ERK signaling in various cell line models, related to Figure 3; Supplementary Figure S8. Par-1b phosphorylation and its effect on KSR:Ras/ERK signaling, related to Figure 3; Supplementary Figure S9. Function and expression of polarity-regulating proteins, related to Figure 4; Supplementary Figure S10. Distribution of polarity-regulating proteins in 3D conditions, related to Figure 4; Supplementary Figure S11. Restoration of ERK activation and proliferation by genetic depletion of Par-3, related to Figure 5; Supplementary Figure S12. Syndecans as crucial cell-surface sensors for the 3D ECM configuration, related to Figure 6; Supplementary Figure S13. Functional role of syndecans in regulating D2.1 cell behaviors in 3D conditions, related to Figure 6; Supplementary Fig. S14. Genetic inactivation of syndecans and its effect on aggressive cell behaviors, related to Figure 7; Supplementary Fig. S15. Concomitant operations of integrin:FAK-mediated pro-proliferative signaling and syndecan-mediated anti-proliferative signaling in the aggressive D2A1 cells, extended experimental results; Supplementary Fig. S16. Restoration of Par-3 and syndecan-1 expression in the B16F10 melanoma cells, extended experimental results; Supplementary Fig. S17. Evidence for genetic alterations to inactivate syndecan-mediated anti-proliferative signaling machinery in human cancers, extended analyses; Supplementary Fig. S18. Syndecan-mediated anti-proliferative signaling machinery that prevents the outgrowth of solitary DTCs, a summary illustration
Supplementary Tables from A ceRNA Circuitry Involving the Long Noncoding RNA Klhl14-AS, Pax8, and Bcl2 Drives Thyroid Carcinogenesis
Authors: Credendino Sara C. , Bellone Maria L. , Lewin Nicole , Amendola Elena , Sanges Remo , Basu Swaraj , Sepe Romina , Decaussin-Petrucci Myriam , Tinto Nadia , Fusco Alfredo , De Felice Mario , De Vita Gabriella
Published: April 2023

Supplementary tables S1-S5. Tab S1: Oligonucleo1des used as primers for qRT-PCR; Tab S2: Oligonucleo1des used for cloning in either reporter or expression vectors. Only gene-specific sequences are reported; Tab S3: Klhl-14-AS specific oligonucleo1des used in RNA pull-down experiments; Tab S4: PITA analysis results of miRNA binding sites. The conserved region of Klhl14-AS was analyzed by using PITA algorithm for the presence of binding sites for miRNAs. Only miRNAs predicted to bind on the conserved sequences in all the species are shown; Tab S5: Rat Pax8 and Bcl-2 MREs. PutaZve MREs on the Bcl2 and Pax8 transcripts were idenZfied by searching for rno-miR-182 and rno-miR-20a-5p canonical (7-8- nt) and marginal (6-nt) seed-matched sites using a custom Perl script.
Figure S1 from Parallel Signaling through IRE1α and PERK Regulates Pancreatic Neuroendocrine Tumor Growth and Survival
Authors: Moore Paul C. , Qi Jenny Y. , Thamsen Maike , Ghosh Rajarshi , Peng Justin , Gliedt Micah J. , Meza-Acevedo Rosa , Warren Rachel E. , Hiniker Annie , Kim Grace E. , Maly Dustin J. , Backes Bradley J. , Papa Feroz R. , Oakes Scott A.
Published: April 2023

Majority of primary human PanNETs show elevated ER stress
Supplementary Material (Table S1-S3, Figure S1-S2) from High Levels of C-Reactive Protein Are Associated with an Increased Risk of Ovarian Cancer: Results from the Ovarian Cancer Cohort Consortium
Authors: Peres Lauren C. , Mallen Adrianne R. , Townsend Mary K. , Poole Elizabeth M. , Trabert Britton , Allen Naomi E. , Arslan Alan A. , Dossus Laure , Fortner Renée T. , Gram Inger T. , Hartge Patricia , Idahl Annika , Kaaks Rudolf , Kvaskoff Marina , Magliocco Anthony M. , Merritt Melissa A. , Quirós J. Ramón , Tjonneland Anne , Trichopoulou Antonia , Tumino Rosario , van Gils Carla H. , Visvanathan Kala , Wentzensen Nicolas , Zeleniuch-Jacquotte Anne , Tworoger Shelley S.
Published: April 2023

Table S1. Association between CRP and ovarian cancer risk by OC3 study Table S2. Association between CRP and ovarian cancer risk for various sensitivity analyses, including exclusion of PLCO, exclusion of women diagnosed within 2 years of blood draw, additional adjustment for aspirin use, and exclusion of women with cardiovascular disease Table S3. Association between CRP and ovarian cancer risk by time between blood draw and diagnosis Figure S1. Restricted cubic splines of the association between CRP and ovarian cancer risk using two approaches to identify CRP outliers Figure S2. Restricted cubic splines of the association between CRP and risk of serous and non-serous ovarian cancer
Figure S4 from Tumor Angiogenesis Is Differentially Regulated by Phosphorylation of Endothelial Cell Focal Adhesion Kinase Tyrosines-397 and -861
Authors: Pedrosa Ana-Rita , Bodrug Natalia , Gomez-Escudero Jesus , Carter Edward P. , Reynolds Louise E. , Georgiou Paraskivi Natalia , Fernandez Isabelle , Lees Delphine M. , Kostourou Vassiliki , Alexopoulou Annika N. , Batista Silvia , Tavora Bernardo , Serrels Bryan , Parsons Maddy , Iskratsch Thomas , Hodivala-Dilke Kairbaan M.
Published: April 2023

Supplementary Figure 4. Loss of endothelial cell FAK-Y397 or FAK-Y861 phosphorylation has no detectable effect on blood vessel perfusion or maturation.
Supplementary Methods from MYC Regulates the HIF2α Stemness Pathway via Nanog and Sox2 to Maintain Self-Renewal in Cancer Stem Cells versus Non-Stem Cancer Cells
Authors: Das Bikul , Pal Bidisha , Bhuyan Rashmi , Li Hong , Sarma Anupam , Gayan Sukanya , Talukdar Joyeeta , Sandhya Sorra , Bhuyan Seema , Gogoi Gayatri , Gouw Arvin M. , Baishya Debabrat , Gotlib Jason R. , Kataki Amal C. , Felsher Dean W.
Published: April 2023

Supplemental Methods elaborate the details of each methodology/approaches being used in the manuscript
Supplementary Figures from MYC Regulates the HIF2α Stemness Pathway via Nanog and Sox2 to Maintain Self-Renewal in Cancer Stem Cells versus Non-Stem Cancer Cells
Authors: Das Bikul , Pal Bidisha , Bhuyan Rashmi , Li Hong , Sarma Anupam , Gayan Sukanya , Talukdar Joyeeta , Sandhya Sorra , Bhuyan Seema , Gogoi Gayatri , Gouw Arvin M. , Baishya Debabrat , Gotlib Jason R. , Kataki Amal C. , Felsher Dean W.
Published: April 2023

Supplemental figures provide additional supporting data to claim that MYC regulates the HIF-2a stemness pathway via Nanog and Sox2 to maintain self-renewal in CSCs versus non-CSCs
Supplementary Data from Selective Targeting of Myoblast Fusogenic Signaling and Differentiation-Arrest Antagonizes Rhabdomyosarcoma Cells
Authors: Granados Valerie A. , Avirneni-Vadlamudi Usha , Dalal Pooja , Scarborough Samuel R. , Galindo Kathleen A. , Mahajan Priya , Galindo Rene L.
Published: April 2023

Included here are Supplemental Methods, as well as four Supplemental Figures. These Figures show data supporting the notions that EGFR inhibitors antagonize RMS in vitro and in vivo, and that Akt1 intracellular activity is an RMS therapeutic target.
Supplementary Figure 5 from Macrophage-Derived IL1β and TNFα Regulate Arginine Metabolism in Neuroblastoma
Authors: Fultang Livingstone , Gamble Laura D. , Gneo Luciana , Berry Andrea M. , Egan Sharon A. , De Bie Fenna , Yogev Orli , Eden Georgina L. , Booth Sarah , Brownhill Samantha , Vardon Ashley , McConville Carmel M. , Cheng Paul N. , Norris Murray D. , Etchevers Heather C. , Murray Jayne , Ziegler David S. , Chesler Louis , Schmidt Ronny , Burchill Susan A. , Haber Michelle , De Santo Carmela , Mussai Francis
Published: April 2023

Supplementary Figure 5 : IL-1ï�¢ï€ and TNF-ï�¡ï€ drive neuroblastoma cell proliferation
Supplementary Table S4 from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

MSI status transcriptional signature and GSEA analysis performed comparing MSI vs MSS samples
Supplementary Figure 4 from Macrophage-Derived IL1β and TNFα Regulate Arginine Metabolism in Neuroblastoma
Authors: Fultang Livingstone , Gamble Laura D. , Gneo Luciana , Berry Andrea M. , Egan Sharon A. , De Bie Fenna , Yogev Orli , Eden Georgina L. , Booth Sarah , Brownhill Samantha , Vardon Ashley , McConville Carmel M. , Cheng Paul N. , Norris Murray D. , Etchevers Heather C. , Murray Jayne , Ziegler David S. , Chesler Louis , Schmidt Ronny , Burchill Susan A. , Haber Michelle , De Santo Carmela , Mussai Francis
Published: April 2023

Supplementary Figure 4 Macrophage infiltration and downstream effects on neuroblastoma tumours
Supplementary Table S1 from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

Baseline characteristics of the 349 enrolled patients.
Supplementary Methods from A Comprehensive PDX Gastric Cancer Collection Captures Cancer Cell–Intrinsic Transcriptional MSI Traits
Authors: Corso Simona , Isella Claudio , Bellomo Sara E. , Apicella Maria , Durando Stefania , Migliore Cristina , Ughetto Stefano , D’Errico Laura , Menegon Silvia , Moya-Rull Daniel , Cargnelutti Marilisa , Capelôa Tânia , Conticelli Daniela , Giordano Jessica , Venesio Tiziana , Balsamo Antonella , Marchiò Caterina , Degiuli Maurizio , Reddavid Rossella , Fumagalli Uberto , De Pascale Stefano , Sgroi Giovanni , Rausa Emanuele , Baiocchi Gian Luca , Molfino Sarah , Pietrantonio Filippo , Morano Federica , Siena Salvatore , Sartore-Bianchi Andrea , Bencivenga Maria , Mengardo Valentina , Rosati Riccardo , Marrelli Daniele , Morgagni Paolo , Rausei Stefano , Pallabazzer Giovanni , De Simone Michele , Ribero Dario , Marsoni Silvia , Sottile Antonino , Medico Enzo , Cassoni Paola , Sapino Anna , Pectasides Eirini , Thorner Aaron R. , Nag Anwesha , Drinan Samantha D. , Wollison Bruce M. , Bass Adam J. , Giordano Silvia
Published: April 2023

Supplementary Methods
Table S2 from Chemotherapy-Induced Extracellular Vesicle miRNAs Promote Breast Cancer Stemness by Targeting ONECUT2
Authors: Shen Meng , Dong Chuan , Ruan Xianhui , Yan Wei , Cao Minghui , Pizzo Donald , Wu Xiwei , Yang Lin , Liu Liang , Ren Xiubao , Wang Shizhen Emily
Published: April 2023

Table S2 showing chemo-EV miRNAs identified by small RNA-seq
Figure S4 from The Deubiquitylase OTUB1 Mediates Ferroptosis via Stabilization of SLC7A11
Authors: Liu Tong , Jiang Le , Tavana Omid , Gu Wei
Published: April 2023

The loss of OTUB1 induces ferroptosis in SK-N-BE(2)C cells
Supplementary Figures from An ERG Enhancer–Based Reporter Identifies Leukemia Cells with Elevated Leukemogenic Potential Driven by ERG-USP9X Feed-Forward Regulation
Authors: Aqaqe Nasma , Yassin Muhammad , Yassin Abed Alkader , Ershaid Nour , Katz-Even Chen , Zipin-Roitman Adi , Kugler Eitan , Lechman Eric R. , Gan Olga I. , Mitchell Amanda , Dick John E. , Izraeli Shai , Milyavsky Michael
Published: April 2023

Supplementary Figures
Movie S2 from Assessment of Tumor Redox Status through (S)-4-(3-[18F]fluoropropyl)-L-Glutamic Acid PET Imaging of System xc− Activity
Authors: McCormick Patrick N. , Greenwood Hannah E. , Glaser Matthias , Maddocks Oliver D.K. , Gendron Thibault , Sander Kerstin , Gowrishankar Gayatri , Hoehne Aileen , Zhang Tong , Shuhendler Adam J. , Lewis David Y. , Berndt Mathias , Koglin Norman , Lythgoe Mark F. , Gambhir Sanjiv S. , Årstad Erik , Witney Timothy H.
Published: April 2023

Movie S2
Movie S1 from Assessment of Tumor Redox Status through (S)-4-(3-[18F]fluoropropyl)-L-Glutamic Acid PET Imaging of System xc− Activity
Authors: McCormick Patrick N. , Greenwood Hannah E. , Glaser Matthias , Maddocks Oliver D.K. , Gendron Thibault , Sander Kerstin , Gowrishankar Gayatri , Hoehne Aileen , Zhang Tong , Shuhendler Adam J. , Lewis David Y. , Berndt Mathias , Koglin Norman , Lythgoe Mark F. , Gambhir Sanjiv S. , Årstad Erik , Witney Timothy H.
Published: April 2023

Movie S1
Legends to Supplementary Tables and Figures from DNA Methylation Controls Metastasis-Suppressive 14q32-Encoded miRNAs
Authors: Oshima Go , Poli Elizabeth C. , Bolt Michael J. , Chlenski Alexandre , Forde Martin , Jutzy Jessica M.S. , Biyani Neha , Posner Mitchell C. , Pitroda Sean P. , Weichselbaum Ralph R. , Khodarev Nikolai N.
Published: April 2023

Legends to Supplementary Tables S1-S4 and Supplementary Figures S1-S8
Supplementary Data from p300 Mediates Muscle Wasting in Lewis Lung Carcinoma
Authors: Sin Thomas K. , Zhu James Z. , Zhang Guohua , Li Yi-Ping
Published: April 2023

Figure S1. Genotyping p300 mKO Figure S2. Lys39 mutation effect on Thr188 phosphorylation Figure S3. Lys39 acetylation is required for muscle mass loss Figure S4. Acetyltransferase activity of p300 is required for muscle mass loss Figure S5. p300 is not required for activation of p38 and NF-kB
Table S4 from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Table S4 contains all apoptotic effects of single agent inhibitors and their combinations (original data of Fig 1C and Fig. S3).
Supplementary Methods from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Additional information on data analysis and experimental procedures are included in the Supplementary Methods.
Supplementary Data from Dual Inhibition of GLUT1 and the ATR/CHK1 Kinase Axis Displays Synergistic Cytotoxicity in KRAS-Mutant Cancer Cells
Authors: Erber Johanna , Steiner Joachim D. , Isensee Jörg , Lobbes Leonard A. , Toschka André , Beleggia Filippo , Schmitt Anna , Kaiser Rainer W. J. , Siedek Florian , Persigehl Thorsten , Hucho Tim , Reinhardt Hans C.
Published: April 2023

Table S6 contains all p-values related to Fig. 4C.
Figure S3 from Prolactin Promotes Fibrosis and Pancreatic Cancer Progression
Authors: Tandon Manuj , Coudriet Gina M. , Criscimanna Angela , Socorro Mairobys , Eliliwi Mouhanned , Singhi Aatur D. , Cruz-Monserrate Zobeida , Bailey Peter , Lotze Michael T. , Zeh Herbert , Hu Jing , Goffin Vincent , Gittes George K. , Biankin Andrew V. , Esni Farzad
Published: April 2023

Total FAK1 and STAT3 are present in KC;Prl-/- PanINs.
Supplementary Methods and oligonucleotide sequences from BRCA1 Deficiency Upregulates NNMT, Which Reprograms Metabolism and Sensitizes Ovarian Cancer Cells to Mitochondrial Metabolic Targeting Agents
Authors: Kanakkanthara Arun , Kurmi Kiran , Ekstrom Thomas L. , Hou Xiaonan , Purfeerst Emma R. , Heinzen Ethan P. , Correia Cristina , Huntoon Catherine J. , O'Brien Daniel , Wahner Hendrickson Andrea E. , Dowdy Sean C. , Li Hu , Oberg Ann L. , Hitosugi Taro , Kaufmann Scott H. , Weroha S. John , Karnitz Larry M.
Published: April 2023

Supplementary Methods file that includes oligonucleotide sequences used in the study.
Supplementary Figure 7 from Secretion of Acid Sphingomyelinase and Ceramide by Endothelial Cells Contributes to Radiation-Induced Intestinal Toxicity
Authors: Leonetti Daniela , Estéphan Hala , Ripoche Natacha , Dubois Nolwenn , Aguesse Audrey , Gouard Sébastien , Brossard Lisa , Chiavassa Sophie , Corre Isabelle , Pecqueur Claire , Neunlist Michel , Hadchity Elie , Gaugler Marie-Hélène , Mahé Maxime M. , Paris François
Published: April 2023

SupFigure7
Supplementary Figure 6 from Secretion of Acid Sphingomyelinase and Ceramide by Endothelial Cells Contributes to Radiation-Induced Intestinal Toxicity
Authors: Leonetti Daniela , Estéphan Hala , Ripoche Natacha , Dubois Nolwenn , Aguesse Audrey , Gouard Sébastien , Brossard Lisa , Chiavassa Sophie , Corre Isabelle , Pecqueur Claire , Neunlist Michel , Hadchity Elie , Gaugler Marie-Hélène , Mahé Maxime M. , Paris François
Published: April 2023

SupFigure6
Figure S7 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Pathway analysis and GSEA based comparison of the independent effects of cancer and chemotherapy show convergence of mitochondrial dysfunction
Figure S6 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Steps outlining parallel independent transcriptome analyses
Figure S4 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

'Kruschke style' hierarchical model graphical diagram
Figure S2 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Longitudinal change in animal weight
Figure S4 from Long-Term Gemcitabine Treatment Reshapes the Pancreatic Tumor Microenvironment and Sensitizes Murine Carcinoma to Combination Immunotherapy
Authors: Principe Daniel R. , Narbutis Matthew , Kumar Sandeep , Park Alex , Viswakarma Navin , Dorman Matthew J. , Kamath Suneel D. , Grippo Paul J. , Fishel Melissa L. , Hwang Rosa F. , Thummuri Dinesh , Underwood Patrick W. , Munshi Hidayatullah G. , Trevino Jose G. , Rana Ajay
Published: April 2023

Gemcitabine alters paracrine interactions between cancer and stromal cells in vitro
Figure S16 from Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy
Authors: Housley Stephen N. , Nardelli Paul , Carrasco Dario I. , Rotterman Travis M. , Pfahl Emily , Matyunina Lilya V. , McDonald John F. , Cope Timothy C.
Published: April 2023

Kv3.3 Immunostaining of neuromuscular junction
Figure S3 from Long-Term Gemcitabine Treatment Reshapes the Pancreatic Tumor Microenvironment and Sensitizes Murine Carcinoma to Combination Immunotherapy
Authors: Principe Daniel R. , Narbutis Matthew , Kumar Sandeep , Park Alex , Viswakarma Navin , Dorman Matthew J. , Kamath Suneel D. , Grippo Paul J. , Fishel Melissa L. , Hwang Rosa F. , Thummuri Dinesh , Underwood Patrick W. , Munshi Hidayatullah G. , Trevino Jose G. , Rana Ajay
Published: April 2023

Cytotoxic chemotherapy alters the immune surface profile of Capan1 and Bxpc3 tumor cells in vitro
Figure S2 from Long-Term Gemcitabine Treatment Reshapes the Pancreatic Tumor Microenvironment and Sensitizes Murine Carcinoma to Combination Immunotherapy
Authors: Principe Daniel R. , Narbutis Matthew , Kumar Sandeep , Park Alex , Viswakarma Navin , Dorman Matthew J. , Kamath Suneel D. , Grippo Paul J. , Fishel Melissa L. , Hwang Rosa F. , Thummuri Dinesh , Underwood Patrick W. , Munshi Hidayatullah G. , Trevino Jose G. , Rana Ajay
Published: April 2023

Gemcitabine alters antigen presentation and tumor-derived cytokine production in primary human tumor cells in vitro
Figure S1 from Long-Term Gemcitabine Treatment Reshapes the Pancreatic Tumor Microenvironment and Sensitizes Murine Carcinoma to Combination Immunotherapy
Authors: Principe Daniel R. , Narbutis Matthew , Kumar Sandeep , Park Alex , Viswakarma Navin , Dorman Matthew J. , Kamath Suneel D. , Grippo Paul J. , Fishel Melissa L. , Hwang Rosa F. , Thummuri Dinesh , Underwood Patrick W. , Munshi Hidayatullah G. , Trevino Jose G. , Rana Ajay
Published: April 2023

Gemcitabine alters antigen presentation and tumor-derived cytokine production in murine tumor cells
Figure S2 from Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer
Authors: Wang Shidan , Rong Ruichen , Yang Donghan M. , Fujimoto Junya , Yan Shirley , Cai Ling , Yang Lin , Luo Danni , Behrens Carmen , Parra Edwin R. , Yao Bo , Xu Lin , Wang Tao , Zhan Xiaowei , Wistuba Ignacio I. , Minna John , Xie Yang , Xiao Guanghua
Published: April 2023

Supplemental Figure S2 Illustration of instance segmentation using the developed HD-Staining model.
Figure S8 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

Basal levels of BRD4 mRNA in NSCLC cell lines
Figure S5 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

ZBC260 effectively decreases BRD4 accompanied with reduction of Mcl-1, Bim and c-FLIP in SCLC cells.
Figure S4 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

ZBC260, dBET and JQ-1 differentially modulate the levels of BET proteins, c-Myc, Mcl-1 and c-FLIP in PC-9 cells.
Figure S2 from BRD4 Levels Determine the Response of Human Lung Cancer Cells to BET Degraders That Potently Induce Apoptosis through Suppression of Mcl-1
Authors: Zong Dan , Gu Jiajia , Cavalcante Giovanna C. , Yao Weilong , Zhang Guojing , Wang Shaomeng , Owonikoko Taofeek K. , He Xia , Sun Shi-Yong
Published: April 2023

ZBC260 exhibits more potent activity than CQ-1 in inducing apoptosis in SCLC cells.
Table S1 from GPD1 Enhances the Anticancer Effects of Metformin by Synergistically Increasing Total Cellular Glycerol-3-Phosphate
Authors: Xie Jianjiang , Ye Jianheng , Cai Zhiduan , Luo Yong , Zhu Xuejin , Deng Yulin , Feng Yuanfa , Liang Yingke , Liu Ren , Han Zhaodong , Liang Yuxiang , Zheng Yu , Mo Rujun , Zhuo Yangjia , Wu Yongding , Jiang Funeng , Zhu Jianguo , Wu Chin-Lee , Zhong Weide
Published: April 2023

Table S1 showed the IC50 values for metformin in cells and GPD1 overexpression cells.
Supplementary Table 7 from Transcriptome-Wide Association Study Identifies New Candidate Susceptibility Genes for Glioma
Authors: Atkins Isabelle , Kinnersley Ben , Ostrom Quinn T. , Labreche Karim , Il'yasova Dora , Armstrong Georgina N. , Eckel-Passow Jeanette E. , Schoemaker Minouk J. , Nöthen Markus M. , Barnholtz-Sloan Jill S. , Swerdlow Anthony J. , Simon Matthias , Rajaraman Preetha , Chanock Stephen J. , Shildkraut Joellen , Bernstein Jonine L. , Hoffmann Per , Jöckel Karl-Heinz , Lai Rose K. , Claus Elizabeth B. , Olson Sara H. , Johansen Christoffer , Wrensch Margaret R. , Melin Beatrice , Jenkins Robert B. , Sanson Marc , Bondy Melissa L. , Houlston Richard S.
Published: April 2023

Supplementary Table 7: S-PrediXcan statistics at each brain tissue for the 31 identified gene associations.
Supplementary information from GPD1 Enhances the Anticancer Effects of Metformin by Synergistically Increasing Total Cellular Glycerol-3-Phosphate
Authors: Xie Jianjiang , Ye Jianheng , Cai Zhiduan , Luo Yong , Zhu Xuejin , Deng Yulin , Feng Yuanfa , Liang Yingke , Liu Ren , Han Zhaodong , Liang Yuxiang , Zheng Yu , Mo Rujun , Zhuo Yangjia , Wu Yongding , Jiang Funeng , Zhu Jianguo , Wu Chin-Lee , Zhong Weide
Published: April 2023

Supplementary Information showed the additional details, such as reagents and assay kit, list of antibodies, sequences, primers and abbreviation.
Figure S4 from GPD1 Enhances the Anticancer Effects of Metformin by Synergistically Increasing Total Cellular Glycerol-3-Phosphate
Authors: Xie Jianjiang , Ye Jianheng , Cai Zhiduan , Luo Yong , Zhu Xuejin , Deng Yulin , Feng Yuanfa , Liang Yingke , Liu Ren , Han Zhaodong , Liang Yuxiang , Zheng Yu , Mo Rujun , Zhuo Yangjia , Wu Yongding , Jiang Funeng , Zhu Jianguo , Wu Chin-Lee , Zhong Weide
Published: April 2023

Figure S4 showed that the extracellular acidification rate assay in GPD1 overexpressing cells and the CCK8 assay and the oxygen consumption rate in GPD1 knock-down cells.
Video S6 from ICOS Is an Indicator of T-cell–Mediated Response to Cancer Immunotherapy
Authors: Xiao Zunyu , Mayer Aaron T. , Nobashi Tomomi W. , Gambhir Sanjiv S.
Published: April 2023

Video S6: PBS i.p group Day 2 PET image
Video S4 from ICOS Is an Indicator of T-cell–Mediated Response to Cancer Immunotherapy
Authors: Xiao Zunyu , Mayer Aaron T. , Nobashi Tomomi W. , Gambhir Sanjiv S.
Published: April 2023

Video S4: PBS i.t group Day 2 PET image
Supplementary Methods from FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy
Authors: Manfrini Nicola , Mancino Marilena , Miluzio Annarita , Oliveto Stefania , Balestra Matteo , Calamita Piera , Alfieri Roberta , Rossi Riccardo L. , Sassoè-Pognetto Marco , Salio Chiara , Cuomo Alessandro , Bonaldi Tiziana , Manfredi Marcello , Marengo Emilio , Ranzato Elia , Martinotti Simona , Cittaro Davide , Tonon Giovanni , Biffo Stefano
Published: April 2023

Detailed methods
Figure S3 from The MDM2/MDMX-p53 Antagonist PM2 Radiosensitizes Wild-Type p53 Tumors
Authors: Spiegelberg Diana , Mortensen Anja C. , Lundsten Sara , Brown Christopher J. , Lane David P. , Nestor Marika
Published: April 2023

Supplemental Figure 3. A) Left: Tumor spheroid sizes of untreated controls and DMSO-treated (1x, 2x and 3x treated with 0.2 % DMSO at 48 h intervals). UM-SCC-74B spheroids at day 8 post start of treatment normalized to percentage of untreated controls. No significant differences were detected between untreated controls and DMSO-treated spheroids. n {greater than or equal to} 4, error bars = SD. Right: Representative images of UM-SCC-74B spheroids for the corresponding treatments. B) Drug efficacy assay in two wt p53 tumor spheroid models. Growth inhibitory effects of PM2 using two different treatment regimens on HCT116 wt p53 spheroids (left) and UM-SCC-74B wt p53 spheroids (right) was followed over time. n{greater than or equal to}5, error bars = 95 % CI. One weekly dose of 20 µM PM2 resulted in the same growth inhibitory effects as three repeated doses of 20 µM at 48 h intervals. C) Tumor spheroid therapy experiments in four tumor spheroid models. Top row: Tumor spheroid of untreated controls, PM2-treated (20 µM), irradiated (2 Gy), and combination (20 µM of PM2 and 2 Gy of irradiation) at day 10 (wt p53 UM-SCC-74A, wt p53 HCT116 and mutant p53 BON) or day 7 (wt p53 UM-SCC-74B) post treatment normalized to percentage of untreated controls. n {greater than or equal to} 5. p-values were calculated using one-way ANOVA followed by Tukey's multiple comparisons test; p<0.05 (*), p<0.01 (**), p<0.001 (***), p<0.0001 (****). Bottom row: Representative images of the spheroids at the corresponding treatments.
Figure S2 from The MDM2/MDMX-p53 Antagonist PM2 Radiosensitizes Wild-Type p53 Tumors
Authors: Spiegelberg Diana , Mortensen Anja C. , Lundsten Sara , Brown Christopher J. , Lane David P. , Nestor Marika
Published: April 2023

Supplemental Figure 2. A) LDH release assay. PM2 and PM2-Scrambled were titrated on to T22 p53 reporter cells and LDH release was measured. The scrambled variant of PM2 has the same amino acid composition as PM2. However the residues that are involved in interacting with p53 (F19, W23, L26) have been interchanged with each other to abrogate binding to p53. B) p53 activation assay. PM2 and PM2-Scrambled were titrated on to T22 p53 reporter cells and their p53 transcriptional activation assessed in the presence of 10 % FCS after 18 h of treatment. C) Dose-response of PM2, assessed by XTT cell viability assay on HCT116 (wt p53) cells. Viability was defined as percent absorbance compared to untreated control. IC50 was calculated to 12.26-19.35 µM (95 % CI). D) Determination of solubility of PM2 in PBS with standard addition assay. A linear regression model was fitted to the experimental data points, where the concentration of PM2 in the cuvette correlates to the X-intercept of the dashed line. The resulting solubility of PM2 in PBS was 54.02 µM. Graph shows mean and SD, n=3.
Supplementary Figure 6 from A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier
Authors: Hilfenhaus Georg , Mompeón Ana , Freshman Jonathan , Prajapati Divya P. , Hernandez Gloria , Freitas Vanessa M. , Ma Feiyang , Langenbacher Adam D. , Mirkov Snezana , Song Dana , Cho Byoung-Kyu , Goo Young Ah , Pellegrini Matteo , Chen Jau-Nian , Damoiseaux Robert , Iruela-Arispe M. Luisa
Published: April 2023

Analysis of scRNAseq findings
Figure S1 from The MDM2/MDMX-p53 Antagonist PM2 Radiosensitizes Wild-Type p53 Tumors
Authors: Spiegelberg Diana , Mortensen Anja C. , Lundsten Sara , Brown Christopher J. , Lane David P. , Nestor Marika
Published: April 2023

Supplemental Figure 1. Western blot analysis of A) HCT116 wt p53, B) HCT116 p53 -/- and C) T22 p53 reporter cells treated with either 50 µM, 25 µM, 12.5 µM and 6.25 µM PM2 or the PM2 scrambled control.
Supplementary Figure 4 from A High-Content Screen Identifies Drugs That Restrict Tumor Cell Extravasation across the Endothelial Barrier
Authors: Hilfenhaus Georg , Mompeón Ana , Freshman Jonathan , Prajapati Divya P. , Hernandez Gloria , Freitas Vanessa M. , Ma Feiyang , Langenbacher Adam D. , Mirkov Snezana , Song Dana , Cho Byoung-Kyu , Goo Young Ah , Pellegrini Matteo , Chen Jau-Nian , Damoiseaux Robert , Iruela-Arispe M. Luisa
Published: April 2023

Effect of drug hits on cortical actin and tumor cell migration and invasion
Supplementary Data from A Novel Locus Predicts Spermatogenic Recovery among Childhood Cancer Survivors Exposed to Alkylating Agents
Authors: Sapkota Yadav , Wilson Carmen L. , Zaidi Asifa K. , Moon Wonjong , Fon Tacer Klementina , Lu Lu , Liu Qi , Baedke Jessica , Dhaduk Rikeenkumar , Wang Zhaoming , Chemaitilly Wassim , Krasin Matthew J. , Berry Fred B. , Zhang Jinghui , Hudson Melissa M. , Robison Leslie L. , Green Daniel M. , Yasui Yutaka
Published: April 2023

Sup Table 1: Age-adjusted testosterone, FSH and LH levels in community controls. Sup Table 2: Non-genetic model for sperm concentration (millions/mL) among 201 unirradiated male survivors who were exposed to CED. Sup Table 3: Sperm characteristics in oligospermic and normospermic semen analysis participants in the discovery sample. Sup Table 4: Rare variant associations for sperm concentration (millions/mL) showing statistical significance in standard burden and SKAT tests and their results based on permutation-based analyses. Sup Table 5: Meta-analysis of discovery and replications results for the chromosome 7q21.3 locus associated with sperm concentration. Sup Table 6: The association of rs7784118 with sperm concentration in the discovery sample, stratified by endocrine parameters. Sup Table 7: Consistency of two different semen analyses for the 16 male survivors in the discovery sample. Sup Figure 1: Principal component analysis (PCA) of survivors in the SJLIFE WGS dataset. Sup Figure 2: Quantile-quantile plot for the common variant analysis of sperm concentration in the discovery sample. Sup Figure 3: Distribution of sperm concentration (millions/mL) with respect to genotypes of rs7784118 in the discovery cohort.
Figure S4 from Notch-Induced Myeloid Reprogramming in Spontaneous Pancreatic Ductal Adenocarcinoma by Dual Genetic Targeting
Authors: Cheung Phyllis F. , Neff Florian , Neander Christian , Bazarna Anna , Savvatakis Konstantinos , Liffers Sven-Thorsten , Althoff Kristina , Lee Chang-Lung , Moding Everett J. , Kirsch David G , Saur Dieter , Bazhin Alexandr V. , Trajkovic-Arsic Marija , Heikenwalder Mathias F. , Siveke Jens T.
Published: April 2023

Neither myeloid-specific Notch activation nor Rbpj knock out exerts systemic effect on immune system; and Stromal characterization of FKP tumors upon Notch modulation.
Figure S3 from Notch-Induced Myeloid Reprogramming in Spontaneous Pancreatic Ductal Adenocarcinoma by Dual Genetic Targeting
Authors: Cheung Phyllis F. , Neff Florian , Neander Christian , Bazarna Anna , Savvatakis Konstantinos , Liffers Sven-Thorsten , Althoff Kristina , Lee Chang-Lung , Moding Everett J. , Kirsch David G , Saur Dieter , Bazhin Alexandr V. , Trajkovic-Arsic Marija , Heikenwalder Mathias F. , Siveke Jens T.
Published: April 2023

Characterization of stromal environment and Notch expression in FKP-based PDAC.
Figure S2 from Notch-Induced Myeloid Reprogramming in Spontaneous Pancreatic Ductal Adenocarcinoma by Dual Genetic Targeting
Authors: Cheung Phyllis F. , Neff Florian , Neander Christian , Bazarna Anna , Savvatakis Konstantinos , Liffers Sven-Thorsten , Althoff Kristina , Lee Chang-Lung , Moding Everett J. , Kirsch David G , Saur Dieter , Bazhin Alexandr V. , Trajkovic-Arsic Marija , Heikenwalder Mathias F. , Siveke Jens T.
Published: April 2023

Induction of bone marrow-derived macrophages (BMDM)
Figure S1 from Notch-Induced Myeloid Reprogramming in Spontaneous Pancreatic Ductal Adenocarcinoma by Dual Genetic Targeting
Authors: Cheung Phyllis F. , Neff Florian , Neander Christian , Bazarna Anna , Savvatakis Konstantinos , Liffers Sven-Thorsten , Althoff Kristina , Lee Chang-Lung , Moding Everett J. , Kirsch David G , Saur Dieter , Bazhin Alexandr V. , Trajkovic-Arsic Marija , Heikenwalder Mathias F. , Siveke Jens T.
Published: April 2023

Stromal characterization of preneoplasia, early and late PDAC, and normal pancreas; and gating strategies in flow cytometry
Figure S2 from Tumor Cell–Derived IL1β Promotes Desmoplasia and Immune Suppression in Pancreatic Cancer
Authors: Das Shipra , Shapiro Beny , Vucic Emily A. , Vogt Sandra , Bar-Sagi Dafna
Published: April 2023

Tumor cell-derived IL-1b regulates stromal immune cell profile and IL-1b production.
Supplementary Data from Hypoxia Induces Resistance to EGFR Inhibitors in Lung Cancer Cells via Upregulation of FGFR1 and the MAPK Pathway
Authors: Lu Yuhong , Liu Yanfeng , Oeck Sebastian , Zhang Gary J. , Schramm Alexander , Glazer Peter M.
Published: April 2023

Supplementary figures 1 to 10 and figure legends.
Figure S1 from Tumor Cell–Derived IL1β Promotes Desmoplasia and Immune Suppression in Pancreatic Cancer
Authors: Das Shipra , Shapiro Beny , Vucic Emily A. , Vogt Sandra , Bar-Sagi Dafna
Published: April 2023

IL-1 signaling in the PDA stroma promotes oncogenesis.
Supplementary Materials and Methods from Dynamics of Genomic, Epigenomic, and Transcriptomic Aberrations during Stepwise Hepatocarcinogenesis
Authors: Jee Byul A , Choi Ji-Hye , Rhee Hyungjin , Yoon Sarah , Kwon So Mee , Nahm Ji Hae , Yoo Jeong Eun , Jeon Youngsic , Choi Gi Hong , Woo Hyun Goo , Park Young Nyun
Published: April 2023

Supplementary Materials and Methods
Table S7 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

A list of significant regulatory mutations in exonic regions.
Table S5 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

Lists of DEEP-Genic and DEEP-intergenic genes.
Supplementary Tables S1-S9 from A DNA Hypomethylating Drug Alters the Tumor Microenvironment and Improves the Effectiveness of Immune Checkpoint Inhibitors in a Mouse Model of Pancreatic Cancer
Authors: Gonda Tamas A. , Fang Jarwei , Salas Martha , Do Catherine , Hsu Emily , Zhukovskaya Anna , Siegel Ariel , Takahashi Ryota , Lopez-Bujanda Zoila A. , Drake Charles G. , Manji Gulam A. , Wang Timothy C. , Olive Kenneth P. , Tycko Benjamin
Published: April 2023

Supplementary tables S1-S9
Supplementary Figures S1-11 from A DNA Hypomethylating Drug Alters the Tumor Microenvironment and Improves the Effectiveness of Immune Checkpoint Inhibitors in a Mouse Model of Pancreatic Cancer
Authors: Gonda Tamas A. , Fang Jarwei , Salas Martha , Do Catherine , Hsu Emily , Zhukovskaya Anna , Siegel Ariel , Takahashi Ryota , Lopez-Bujanda Zoila A. , Drake Charles G. , Manji Gulam A. , Wang Timothy C. , Olive Kenneth P. , Tycko Benjamin
Published: April 2023

Supplementary figures S1-S11
Table S3 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

Significant peaks identified from the prostate ATAC-Seq experiment.
Figure S2 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

VAF comparison among deleterious, benign mutations and the genome background. All mutations are localized in gene promoter regions. P values were derived from Wilcoxon rank-sum test by comparing each mutation group against the genome background.
Figure S1 from A Deep Learning Framework Identifies Pathogenic Noncoding Somatic Mutations from Personal Prostate Cancer Genomes
Authors: Wang Cheng , Li Jingjing
Published: April 2023

The DEEP Neural Network Architecture and workflow of the DEEP score calculation for simple somatic mutations in prostate cancer. Layer1: convolution layer, kernels:320, window size:8, step size:1 Layer2: convolution layer, kernels:320, window size:8, step size:1 Layer3: pooling layer, kernel size: 4; step size:4; Layer4: convolution layer, kernels:480, window size:8, step size:1 Layer5: convolution layer, kernels:480, window size:8, step size:1 Layer6: pooling layer, kernel size: 4; step size:4; Layer7: convolution layer, kernels:640, window size:8, step size:1 Layer8: convolution layer, kernels:640, window size:8, step size:1 Layer9,10: fully connected layers; Layer11: Sigmoid output layer; All convolution layers were ReLU activated. 20% dropout were performed before the pooling layers. The weight (W) is a function that decays with the increased distance between mutations and the 200bp windows. We used k=5 as a magnifier. Finally, absolute values of the summed scores from two strands were taken to derive the DEEP scores.
Supplementary Tables from LDtrait: An Online Tool for Identifying Published Phenotype Associations in Linkage Disequilibrium
Authors: Lin Shu-Hong , Brown Derek W. , Machiela Mitchell J.
Published: April 2023

Example LDTrait queries and output for three variants: rs6983267, rs2736100, and rs2887399
Supplementary Data 6 from Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments
Authors: Kimmel Gregory J. , Dane Mark , Heiser Laura M. , Altrock Philipp M. , Andor Noemi
Published: April 2023

Simulation shown in Fig. 4F
Supplementary Figures from ARC Is a Critical Protector against Inflammatory Bowel Disease (IBD) and IBD-Associated Colorectal Tumorigenesis
Authors: Wang Qiushi , Zhang Tianshun , Chang Xiaoyu , Lim Do Young , Wang Keke , Bai Ruihua , Wang Ting , Ryu Joohyun , Chen Hanyong , Yao Ke , Ma Wei-Ya , Boardman Lisa A. , Bode Ann M. , Dong Zigang
Published: April 2023

Supplementary Figure 1-6
Supplementary Data 3 from Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments
Authors: Kimmel Gregory J. , Dane Mark , Heiser Laura M. , Altrock Philipp M. , Andor Noemi
Published: April 2023

Observed (experimentally measured) 1D growth patterns
Supplementary Table 1 from Brain Metastasis Cell Lines Panel: A Public Resource of Organotropic Cell Lines
Authors: Valiente Manuel , Van Swearingen Amanda E.D. , Anders Carey K. , Bairoch Amos , Boire Adrienne , Bos Paula D. , Cittelly Diana M. , Erez Neta , Ferraro Gino B. , Fukumura Dai , Gril Brunilde , Herlyn Meenhard , Holmen Sheri L. , Jain Rakesh K. , Joyce Johanna A. , Lorger Mihaela , Massague Joan , Neman Josh , Sibson Nicola R. , Steeg Patricia S. , Thorsen Frits , Young Leonie S. , Varešlija Damir , Vultur Adina , Weis-Garcia Frances , Winkler Frank
Published: April 2023

Table containing all brain metastatic cell lines in the BrMPanel
Table S1, Table S2 from YAP-Mediated Repression of HRK Regulates Tumor Growth, Therapy Response, and Survival Under Tumor Environmental Stress in Neuroblastoma
Authors: Shim Jenny , Lee Jasmine Y. , Jonus Hunter C. , Arnold Amanda , Schnepp Robert W. , Janssen Kaitlyn M. , Maximov Victor , Goldsmith Kelly C.
Published: April 2023

Primer sequences and Neuroblastoma cell line mutations
Figure S7, Figure S8 from YAP-Mediated Repression of HRK Regulates Tumor Growth, Therapy Response, and Survival Under Tumor Environmental Stress in Neuroblastoma
Authors: Shim Jenny , Lee Jasmine Y. , Jonus Hunter C. , Arnold Amanda , Schnepp Robert W. , Janssen Kaitlyn M. , Maximov Victor , Goldsmith Kelly C.
Published: April 2023

HRK primary tumor gene expression by MYCN status and stage; Apoptosis in hypoxic conditions of shYAP model
Figure S5, Figure S6 from YAP-Mediated Repression of HRK Regulates Tumor Growth, Therapy Response, and Survival Under Tumor Environmental Stress in Neuroblastoma
Authors: Shim Jenny , Lee Jasmine Y. , Jonus Hunter C. , Arnold Amanda , Schnepp Robert W. , Janssen Kaitlyn M. , Maximov Victor , Goldsmith Kelly C.
Published: April 2023

Etoposide treated shYAP model Apoptosis; BCL-2 family protein expression and BIM binding patterns in shYAP models
Figure S5 from Oncogenic BRAFV600E Governs Regulatory T-cell Recruitment during Melanoma Tumorigenesis
Authors: Shabaneh Tamer B. , Molodtsov Aleksey K. , Steinberg Shannon M. , Zhang Peisheng , Torres Gretel M. , Mohamed Gadisti A. , Boni Andrea , Curiel Tyler J. , Angeles Christina V. , Turk Mary Jo
Published: April 2023

Chemokine protein levels and effects of neutralization
Figure S4 from Oncogenic BRAFV600E Governs Regulatory T-cell Recruitment during Melanoma Tumorigenesis
Authors: Shabaneh Tamer B. , Molodtsov Aleksey K. , Steinberg Shannon M. , Zhang Peisheng , Torres Gretel M. , Mohamed Gadisti A. , Boni Andrea , Curiel Tyler J. , Angeles Christina V. , Turk Mary Jo
Published: April 2023

Input population of tumor-experience Tregs; and effects of pertussis toxin treatment
Supplementary Figures from Determination of Tumor Margins with Surgical Specimen Mapping Using Near-Infrared Fluorescence
Authors: Gao Rebecca W. , Teraphongphom Nutte T. , van den Berg Nynke S. , Martin Brock A. , Oberhelman Nicholas J. , Divi Vasu , Kaplan Michael J. , Hong Steven S. , Lu Guolan , Ertsey Robert , Tummers Willemieke S.F.J. , Gomez Adam J. , Holsinger F. Christopher , Kong Christina S. , Colevas Alexander D. , Warram Jason M. , Rosenthal Eben L.
Published: April 2023

1. Supplementary Figure 1: Patient and tumor characteristics. 2. Supplementary Figure 2: Flow diagram of tumor-mapping analysis. The primary tumor specimen (A) is imaged using a closed-field fluorescence imaging device (B) and sectioned into breadloafs (C). H&E slides with areas of tumor tissue marked by a board-certified pathologist are analyzed, and tumor tissue distance to the deep margin surface is measured. Tumor depth in areas with fluorescence are compared to tumor depth in areas without fluorescence. 3. Supplementary Table 1: Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of fluorescence signal for areas of the primary tumor specimen with tumor tissue {less than or equal to} 1 mm from the deep margin surface given by cohort. 4. Supplementary Table 2: Sensitivity, specificity, PPV, and NPV of fluorescence signal for areas of the primary tumor specimen with tumor tissue {less than or equal to} 2 mm from the deep margin surface given by cohort.