bluuebunny/crossref_metadata_2025 huggingface dataset:
Fig. S6 from Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes
Authors: Oakes Robert S. , Bushnell Grace G. , Orbach Sophia M. , Kandagatla Pridvi , Zhang Yining , Morris Aaron H. , Hall Matthew S. , LaFaire Petrina , Decker Joseph T. , Hartfield Rachel M. , Brooks Michael D. , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

Statistical plots to support heatmaps in main text and supplementary materials. (a) Box plots for gene panel heatmap in Fig. 1f show the median, 25th-75th percentiles and most extreme data points that were not considered outliers (outliers are visually indicated by red +). TB cohort expression is centered relative to the time-matched TFC cohort median. Scale depicts the log2-transformed fold change. A two-way MANOVA showed a significant interaction effect between condition and time (Pillai's Trace=1.276, F(20,28)=2.465, p=0.014). Post hoc univariate ANOVA showed significant differences within the diseased cohort over time (indicated by #, df=(2,22), p<0.05). Simple effects analysis showed significant differences between diseased and time-matched TFC (indicated by *, Å idÃ¡k adjusted p<0.05 adjusted). (b) Tumor growth curve for 4T1 mice starting at Day 7, with a power regression line, error bars are standard deviation. (c) Box plots of gene expression to support the data in the C57BL/6-Lu.2 heatmap in Fig. 2b. * indicates significance (Dunn-Å idÃ¡k corrected to p<0.005) from independent two-tailed t-tests comparing TB to TFC (n=5 per condition). (d) Box plots of gene expression for blood data to support the heatmap found in Fig. 1. Tumor-bearing Implant Free Controls (IFCs) are shown to illustrate that the implants do not alter the gene expression of blood leukocytes. A two-way MANOVA showed a significant interaction effect between condition and time (Pillai's Trace=2.527, F(36,40)=1.907, p=0.024). Post hoc univariate and simple effects analysis showed significant differences within the diseased cohort over time as indicated as # (df=(2,15), p<0.001) and * indicates significant differences compared to time matched controls (Å idÃ¡k adjusted p<0.05 adjusted). (e) Gene expression data from the lung tissue heatmap in Fig. 2a. * indicates significance (Dunn-Å idÃ¡k corrected to p<0.005) from independent two-tailed t-tests comparing TB to TFC (n=4 per condition). For full statistical values see Data File 4 for exact F and p values.
Video S4 from A Tissue-Engineered 3D Microvessel Model Reveals the Dynamics of Mosaic Vessel Formation in Breast Cancer
Authors: Silvestri Vanesa L. , Henriet Elodie , Linville Raleigh M. , Wong Andrew D. , Searson Peter C. , Ewald Andrew J.
Published: April 2023

Intravasation event is preceded by mosaic vessel formation.
Video S3 from A Tissue-Engineered 3D Microvessel Model Reveals the Dynamics of Mosaic Vessel Formation in Breast Cancer
Authors: Silvestri Vanesa L. , Henriet Elodie , Linville Raleigh M. , Wong Andrew D. , Searson Peter C. , Ewald Andrew J.
Published: April 2023

Vessel barrier function is retained at the site of mosaic vessel formation in a 3D tumor-microvessel model.
Fig. S4 from Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes
Authors: Oakes Robert S. , Bushnell Grace G. , Orbach Sophia M. , Kandagatla Pridvi , Zhang Yining , Morris Aaron H. , Hall Matthew S. , LaFaire Petrina , Decker Joseph T. , Hartfield Rachel M. , Brooks Michael D. , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

Gating scheme for flow cytometry analysis of adoptive transferred cells. Supporting Fig. 2 these plots indicate the (a) cells and (b) singlet gating prior to (c) gating for DiO and DiD fluorescent lipophilic dyes. Axes in panel C are identical to those in panels D-F. Numbers on plots indicate percentage of gated cells in comparison to a) total events, b) gated cells, and c) single cells. Representative flow cytometry plots and gating for (d) PBS injected control mice and adoptively transferred Ly6G+ and Gr1+Ly6G- populations into (e) TFC and (f) TB mice.
Video S2 from A Tissue-Engineered 3D Microvessel Model Reveals the Dynamics of Mosaic Vessel Formation in Breast Cancer
Authors: Silvestri Vanesa L. , Henriet Elodie , Linville Raleigh M. , Wong Andrew D. , Searson Peter C. , Ewald Andrew J.
Published: April 2023

Mosaic vessel formation in a 3D tumor-microvessel model.
Video S1 from A Tissue-Engineered 3D Microvessel Model Reveals the Dynamics of Mosaic Vessel Formation in Breast Cancer
Authors: Silvestri Vanesa L. , Henriet Elodie , Linville Raleigh M. , Wong Andrew D. , Searson Peter C. , Ewald Andrew J.
Published: April 2023

Tumor organoids induce transient focal leaks in a tissue-engineered microvessel model.
Fig. S10 from Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes
Authors: Oakes Robert S. , Bushnell Grace G. , Orbach Sophia M. , Kandagatla Pridvi , Zhang Yining , Morris Aaron H. , Hall Matthew S. , LaFaire Petrina , Decker Joseph T. , Hartfield Rachel M. , Brooks Michael D. , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

Kaplan-Meier survival curves correlated with high and low gene expression from breast cancer patient samples. (a) Microarray (GEO via KMPlot) and prognosis data were queried for genes selected for the 10-gene panel derived from tissue within implants to determine the expression level relevance in primary tumors on the clinical outcome of systemically untreated breast cancer patients (n=818). Kaplan-Meier plots indicate as separation of two profiles separating high and low gene expression that are automatically divided by the median expression of the genes for all samples. Plots indicate the Hazard Ratio (HR) which is highest for S100a9 and logrank significance comparing high and low expression as a function of recurrence-free survival. FDR 10% corrected significance (p<0.011) and FDR 5% corrected significance (p<0.00099). (b) Metrics on overall survival (n=379 patients) were calculated in the same manner as that for recurrence-free survival. FDR 10% corrected significance (p<0.0123) and FDR 5% corrected significance (p<0.005).
Fig. S1 from Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes
Authors: Oakes Robert S. , Bushnell Grace G. , Orbach Sophia M. , Kandagatla Pridvi , Zhang Yining , Morris Aaron H. , Hall Matthew S. , LaFaire Petrina , Decker Joseph T. , Hartfield Rachel M. , Brooks Michael D. , Wicha Max S. , Jeruss Jacqueline S. , Shea Lonnie D.
Published: April 2023

Development of the pre-metastatic niche (preMN), metastatic niche (MN), and synthetic diagnostic site. Circulating tumor cells exhibit a tropism for specific distal microenvironments, thus indicating that metastasis is pre-determined. Development of these predetermined sites is driven by (1) systemic conditioning from the primary tumor through secretion of factors and exosomes, which is amplified by simultaneous conditioning of the bone-marrow and alterations in bone-marrow derived cells. (2) This process conditions distal tissues and contributes to the (3) aggregation of pre-metastatic immune cells and extracellular matrix proteins. (4) These primed distal microenvironments are denoted as the preMN and facilitate homing then colonization of (5) circulating tumor cells which (6) extravasate and (7) migrate into distal organs where they may become a (8) disseminated tumor cells if the conditions are hospitable. This disseminated tumor cell may then undergo a phenotypic shift to initiate a (9) metastatic secondary growth, thus leading to development of a metastatic niche. Given that the preMN contains a unique mixture of soluble factors, extracellular matrix, stromal and immune cells (e.g., cancer-associated fibroblasts and myeloid-derived suppressor cells, MDSCs), it is reasonable that preMN function could be synthesized through the recapitulation these unique factors at a synthetic site in vivo. This rationale underpins the development of material based synthetic diagnostic site that (2.1) is conditioned, (3.1) populated by disease associated immune cells, (4.1) develops characteristics of a preMN, and (7.1) captures metastatic tumor cells.
Supplementary Figure Legends from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation
Authors: Saha Shekhar , Kiran Manjari , Kuscu Canan , Chatrath Ajay , Wotton David , Mayo Marty W. , Dutta Anindya
Published: April 2023

Text for the Supplementary Figures
Figure S4 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation
Authors: Saha Shekhar , Kiran Manjari , Kuscu Canan , Chatrath Ajay , Wotton David , Mayo Marty W. , Dutta Anindya
Published: April 2023

Defining the minimal region of DRAIC that inhibits tumorigenic property in cancer cell lines
Figure S3 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation
Authors: Saha Shekhar , Kiran Manjari , Kuscu Canan , Chatrath Ajay , Wotton David , Mayo Marty W. , Dutta Anindya
Published: April 2023

Specificity of DRAIC's association with IKK by depletion of IKK complex using siRNA and immunoprecipitation of the residual subunit of IKK complex in LNCaP cells
Figure S2 from Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation
Authors: Saha Shekhar , Kiran Manjari , Kuscu Canan , Chatrath Ajay , Wotton David , Mayo Marty W. , Dutta Anindya
Published: April 2023

DRAIC KO validation
Table 8 from Noncanonical IL6 Signaling-Mediated Activation of YAP Regulates Cell Migration and Invasion in Ovarian Clear Cell Cancer
Authors: Azar Walid J. , Christie Elizabeth L. , Mitchell Chris , Liu David S. , Au-Yeung George , Bowtell David D.L.
Published: April 2023

Selected compounds for secondary screen
Table 7 from Noncanonical IL6 Signaling-Mediated Activation of YAP Regulates Cell Migration and Invasion in Ovarian Clear Cell Cancer
Authors: Azar Walid J. , Christie Elizabeth L. , Mitchell Chris , Liu David S. , Au-Yeung George , Bowtell David D.L.
Published: April 2023

Primary hits-JHOC-5
Table 6 from Noncanonical IL6 Signaling-Mediated Activation of YAP Regulates Cell Migration and Invasion in Ovarian Clear Cell Cancer
Authors: Azar Walid J. , Christie Elizabeth L. , Mitchell Chris , Liu David S. , Au-Yeung George , Bowtell David D.L.
Published: April 2023

Primary hits-TOV21G
Table 3 from Noncanonical IL6 Signaling-Mediated Activation of YAP Regulates Cell Migration and Invasion in Ovarian Clear Cell Cancer
Authors: Azar Walid J. , Christie Elizabeth L. , Mitchell Chris , Liu David S. , Au-Yeung George , Bowtell David D.L.
Published: April 2023

Drug list
Supplementary Table 4 from Targeting the E3 Ubiquitin Ligase PJA1 Enhances Tumor-Suppressing TGFβ Signaling
Authors: Chen Jian , Mitra Abhisek , Li Shulin , Song Shumei , Nguyen Bao-Ngoc , Chen Jiun-Sheng , Shin Ji-Hyun , Gough Nancy R. , Lin Paul , Obias Vincent , He Aiwu Ruth , Yao Zhixing , Malta Tathiane M. , Noushmehr Houtan , Latham Patricia S. , Su Xiaoping , Rashid Asif , Mishra Bibhuti , Wu Ray-Chang , Mishra Lopa
Published: April 2023

Characteristics of HCC patients with PJA1 genetic alterations
Supplementary Materials and Methods-PJA1-Cancer research from Targeting the E3 Ubiquitin Ligase PJA1 Enhances Tumor-Suppressing TGFβ Signaling
Authors: Chen Jian , Mitra Abhisek , Li Shulin , Song Shumei , Nguyen Bao-Ngoc , Chen Jiun-Sheng , Shin Ji-Hyun , Gough Nancy R. , Lin Paul , Obias Vincent , He Aiwu Ruth , Yao Zhixing , Malta Tathiane M. , Noushmehr Houtan , Latham Patricia S. , Su Xiaoping , Rashid Asif , Mishra Bibhuti , Wu Ray-Chang , Mishra Lopa
Published: April 2023

Supplementary Materials and Methods
Video from Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity
Authors: Melms Johannes C. , Vallabhaneni Sreeram , Mills Caitlin E. , Yapp Clarence , Chen Jia-Yun , Morelli Eugenio , Waszyk Patricia , Kumar Sushil , Deming Derrick , Moret Nienke , Rodriguez Steven , Subramanian Kartik , Rogava Meri , Cartwright Adam N.R. , Luoma Adrienne , Mei Shaolin , Brinker Titus J. , Miller David M. , Spektor Alexander , Schadendorf Dirk , Riggi Nicolo , Wucherpfennig Kai W. , Sorger Peter K. , Izar Benjamin
Published: April 2023

Video CX
Supplementary Figures from Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity
Authors: Melms Johannes C. , Vallabhaneni Sreeram , Mills Caitlin E. , Yapp Clarence , Chen Jia-Yun , Morelli Eugenio , Waszyk Patricia , Kumar Sushil , Deming Derrick , Moret Nienke , Rodriguez Steven , Subramanian Kartik , Rogava Meri , Cartwright Adam N.R. , Luoma Adrienne , Mei Shaolin , Brinker Titus J. , Miller David M. , Spektor Alexander , Schadendorf Dirk , Riggi Nicolo , Wucherpfennig Kai W. , Sorger Peter K. , Izar Benjamin
Published: April 2023

Suppl. F1: On-target activity and toxicity of CX-6258 Suppl. F2: On-target activity of CX-6258 and siRNA KD of Haspin Suppl. F3: Effects of CX-6258 on cell-cycle and cGAS recruitment Suppl. F4: In vivo effects of CX-6258
Wound Assay vehicle from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Wound Assay vehicle
Fig Supp 6 from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer
Authors: Banik Debarati , Noonepalle Satish , Hadley Melissa , Palmer Erica , Gracia-Hernandez Maria , Zevallos-Delgado Christian , Manhas Namratta , Simonyan Hayk , Young Colin N. , Popratiloff Anastas , Chiappinelli Katherine B. , Fernandes Rohan , Sotomayor Eduardo M. , Villagra Alejandro
Published: April 2023

Fig Supp 6
Table S4 from Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds
Authors: Peuget Sylvain , Zhu Jiawei , Sanz Gema , Singh Madhurendra , Gaetani Massimiliano , Chen Xinsong , Shi Yao , Saei Amir Ata , Visnes Torkild , Lindström Mikael S. , Rihani Ali , Moyano-Galceran Lidia , Carlson Joseph W. , Hjerpe Elisabet , Joneborg Ulrika , Lehti Kaisa , Hartman Johan , Helleday Thomas , Zubarev Roman , Selivanova Galina
Published: April 2023

GO biological processes affected by RITA, AF and Onc-1.
Table S2 from Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds
Authors: Peuget Sylvain , Zhu Jiawei , Sanz Gema , Singh Madhurendra , Gaetani Massimiliano , Chen Xinsong , Shi Yao , Saei Amir Ata , Visnes Torkild , Lindström Mikael S. , Rihani Ali , Moyano-Galceran Lidia , Carlson Joseph W. , Hjerpe Elisabet , Joneborg Ulrika , Lehti Kaisa , Hartman Johan , Helleday Thomas , Zubarev Roman , Selivanova Galina
Published: April 2023

qPCR primers
Table S1 from Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds
Authors: Peuget Sylvain , Zhu Jiawei , Sanz Gema , Singh Madhurendra , Gaetani Massimiliano , Chen Xinsong , Shi Yao , Saei Amir Ata , Visnes Torkild , Lindström Mikael S. , Rihani Ali , Moyano-Galceran Lidia , Carlson Joseph W. , Hjerpe Elisabet , Joneborg Ulrika , Lehti Kaisa , Hartman Johan , Helleday Thomas , Zubarev Roman , Selivanova Galina
Published: April 2023

Cell lines
Supplementary Data from Mathematical Modeling of Preclinical Alpha-Emitter Radiopharmaceutical Therapy
Authors: Karimian Alireza , Ji Nathan T. , Song Hong , Sgouros George
Published: April 2023

Supplementary table and figures. Table S1: Simulated survival time following fractionated, 200 nCi-administration of 225Ac-7.16.4 antibody; Figure S1: Simulated antibody kinetics, showing that the greater median survival occurs only when the second injection is administered after the first has cleared. Figure S2: Impact of fractionation when radiosensitivity is reduced by 50%. Each plot shows a comparison of 4 simulations: no treatment (blue), single, 400 nCi injection (red), fractionated without (green) or with (purple) reduction in sensitivity. Results are shown for a 2-fraction (a and b) and 4-fraction (c and d) protocol with 10 (a and c) or 20 (b and d) days between administrations; Figure S3: Impact of fractionation when growth rate is increased by 50%. Each plot shows a comparison of 4 simulations: no treatment (blue), single, 400 nCi injection (red), fractionated without (green) or with (purple) increase in growth rate. Results are shown for a 2-fraction (a and b) and 4-fraction (c and d) protocol with 10 (a and c) or 20 (b and d) days between administrations.
Table S3 from An Integrative Gene Expression and Mathematical Flux Balance Analysis Identifies Targetable Redox Vulnerabilities in Melanoma Cells
Authors: Paudel B. Bishal , Lewis Joshua E. , Hardeman Keisha N. , Hayford Corey E. , Robbins Charles J. , Stauffer Philip E. , Codreanu Simona G. , Sherrod Stacy D. , McLean John A. , Kemp Melissa L. , Quaranta Vito
Published: April 2023

Table S3
Figure S5 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

IRF8 enhances AR degradation through ubiquitin dependent pathways.
Figure S1 from Dual Oxidase-Induced Sustained Generation of Hydrogen Peroxide Contributes to Pharmacologic Ascorbate-Induced Cytotoxicity
Authors: Gibson Adrienne R. , O'Leary Brianne R. , Du Juan , Sarsour Ehab H. , Kalen Amanda L. , Wagner Brett A. , Stolwijk Jeffrey M. , Falls-Hubert Kelly C. , Alexander Matthew S. , Carroll Rory S. , Spitz Douglas R. , Buettner Garry R. , Goswami Prabhat C. , Cullen Joseph J.
Published: April 2023

Basal oxygen consumption rate is sustained after exposure to P-AscH- in MIA PaCa-2 cells.
Figure S3 from Loss of a Negative Feedback Loop between IRF8 and AR Promotes Prostate Cancer Growth and Enzalutamide Resistance
Authors: Wu Hongxi , You Linjun , Li Yan , Zhao Zhili , Shi Guangjiang , Chen Zhen , Wang Zhuo , Li Xianjing , Du Shijia , Ye Wanli , Gao Xiaofang , Duan Jingjing , Cheng Yan , Tao Weiyan , Bian Jinsong , Zhou Jin-Rong , Zhu Qingyi , Yang Yong
Published: April 2023

Disruption of IRF8 in PCa cells affects cell growth in vitro and tumorigenesis in vivo.
Supplementary Figure S6 from NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors
Authors: Ford Kirsty , Hanley Christopher J. , Mellone Massimiliano , Szyndralewiez Cedric , Heitz Freddy , Wiesel Philippe , Wood Oliver , Machado Maria , Lopez Maria-Antoinette , Ganesan Anusha-Preethi , Wang Chuan , Chakravarthy Ankur , Fenton Tim R. , King Emma V. , Vijayanand Pandurangan , Ottensmeier Christian H. , Al-Shamkhani Aymen , Savelyeva Natalia , Thomas Gareth J.
Published: April 2023

Supplementary Figure S6
Supplementary Data from NOX4 Inhibition Potentiates Immunotherapy by Overcoming Cancer-Associated Fibroblast-Mediated CD8 T-cell Exclusion from Tumors
Authors: Ford Kirsty , Hanley Christopher J. , Mellone Massimiliano , Szyndralewiez Cedric , Heitz Freddy , Wiesel Philippe , Wood Oliver , Machado Maria , Lopez Maria-Antoinette , Ganesan Anusha-Preethi , Wang Chuan , Chakravarthy Ankur , Fenton Tim R. , King Emma V. , Vijayanand Pandurangan , Ottensmeier Christian H. , Al-Shamkhani Aymen , Savelyeva Natalia , Thomas Gareth J.
Published: April 2023

Supplementary data - Figure legends and table descriptions
Supplementary Figure S1 from Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition
Authors: Liang Junbo , Zhao Hong , Diplas Bill H. , Liu Song , Liu Jianmei , Wang Dingding , Lu Yan , Zhu Qing , Wu Jiayu , Wang Wenjia , Yan Hai , Zeng Yi-Xin , Wang Xiaoyue , Jiao Yuchen
Published: April 2023

Figure S1. Validation of ATRX KO in PLC/PRF/5 and HuH-7 cells.
Supplementary Data File 3 from Localized Metabolomic Gradients in Patient-Derived Xenograft Models of Glioblastoma
Authors: Randall Elizabeth C. , Lopez Begoña G.C. , Peng Sen , Regan Michael S. , Abdelmoula Walid M. , Basu Sankha S. , Santagata Sandro , Yoon Haejin , Haigis Marcia C. , Agar Jeffrey N. , Tran Nhan L. , Elmquist William F. , White Forest M. , Sarkaria Jann N. , Agar Nathalie Y.R.
Published: April 2023

Heatmap of mRNA sequencing data, highlighting the activated genes within pathways for glycolysis.
Supplementary Data File 2 from Localized Metabolomic Gradients in Patient-Derived Xenograft Models of Glioblastoma
Authors: Randall Elizabeth C. , Lopez Begoña G.C. , Peng Sen , Regan Michael S. , Abdelmoula Walid M. , Basu Sankha S. , Santagata Sandro , Yoon Haejin , Haigis Marcia C. , Agar Jeffrey N. , Tran Nhan L. , Elmquist William F. , White Forest M. , Sarkaria Jann N. , Agar Nathalie Y.R.
Published: April 2023

Heatmap of mRNA sequencing data, highlighting the activated genes within pathways for fatty acid metabolism.
Figure S6 from Oxygen-Enhanced Optoacoustic Tomography Reveals the Effectiveness of Targeting Heme and Oxidative Phosphorylation at Normalizing Tumor Vascular Oxygenation
Authors: Ghosh Poorva , Guo Yihang , Ashrafi Adnin , Chen Jingyu , Dey Sanchareeka , Zhong Shigen , Liu Jie , Campbell James , Konduri Purna Chaitanya , Gerberich Jeni , Garrossian Massoud , Mason Ralph P. , Zhang Li , Liu Li
Published: April 2023

Fig. S6 Analysis of correlation between tumor sizes and MSOT metrics. (A, B, & C) sO2 (Air), sO2 (O2), and Î"sO2 as derived from MSOT data. No significant correlation was detected between any MSOT metric with tumor sizes measured ex vivo. (D) Summary of p-values and r correlations of MSOT and OE-MSOT metrics with tumor sizes. For statistical analysis, the levels in treated tumors were compared to the levels in control tumors with a Welch 2-sample t-test or Pearson r correlation.
Figure S5 from Oxygen-Enhanced Optoacoustic Tomography Reveals the Effectiveness of Targeting Heme and Oxidative Phosphorylation at Normalizing Tumor Vascular Oxygenation
Authors: Ghosh Poorva , Guo Yihang , Ashrafi Adnin , Chen Jingyu , Dey Sanchareeka , Zhong Shigen , Liu Jie , Campbell James , Konduri Purna Chaitanya , Gerberich Jeni , Garrossian Massoud , Mason Ralph P. , Zhang Li , Liu Li
Published: April 2023

Fig. S5. (A & B) The effect of HSP2 on subcutaneous NSCLC H1299-luc tumor xenografts after 1.5 weeks of treatment (mid-point for treatment shown in Fig. 2). (A) Photos of excised tumors from mice treated with saline (control) or HSP2. (B) Average masses for control and treated tumors shown in A. (C-E) Comparison of sO2 and Î"sO2 levels in mid-point and end-point control and HSP2-treated tumors. (C) Representative tumor images of spatial distribution of oxygen saturation [sO2 (O2)] after the oxygen challenge in mid-point and end-point control and HSP2-treated tumors. (D) Quantification of sO2 levels in in mid-point and end-point control and HSP2-treated tumors. (E) Representative tumor images of the amplitude of signal change (Î"sO2) from breathing air to breathing 100% oxygen in mid-point and end-point control and HSP2-treated tumors. The change in sO2 (Î"sO2) is calculated by subtracting the average tumor sO2 while breathing air from the average tumor sO2 while breathing oxygen. (F) Quantification of Î"sO2 levels in mid-point and end-point control and HSP2-treated tumors. Tumor sizes are listed in Materials and Methods. Specifically the sizes of the four shown tumors were: Control: mid-point: 54.4 mm3, end-point: 369 mm3; HSP2: mid-point: 35.7 mm3, end-point 88.4 mm3. ***, P < 0.001; *, P < 0.05. The P values for the comparison of end-point HSP2-treated tumors and mid-point control tumors are listed under the plots in D and F.
Table S8 from Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology
Authors: Failmezger Henrik , Muralidhar Sathya , Rullan Antonio , de Andrea Carlos E. , Sahai Erik , Yuan Yinyin
Published: April 2023

Comparison of pathways enriched for genes correlated with stromal clustering, as identified by CNx and lol
Supplementary Figure1 from Differential Contributions of Pre- and Post-EMT Tumor Cells in Breast Cancer Metastasis
Authors: Lourenco Ana Rita , Ban Yi , Crowley Michael J. , Lee Sharrell B. , Ramchandani Divya , Du Wei , Elemento Olivier , George Jason T. , Jolly Mohit Kumar , Levine Herbert , Sheng Jianting , Wong Stephen T. , Altorki Nasser K. , Gao Dingcheng
Published: April 2023

GSEA of bulk RNA-seq of RFP+ and GFP+ Tri-PyMT cells.
Table S4 from ARRB1-Promoted NOTCH1 Degradation Is Suppressed by OncomiR miR-223 in T-cell Acute Lymphoblastic Leukemia
Authors: Shu Yi , Wang Yi , Lv Wen-Qiong , Peng Dan-Yi , Li Juan , Zhang Hang , Jiang Guang-Jie , Yang Bi-Jie , Liu Shan , Zhang Jia , Chen Yan-Hua , Tang Shi , Wan Ke-Xing , Yuan Jun-Tao , Guo Wei , Fu Guo , Qi Xin-Kun , Liu Zhi-Dai , Liu Hai-Yan , Yang Chao , Zhang Ling-Huan , Liu Fang-Jie , Yu Jie , Zhang Peng-Hui , Qu Bin , Zhao Hui , He Tong-Chuan , Zou Lin
Published: April 2023

Table S4, Supplementary Table 4. RNA-Seq analysis of ARRB1-silenced and overexpression Jurkat cells
Table S1 from ARRB1-Promoted NOTCH1 Degradation Is Suppressed by OncomiR miR-223 in T-cell Acute Lymphoblastic Leukemia
Authors: Shu Yi , Wang Yi , Lv Wen-Qiong , Peng Dan-Yi , Li Juan , Zhang Hang , Jiang Guang-Jie , Yang Bi-Jie , Liu Shan , Zhang Jia , Chen Yan-Hua , Tang Shi , Wan Ke-Xing , Yuan Jun-Tao , Guo Wei , Fu Guo , Qi Xin-Kun , Liu Zhi-Dai , Liu Hai-Yan , Yang Chao , Zhang Ling-Huan , Liu Fang-Jie , Yu Jie , Zhang Peng-Hui , Qu Bin , Zhao Hui , He Tong-Chuan , Zou Lin
Published: April 2023

Table S1, Suppl. Table1. The characteristics of T-ALL cell lines
Supplementary Data from ERK-Mediated Loss of miR-199a-3p and Induction of EGR1 Act as a “Toggle Switch” of GBM Cell Dedifferentiation into NANOG- and OCT4-Positive Cells
Authors: Almairac Fabien , Turchi Laurent , Sakakini Nathalie , Debruyne David Nicolas , Elkeurti Sarah , Gjernes Elisabet , Polo Beatrice , Bianchini Laurence , Fontaine Denys , Paquis Philippe , Chneiweiss Herve , Junier Marie-Pierre , Verrando Patrick , Burel-Vandenbos Fanny , Virolle Thierry
Published: April 2023

These figures describe the identification of three clusters of genes that are regulated by ERK upon EGF-mediated dedifferentiation (sup fig 8) and the probability of survival of patients expressing these clusters at a level above or below the median of expression (sup fig 9).
Supplementary Data 4 from Gain-of-Function Mutant p53 R273H Interacts with Replicating DNA and PARP1 in Breast Cancer
Authors: Xiao Gu , Lundine Devon , Annor George K. , Canar Jorge , Ellison Viola , Polotskaia Alla , Donabedian Patrick L. , Reiner Thomas , Khramtsova Galina F. , Olopade Olufunmilayo I. , Mazo Alexander , Bargonetti Jill
Published: April 2023

S4 Examples of manually scored p53 and PARP1 staining intensity categories.
Supplementary Data 3 from Gain-of-Function Mutant p53 R273H Interacts with Replicating DNA and PARP1 in Breast Cancer
Authors: Xiao Gu , Lundine Devon , Annor George K. , Canar Jorge , Ellison Viola , Polotskaia Alla , Donabedian Patrick L. , Reiner Thomas , Khramtsova Galina F. , Olopade Olufunmilayo I. , Mazo Alexander , Bargonetti Jill
Published: April 2023

S3 Mutant p53/PARP and Mutant p53/Edu Complexes in MDA-MB-468 and PANC-1 Cells.
Table S2 from Hybrid Epithelial–Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors
Authors: Selvaggio Gianluca , Canato Sara , Pawar Archana , Monteiro Pedro T. , Guerreiro Patrícia S. , Brás M. Manuela , Janody Florence , Chaouiya Claudine
Published: April 2023

Phenotypes reached upon systematic in silico analysis of single and double mutants.
Figure S4 from CXCR4 in Tumor Epithelial Cells Mediates Desmoplastic Reaction in Pancreatic Ductal Adenocarcinoma
Authors: Morita Toshihiro , Kodama Yuzo , Shiokawa Masahiro , Kuriyama Katsutoshi , Marui Saiko , Kuwada Takeshi , Sogabe Yuko , Matsumori Tomoaki , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Nishikawa Yoshihiro , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Nagasawa Takashi , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Cxcr4 KO result in up-regulation of epithelial mesenchymal transition in Microarray analysis.
Figure S3 from CXCR4 in Tumor Epithelial Cells Mediates Desmoplastic Reaction in Pancreatic Ductal Adenocarcinoma
Authors: Morita Toshihiro , Kodama Yuzo , Shiokawa Masahiro , Kuriyama Katsutoshi , Marui Saiko , Kuwada Takeshi , Sogabe Yuko , Matsumori Tomoaki , Kakiuchi Nobuyuki , Tomono Teruko , Mima Atsushi , Ueda Tatsuki , Tsuda Motoyuki , Yamauchi Yuki , Nishikawa Yoshihiro , Sakuma Yojiro , Ota Yuji , Maruno Takahisa , Uza Norimitsu , Nagasawa Takashi , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

Cxcr4 KO does not affect tumor infiltration of immune cells.
Supplementary Figures S1-S8 from Hybrid Epithelial–Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors
Authors: Selvaggio Gianluca , Canato Sara , Pawar Archana , Monteiro Pedro T. , Guerreiro Patrícia S. , Brás M. Manuela , Janody Florence , Chaouiya Claudine
Published: April 2023

Supplementary Figures S1-S8
Supplementary Table S1-6 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

Table S1. Primer information Table S2. The list of genes which were changed expression of mRNA by BACH1 silencing Table S3. The list of genes which were changed in their mRNA expression by BACH1 deletion Table S4. Clinicopathological features in PDAC Table S5. Variate analysis in PDAC Table S6. Clinicopathological features in PDAC of the TCGA
Supplementary Figure S6 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

Examination of metastatic activity of BACH1 knockout AsPC1 cells. Details are described in methods and legends file (Supplementary_methods_and_legends).
Supplementary Methods from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Detailed methods
Supplementary Figure S2 from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

Gene ontology, KEGG pathway and Gene set enrichment analysis of BACH1 silenced AsPC-1. Details are described in methods and legends file (Supplementary_methods_and_legends).
Supplementary Data from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

The 16 Supplementary Tables in the document provide information (including raw data) related to data throughout the manuscript
Figures S5 and S6 from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Related to Figure 4: Lipidomic profiling of SCLC cells
Supplementary Data from BACH1 Promotes Pancreatic Cancer Metastasis by Repressing Epithelial Genes and Enhancing Epithelial–Mesenchymal Transition
Authors: Sato Masaki , Matsumoto Mitsuyo , Saiki Yuriko , Alam Mahabub , Nishizawa Hironari , Rokugo Masahiro , Brydun Andrey , Yamada Shinji , Kaneko Mika K. , Funayama Ryo , Ito Mamoru , Kato Yukinari , Nakayama Keiko , Unno Michiaki , Igarashi Kazuhiko
Published: April 2023

Methods and legends for supplementary figures and tables
Supplementary Movie 1 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Supplementary Movie 1
Figure S1 from The MEK5–ERK5 Kinase Axis Controls Lipid Metabolism in Small-Cell Lung Cancer
Authors: Cristea Sandra , Coles Garry L. , Hornburg Daniel , Gershkovitz Maya , Arand Julia , Cao Siqi , Sen Triparna , Williamson Stuart C. , Kim Jun W. , Drainas Alexandros P. , He Andrew , Cam Laurent Le , Byers Lauren Averett , Snyder Michael P. , Contrepois Kévin , Sage Julien
Published: April 2023

Related to Figure 1: MEK5 and ERK5 mRNA and protein knock-down inhibits the expansion of SCLC cells in culture
Supplementary Materials and Methods from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Materials and Methods
Supplementary Figure S7 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S7 shows infiltration of TALL-104 cells into bi-layer GelMA hydrogels containing cancer cells (MDA-MB-231), monocytes (THP-1), and endothelial cells.
Supplementary Figure S6 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S6 shows the TALL-104 cell distribution within the bi-layer GelMA hydrogels loaded with MCF-7 cancer cells and monocytes.
Supplementary Figure S3 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S3 shows the mechanical characterization of the GelMA hydrogels.
Supplementary Figure S2 from An Engineered Tumor-on-a-Chip Device with Breast Cancer–Immune Cell Interactions for Assessing T-cell Recruitment
Authors: Aung Aereas , Kumar Vardhman , Theprungsirikul Jomkuan , Davey Shruti K. , Varghese Shyni
Published: April 2023

Figure S2 shows the characterization of the endothelial layer.
Figure S1 from A Novel Micropeptide Encoded by Y-Linked LINC00278 Links Cigarette Smoking and AR Signaling in Male Esophageal Squamous Cell Carcinoma
Authors: Wu Siqi , Zhang Liyuan , Deng Jieqiong , Guo Binbin , Li Fang , Wang Yirong , Wu Rui , Zhang Shenghua , Lu Jiachun , Zhou Yifeng
Published: April 2023

Fig. S1 Generation of YY1BM-knockout ESCC cell lines using CRISPR/Cas9 system and silencing genes in ESCC cell lines using siRNAs or shRNAs.
Supplementary Tables from Transcriptionally Active Androgen Receptor Splice Variants Promote Hepatocellular Carcinoma Progression
Authors: Dauki Anees M. , Blachly James S. , Kautto Esko A. , Ezzat Sameera , Abdel-Rahman Mohamed H. , Coss Christopher C.
Published: April 2023

These tables contain relevant patient characteristics, primer sequence information for RT-PCR, whole genome sequencing read statistics, and a tabulation of DEGS from publicly available HCC cell RNA-seq data.
Supplementary Information from miR-149 Suppresses Breast Cancer Metastasis by Blocking Paracrine Interactions with Macrophages
Authors: Sánchez-González Ismael , Bobien Anja , Molnar Christian , Schmid Simone , Strotbek Michaela , Boerries Melanie , Busch Hauke , Olayioye Monilola A.
Published: April 2023

Supplementary Material and Methods and Supplementary Figure Legends
Supplementary Figure 1 from Postpartum Involution and Cancer: An Opportunity for Targeted Breast Cancer Prevention and Treatments?
Authors: Borges Virginia F. , Lyons Traci R. , Germain Doris , Schedin Pepper
Published: April 2023

H&E and special stains of human breast tissue
Supplementary Tables from MiR-30e-3p Influences Tumor Phenotype through MDM2/TP53 Axis and Predicts Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Gramantieri Laura , Pollutri Daniela , Gagliardi Martina , Giovannini Catia , Quarta Santina , Ferracin Manuela , Casadei-Gardini Andrea , Callegari Elisa , De Carolis Sabrina , Marinelli Sara , Benevento Francesca , Vasuri Francesco , Ravaioli Matteo , Cescon Matteo , Piscaglia Fabio , Negrini Massimo , Bolondi Luigi , Fornari Francesca
Published: April 2023

ST1: Discovery and validation surgical patient cohorts. ST2: Advanced HCC patient cohort. ST3: Primer sequences for luciferase assay. ST4: Primer sequences for PCR and qPCR. ST5: Antibodies. ST6: Probe sequences for EMSA. ST7: Deregulated miR-30 family members in rat model.
Supplementary Figures from MiR-30e-3p Influences Tumor Phenotype through MDM2/TP53 Axis and Predicts Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Gramantieri Laura , Pollutri Daniela , Gagliardi Martina , Giovannini Catia , Quarta Santina , Ferracin Manuela , Casadei-Gardini Andrea , Callegari Elisa , De Carolis Sabrina , Marinelli Sara , Benevento Francesca , Vasuri Francesco , Ravaioli Matteo , Cescon Matteo , Piscaglia Fabio , Negrini Massimo , Bolondi Luigi , Fornari Francesca
Published: April 2023

This file contains Supplementary Figures. SF1: Correlations between miR-30 family member in human tissues. SF2: Microarray analysis of miRNAs in the rat model. SF3: miR-30e locus and p53 regulation. SF4: MDM2 regulation by miR-30e-3p in HCC cells. SF5: MiR-30e-3p regulates cell growth and cell invasion in HCC cells. SF6: MiR-30e-3p regulates stem cell phenotype in HCC cells. SF7: MiR-30e-3p regulates drug resistance in TP53 deleted HepG2 cells. SF8: MiR-30e-3p regulates drug resistance in TP53 mutated Huh-7 cells. SF9: Circulating miR-30e-3p levels predicts sorafenib response in HCC preclinical models.
Supplementary Video 6 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of mucinous carcinoma
Supplementary Video 4 from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

OCT and QME of invasive ductal carcinoma with stroma
Supplementary Figure 3 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

Non-tumor mesenchymal cell lines and Rb-WT/p53-deficient MFS/UPS cell lines are less sensitive to SKP2 knockdown
Supplementary Figure 2 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

RB1 and TP53 deletion or loss-of-function mutation associates with negative protein expression
Supplementary Figure 1 from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

Comparison of rates of RB1 and TP53 copy number alterations in MFS and UPS samples across 3 large genomic databases
Supplementary Data from Rb and p53-Deficient Myxofibrosarcoma and Undifferentiated Pleomorphic Sarcoma Require Skp2 for Survival
Authors: Li George Z. , Okada Tomoyo , Kim Young-Mi , Agaram Narasimhan P. , Sanchez-Vega Francisco , Shen Yawei , Tsubokawa Norifumi , Rios Jordan , Martin Axel S. , Dickson Mark A. , Qin Li-Xuan , Socci Nicholas D. , Singer Samuel
Published: April 2023

Supplementary tables and figure legends. Supplementary Table 1. siRNA targeting sequences; Supplementary Table 2. pLKO.1 shRNA sequences; Supplementary Table 3. Antibodies Supplementary Table 4. PCR primers
Supplementary Data from Diagnostic Accuracy of Quantitative Micro-Elastography for Margin Assessment in Breast-Conserving Surgery
Authors: Kennedy Kelsey M. , Zilkens Renate , Allen Wes M. , Foo Ken Y. , Fang Qi , Chin Lixin , Sanderson Rowan W. , Anstie James , Wijesinghe Philip , Curatolo Andrea , Tan Hsern Ern I. , Morin Narelle , Kunjuraman Bindu , Yeomans Chris , Chin Synn Lynn , DeJong Helen , Giles Katharine , Dessauvagie Benjamin F. , Latham Bruce , Saunders Christobel M. , Kennedy Brendan F.
Published: April 2023

Reader stats, Read-Eng1, Read-Eng2, Read-Path, Read-Res, Read-Truth, Read-Son, Read-Surg1, Read-Surg2
Table S6 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Association between a genetic predisposition to breast cancer and mammographic features among women who did not develop breast cancer during follow-up
Table S3 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Univariate ACE estimates for % mammographic density
Supplementary Figure 1 from Heritability of Mammographic Breast Density, Density Change, Microcalcifications, and Masses
Authors: Holowko Natalie , Eriksson Mikael , Kuja-Halkola Ralf , Azam Shadi , He Wei , Hall Per , Czene Kamila
Published: April 2023

Illustration of microcalcifications and masses in the breast
Supplementary Figure legends from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

Supplementary Figure legends
Supplementary Figure 5 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure validates the tumor data in a second mouse experiment.
Supplementary Figure 7 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S7 shows that high NAMPT expression correlates with a poorer survival.
Supplementary Figure 3 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure show alternative analysis for cell death in the tumors.
Supplementary Figure 6 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S6 shows that conditioned media is not sufficient to induce senescence.
Supplementary Figure 2 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure validates the tumor growth data with another autophagy gene.
Supplementary Figure 1 from Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation
Authors: Matthew-Onabanjo Asia N. , Janusis Jenny , Mercado-Matos Jose , Carlisle Anne E. , Kim Dohoon , Levine Fayola , Cruz-Gordillo Peter , Richards Ryan , Lee Michael J. , Shaw Leslie M.
Published: April 2023

This Figure validates Beclin 1 regulation of HRS phosphorylation.
Supplementary Figure 4 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S4 shows that genetically knocking down NAMPT suppresses ovarian cancer stem-like cells.
Supplementary Figure 2 from NAMPT Inhibition Suppresses Cancer Stem-like Cells Associated with Therapy-Induced Senescence in Ovarian Cancer
Authors: Nacarelli Timothy , Fukumoto Takeshi , Zundell Joseph A. , Fatkhutdinov Nail , Jean Stephanie , Cadungog Mark G. , Borowsky Mark E. , Zhang Rugang
Published: April 2023

Figure S2 shows that NAMPT inhibition suppresses the SASP induced by carboplatin.