bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 1-4 from Inhibition of ATM Increases Interferon Signaling and Sensitizes Pancreatic Cancer to Immune Checkpoint Blockade Therapy
Authors: Zhang Qiang , Green Michael D. , Lang Xueting , Lazarus Jenny , Parsels Joshua D. , Wei Shuang , Parsels Leslie A. , Shi Jiaqi , Ramnath Nithya , Wahl Daniel R. , Pasca di Magliano Marina , Frankel Timothy L. , Kryczek Ilona , Lei Yu L. , Lawrence Theodore S. , Zou Weiping , Morgan Meredith A.
Published: April 2023

SF1: ATM regulates type I interferon signaling in pancreatic cancer. SF2: ATM regulation of the type I interferon pathway is cGAS/STING independent but SRC dependent. SF3: ATM inhibition cooperates with radiation to activate type I interferon signaling. SF4: ATM regulates pancreatic tumor immunity and ICB efficacy in vivo.
Supplementary Materials and Methods from Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression
Authors: Hughes Robert M. , Simons Brian W. , Khan Hamda , Miller Rebecca , Kugler Valentina , Torquato Samantha , Theodros Debebe , Haffner Michael C. , Lotan Tamara , Huang Jessie , Davicioni Elai , An Steven S. , Riddle Ryan C. , Thorek Daniel L.J. , Garraway Isla P. , Fertig Elana J. , Isaacs John T. , Brennen W. Nathaniel , Park Ben H. , Hurley Paula J.
Published: April 2023

Supplementary Materials and Methods
Supplementary Tables from The Cdk2–c-Myc–miR-571 Axis Regulates DNA Replication and Genomic Stability by Targeting Geminin
Authors: Zhang Yi , Li Zhuqing , Hao Qiang , Tan Wei , Sun Jing , Li Jing , Chen Chi-wei , Li Zongzhu , Meng Yunxiao , Zhou Yuan , Han Zhiyong , Pei Huadong , DePamphilis Melvin L. , Zhu Wenge
Published: April 2023

Supplementary Table 1. List of DNA probes in ligation assay. Supplementary Table 2. List of DNA probes in EMSA assay. Supplementary Table 3. miRNAs identified by HTS that could induce excess DNA replication (Cut-off {greater than or equal to}25%). Supplementary Table 4. Prediction of seed-binding sites in miR-571 and 3'-UTR region (88-94) of GMNN (Geminin) based on Targetscan software. Supplementary Table 5. List of Major DNA replication and cell cycle related genes (n=105)
Supplementary Figure 6 from SUMO-Specific Protease 1 Is Critical for Myeloid-Derived Suppressor Cell Development and Function
Authors: Huang Xian , Zuo Yong , Wang Xiuzhi , Wu Xuefeng , Tan Hongsheng , Fan Qiuju , Dong Baijun , Xue Wei , Chen Guo-Qiang , Cheng Jinke
Published: April 2023

CD45 but not PTP1B is involved in expansion of Senp1-/- MDSC
Supplementary Figure 5 from SUMO-Specific Protease 1 Is Critical for Myeloid-Derived Suppressor Cell Development and Function
Authors: Huang Xian , Zuo Yong , Wang Xiuzhi , Wu Xuefeng , Tan Hongsheng , Fan Qiuju , Dong Baijun , Xue Wei , Chen Guo-Qiang , Cheng Jinke
Published: April 2023

Myeloid precursor cells shown no effects on myelopoiesis in Senp1-/- -BMT mice
Supplementary Table S3 from Deletion of the Miz-1 POZ Domain Increases Efficacy of Cytarabine Treatment in T- and B-ALL/Lymphoma Mouse Models
Authors: Ross Julie , Rashkovan Marissa , Fraszczak Jennifer , Joly-Beauparlant Charles , Vadnais Charles , Winkler René , Droit Arnaud , Kosan Christian , Möröy Tarik
Published: April 2023

GSEA p53
Figure S6 from LINE-1 Retrotransposition Promotes the Development and Progression of Lung Squamous Cell Carcinoma by Disrupting the Tumor-Suppressor Gene FGGY
Authors: Zhang Rui , Zhang Fan , Sun Zeguo , Liu Pengpeng , Zhang Xiao , Ye Yingnan , Cai Beiqi , Walsh Martin J. , Ren Xiubao , Hao Xishan , Zhang Weijia , Yu Jinpu
Published: April 2023

The schematic diagram for the hypothesis of smoking-induced genome disturbance and tumor development and progression. The red oval indicates upregulation, and the green oval indicates downregulation.
sFigure5 from KRAS Oncoprotein Expression Is Regulated by a Self-Governing eIF5A-PEAK1 Feed-Forward Regulatory Loop
Authors: Fujimura Ken , Wang Huawei , Watson Felicia , Klemke Richard L.
Published: April 2023

Pharmacological perturbation of glutamine metabolism and eIF5A inhibit cancer cell growth
Supplementary Figure 8 from 2-Hydroxyglutarate-Mediated Autophagy of the Endoplasmic Reticulum Leads to an Unusual Downregulation of Phospholipid Biosynthesis in Mutant IDH1 Gliomas
Authors: Viswanath Pavithra , Radoul Marina , Izquierdo-Garcia Jose Luis , Ong Wei Qiang , Luchman Hema Artee , Cairncross J. Gregory , Huang Bo , Pieper Russell O. , Phillips Joanna J. , Ronen Sabrina M.
Published: April 2023

ER-phagy is linked to phospholipid biosynthesis in BT54 neurospheres (A-C), orthotopic IDHmut tumor xenografts (D-J) and IDHmut patient biopsies (K-Q).
sFigure 1 from KRAS Oncoprotein Expression Is Regulated by a Self-Governing eIF5A-PEAK1 Feed-Forward Regulatory Loop
Authors: Fujimura Ken , Wang Huawei , Watson Felicia , Klemke Richard L.
Published: April 2023

Schematic showing hypusination of lysine 50 of eIF5A
Supplementary Figure 3 from 2-Hydroxyglutarate-Mediated Autophagy of the Endoplasmic Reticulum Leads to an Unusual Downregulation of Phospholipid Biosynthesis in Mutant IDH1 Gliomas
Authors: Viswanath Pavithra , Radoul Marina , Izquierdo-Garcia Jose Luis , Ong Wei Qiang , Luchman Hema Artee , Cairncross J. Gregory , Huang Bo , Pieper Russell O. , Phillips Joanna J. , Ronen Sabrina M.
Published: April 2023

2-HG induces a reduction in ER area in IDHmut glioma cells.
Figure S4 from KRAS Oncoprotein Expression Is Regulated by a Self-Governing eIF5A-PEAK1 Feed-Forward Regulatory Loop
Authors: Fujimura Ken , Wang Huawei , Watson Felicia , Klemke Richard L.
Published: April 2023

Role of eIF5A and mTOR signaling in regulation of KRas protein expression.
Movie S1 from A Human Organotypic Microfluidic Tumor Model Permits Investigation of the Interplay between Patient-Derived Fibroblasts and Breast Cancer Cells
Authors: Truong Danh D. , Kratz Alexander , Park Jin G. , Barrientos Eric S. , Saini Harpinder , Nguyen Toan , Pockaj Barbara , Mouneimne Ghassan , LaBaer Joshua , Nikkhah Mehdi
Published: April 2023

Time-lapse imaging of SUM-159 breast cancer cells migrating through the 3D stroma in absence of CAFs.
Figure S5 from The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3
Authors: Gambi Giovanni , Di Simone Elisabetta , Basso Veronica , Ricci Luisa , Wang Rui , Verma Akanksha , Elemento Olivier , Ponzoni Maurilio , Inghirami Giorgio , Icardi Laura , Mondino Anna
Published: April 2023

Data reproduce the effect of Sin3A deletion with a second shRNA
Figure S4 from The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3
Authors: Gambi Giovanni , Di Simone Elisabetta , Basso Veronica , Ricci Luisa , Wang Rui , Verma Akanksha , Elemento Olivier , Ponzoni Maurilio , Inghirami Giorgio , Icardi Laura , Mondino Anna
Published: April 2023

Data describe the effect of Resveratrol inhibits STAT3 acetylation and binding to Sin3A in LIF-stimulated cells.
Supplementary Figure from Anthropometric Risk Factors for Cancers of the Biliary Tract in the Biliary Tract Cancers Pooling Project
Authors: Jackson Sarah S. , Van Dyke Alison L. , Zhu Bin , Pfeiffer Ruth M. , Petrick Jessica L. , Adami Hans-Olov , Albanes Demetrius , Andreotti Gabriella , Beane Freeman Laura E. , Berrington de González Amy , Buring Julie E. , Chan Andrew T. , Chen Yu , Fraser Gary E. , Freedman Neal D. , Gao Yu-Tang , Gapstur Susan M. , Gaziano J. Michael , Giles Graham G. , Grant Eric J. , Grodstein Francine , Hartge Patricia , Jenab Mazda , Kitahara Cari M. , Knutsen Synnove F. , Koh Woon-Puay , Larsson Susanna C. , Lee I-Min , Liao Linda M. , Luo Juhua , McGee Emma E. , Milne Roger L. , Monroe Kristine R. , Neuhouser Marian L. , O’Brien Katie M. , Peters Ulrike , Poynter Jenny N. , Purdue Mark P. , Robien Kim , Sandler Dale P. , Sawada Norie , Schairer Catherine , Sesso Howard D. , Simon Tracey G. , Sinha Rashmi , Stolzenberg-Solomon Rachael Z. , Tsugane Shoichiro , Wang Renwei , Weiderpass Elisabete , Weinstein Stephanie J. , White Emily , Wolk Alicja , Yuan Jian-Min , Zeleniuch-Jacquotte Anne , Zhang Xuehong , McGlynn Katherine A. , Campbell Peter T. , Koshiol Jill
Published: April 2023

This file contains Supplementary Figure 1, parts A - D, and the figure description.
Supplementary Tables from HER2 Overexpression Triggers an IL1α Proinflammatory Circuit to Drive Tumorigenesis and Promote Chemotherapy Resistance
Authors: Liu Shou , Lee Ji Shin , Jie Chunfa , Park Min Ho , Iwakura Yoichiro , Patel Yogin , Soni Mithil , Reisman David , Chen Hexin
Published: April 2023

Supplementary Tables - Supplementary Tables S1, S3 and S4. S1 shows frequency of CSCs after transplantation of the indicated cells. S3 shows multivariate Cox regression data. S4 Positive correlation between IL-1α and HER2 or IL6 expression in breast cancer tissues.
Supplementary Figure S1-S4 from Aptamer-Conjugated Extracellular Nanovesicles for Targeted Drug Delivery
Authors: Wan Yuan , Wang Lixue , Zhu Chuandong , Zheng Qin , Wang Guoxiang , Tong Jinlong , Fang Yuan , Xia Yiqiu , Cheng Gong , He Xia , Zheng Si-Yang
Published: April 2023

Supplementary Figure S1: Optimization of PEGylated cholesterol amount for cell labeling. Supplementary Figure S2: Morphology and characterization of isolated bone marrow dendritic cells. Supplementary Figure S3: Characterization of AS1411-ENVs prepared by direct incubation of ENVs with AS1411-PEG2000-Chol. Supplementary Figure S4: HE staining of major organs and tumor in three negative control groups.
Figures S1-S4 from Inactivation of Proprotein Convertases in T Cells Inhibits PD-1 Expression and Creates a Favorable Immune Microenvironment in Colorectal Cancer
Authors: Tomé Mercedes , Pappalardo Angela , Soulet Fabienne , López José Javier , Olaizola Jone , Leger Yannick , Dubreuil Marielle , Mouchard Amandine , Fessart Delphine , Delom Frédéric , Pitard Vincent , Bechade Dominique , Fonck Mariane , Rosado Juan Antonio , Ghiringhelli François , Déchanet-Merville Julie , Soubeyran Isabelle , Siegfried Geraldine , Evrard Serge , Khatib Abdel-Majid
Published: April 2023

PCs expression in T cells and effect of PC inhibition on PD-1 expression, T cell signaling, survival and cytotoxicity.
Table S3 from Low-Dose IFNγ Induces Tumor Cell Stemness in Tumor Microenvironment of Non–Small Cell Lung Cancer
Authors: Song Mengjia , Ping Yu , Zhang Kai , Yang Li , Li Feng , Zhang Chaoqi , Cheng Shaoyan , Yue Dongli , Maimela Nomathamsanqa Resegofetse , Qu Jiao , Liu Shasha , Sun Ting , Li Zihai , Xia Jianchuan , Zhang Bin , Wang Liping , Zhang Yi
Published: April 2023

Association of ICAM1 expression with clinicopathological features in patients with NSCLC.
Supp Legends and Table S1 and S2 from Frizzled-7 Is Required for Wnt Signaling in Gastric Tumors with and Without Apc Mutations
Authors: Flanagan Dustin J. , Barker Nick , Costanzo Natasha S. Di , Mason Elizabeth A. , Gurney Austin , Meniel Valerie S. , Koushyar Sarah , Austin Chloe R. , Ernst Matthias , Pearson Helen B. , Boussioutas Alex , Clevers Hans , Phesse Toby J. , Vincan Elizabeth
Published: April 2023

Supplemental Figure Legends. And Supp Table S1. List of Antibodies used. Table S2. Differential expression of genes in gp130 gastric adenomas compared to wild-type and following deletion of Fzd7.
Figure S3 from mTORC2 Suppresses GSK3-Dependent Snail Degradation to Positively Regulate Cancer Cell Invasion and Metastasis
Authors: Zhang Shuo , Qian Guoqing , Zhang Qian-Qian , Yao Yuying , Wang Dongsheng , Chen Zhuo G. , Wang Li-Jing , Chen Mingwei , Sun Shi-Yong
Published: April 2023

TORKinibs suppress cell migration (A) including TGFb-induced migration (B)
Fig S4 from Frizzled-7 Is Required for Wnt Signaling in Gastric Tumors with and Without Apc Mutations
Authors: Flanagan Dustin J. , Barker Nick , Costanzo Natasha S. Di , Mason Elizabeth A. , Gurney Austin , Meniel Valerie S. , Koushyar Sarah , Austin Chloe R. , Ernst Matthias , Pearson Helen B. , Boussioutas Alex , Clevers Hans , Phesse Toby J. , Vincan Elizabeth
Published: April 2023

Figure S4. Fzd7 inhibition is rescued by Fzd7 expression in GC cells. Fzd7 deletion in gp130F/F mice reduces adenoma burden and induces cell differentiation and changes to Wnt target gene transcription.
Fig S2 from Frizzled-7 Is Required for Wnt Signaling in Gastric Tumors with and Without Apc Mutations
Authors: Flanagan Dustin J. , Barker Nick , Costanzo Natasha S. Di , Mason Elizabeth A. , Gurney Austin , Meniel Valerie S. , Koushyar Sarah , Austin Chloe R. , Ernst Matthias , Pearson Helen B. , Boussioutas Alex , Clevers Hans , Phesse Toby J. , Vincan Elizabeth
Published: April 2023

Figure S2. Gastric cancer cell xenografts treated with vehicle or OMP-18R5.
Figure S2 from Activation of the VEGFC/VEGFR3 Pathway Induces Tumor Immune Escape in Colorectal Cancer
Authors: Tacconi Carlotta , Ungaro Federica , Correale Carmen , Arena Vincenzo , Massimino Luca , Detmar Michael , Spinelli Antonino , Carvello Michele , Mazzone Massimiliano , Oliveira Ana I. , Rubbino Federica , Garlatti Valentina , Spanò Salvatore , Lugli Enrico , Colombo Federico S. , Malesci Alberto , Peyrin-Biroulet Laurent , Vetrano Stefania , Danese Silvio , D’Alessio Silvia
Published: April 2023

VEGFC induced tumor growth is not associated with intestinal inflammation. Related to Figure 2
Fig S6. from miR-192-5p Silencing by Genetic Aberrations Is a Key Event in Hepatocellular Carcinomas with Cancer Stem Cell Features
Authors: Gu Yuanzhuo , Wei Xiyang , Sun Yulin , Gao Hongjun , Zheng Xin , Wong Linda L. , Jin Ling , Liu Niya , Hernandez Brenda , Peplowska Karolina , Zhao Xiaohang , Zhan Qi-Min , Feng Xin-Hua , Tang Zhao-You , Ji Junfang
Published: April 2023

The Up-stream regulation of miR-192-5p expression.
Figure S2: PMTRIPs FISH-PLA is specific, effective, and sensitive without dextran sulfate. from Quantification and Localization of Protein–RNA Interactions in Patient-Derived Archival Tumor Tissue
Authors: Blanchard Emmeline L. , Argyropoulou Danae , Zurla Chiara , Bhosle Sushma M. , Vanover Daryll , Santangelo Philip J.
Published: April 2023

Supplementary Figure 2: PMTRIPs FISH-PLA is specific, effective, and sensitive without dextran sulfate. A). 5 nM of V5-tagged PMTRIPs targeting polyadenylated mRNA were delivered as FISH probes, with FISH hybridization buffer containing either 0%, 5% or 10% dextran sulfate. PLA (white) was performed between the V5 tag and HuR. Extended focus images are shown. Scale bars indicate 10 µm. B) Quantification of PLA is shown. Statistics were performed with a one-way ANOVA with a Dunn's multiple comparisons test, where n=30 and **** p < 0.0001. 95% confidence intervals are shown in red. C) 5 nM V5 tagged MTRIPs targeting polyadenylated mRNA were assembled using either PNA or 2'OM oligos and were delivered as FISH probes. PLA (white) was performed between the V5 tag and HuR. Extended focus images are shown. Scale bars indicate 10 µm. Quantification of PLA is shown. Statistics were performed with a one-way ANOVA with a Dunn's multiple comparisons test, where n=30 and ** p < 0.002 and **** p < 0.0001. 95% confidence intervals are shown in black. D) Representative extended focus control images for figure 2A are shown. PLA is in white. Scale bars indicate 10 µm. E) Representative extended focus control images for figure 2B are shown. PLA is in white. Scale bars indicate 10 µm. F) Representative extended focus control images for figure 2C are shown. PLA is in white. Scale bars indicate 10 µm. G) Representative extended focus control images for figure 2D are shown. PLA is in white. Scale bars indicate 10 µm.
Supplementary Figures S1-6. 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 Figures S1-6. Supplementary Fig. S1 shows that CDK12 depletion alters ATP and ADP levels without affecting glycolysis in cell lines. Supplementary Fig. S2 shows that BRCA1 depletion does not affect glycolysis, that CDK12 and BRCA1 depletion reduce ATP levels in ex vivo HGSOC PDX cultures, that transient BRCA1 expression increase OCR in BRCA1-deficient cells, that CDK12 and BRCA1 depletion do not affect mitochondrial DNA levels, and levels of BRCA1 and CDK12 mRNA expression in cells transfected with CDK12 siRNAs and BRCA1 expression plasmid. Supplementary Fig. S3 shows BRCA2 and RAD51 depletion do not affect OCR but do sensitize to olaparib. Supplementary Fig. S4 shows a map of known BRCA1 transcripts, the exons that are targeted by the BRCA1 siRNAs used in this study, primers used to assess expression of alternative BRCA1 transcripts, NNMT mRNA expression in cells transfected with BRCA1 siRNAs, and binding of BRCA1 to the NNMT promoter using ChIP. Supplementary S5 shows that BRCA2 and RAD51 depletion do not sensitize to VLX600 but do sensitize to olaparib. Supplementary Fig. S6 shows that CDK12 and BRCA1 depletion does not further suppress ATP levels in NNMT-overexpressing cells.
Supplementary File 4 from Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids
Authors: Laddha Saurabh V. , da Silva Edaise M. , Robzyk Kenneth , Untch Brian R. , Ke Hua , Rekhtman Natasha , Poirier John T. , Travis William D. , Tang Laura H. , Chan Chang S.
Published: April 2023

Differentially methylated CpG probes and CpG islands
Supplementary File 2 from Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids
Authors: Laddha Saurabh V. , da Silva Edaise M. , Robzyk Kenneth , Untch Brian R. , Ke Hua , Rekhtman Natasha , Poirier John T. , Travis William D. , Tang Laura H. , Chan Chang S.
Published: April 2023

Mutational profile of lung carcinoid and gene ontology of mutated genes
Supplementary Data from Clonal Mutations Activate the NF-κB Pathway to Promote Recurrence of Nasopharyngeal Carcinoma
Authors: You Rui , Liu You-Ping , Lin De-Chen , Li Qing , Yu Tao , Zou Xiong , Lin Mei , Zhang Xiao-Long , He Gui-Ping , Yang Qi , Zhang Yi-Nuan , Xie Yu-Long , Jiang Rou , Wu Chen-Yan , Zhang Chao , Cui Cheng , Wang Jing-Qi , Wang Yue , Zhuang Ai-Hua , Guo Gui-Fang , Hua Yi-Jun , Sun Rui , Yun Jing-Ping , Zuo Zhi-Xiang , Liu Ze-Xian , Zhu Xiao-Feng , Kang Tie-Bang , Qian Chao-Nan , Mai Hai-Qiang , Sun Ying , Zeng Mu-Sheng , Feng Lin , Zeng Yi-Xin , Chen Ming-Yuan
Published: April 2023

All Supplementary Tables in one file. Supplementary Table 1. Clinical data on the rNPC and pNPC for whole-exome and whole-genome sequencing. Supplementary Table 2.Clinical characteristics of rNPC and pNPC FFPE samples. Supplementary Table 3. The correspondence between sample ID in the manuscript and sample alias in the database (HRA000053) Supplementary Table 4. Summary of WES/WGS on 55rNPC and 44pNPC. Supplementary Table 5. Summary of mutation in 55 rNPC and 44 pNPC cases. Supplementary Table 6. Somatic SNVs and indels of coding regions in 55 rNPC and 44 pNPC cases. Supplementary table 7. Validation of somatic mutations in rNPC and pNPC. Supplementary Table 8. Summary of WES in 7 paired rNPC and pNPC samples. Supplementary table 9. Somatic SNVs and indels of coding regions in pired rNPC and pNPC cases. Supplementary Table 10. Overlapped somatic SNVs and indels of coding regions in 7 paired rNPC and pNPC cases. Supplementary table 11. Summary of CNVs and SVs in 55 rNPC and 44 pNPC cases. Supplementary Table 12. Summary of survival analyses by multivariate Cox proportional hazards model by overall survival. Supplementary Table 13. Summary of survival analyses by multivariate Cox proportional hazards model by loco-regional relapse-free survival.
Supplementary Tables from Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas
Authors: Ohka Fumiharu , Shinjo Keiko , Deguchi Shoichi , Matsui Yusuke , Okuno Yusuke , Katsushima Keisuke , Suzuki Miho , Kato Akira , Ogiso Noboru , Yamamichi Akane , Aoki Kosuke , Suzuki Hiromichi , Sato Shinya , Arul Rayan Nirmala , Prabhakar Shyam , Göke Jonathan , Shimamura Teppei , Maruyama Reo , Takahashi Satoru , Suzumura Akio , Kimura Hiroshi , Wakabayashi Toshihiko , Zong Hui , Natsume Atsushi , Kondo Yutaka
Published: April 2023

ST1: Primer list; ST2: The most differentially expressed 401 transcripts (top 1%) in MADM tumors compared with normal brains; ST3: Upregulated 544 genes specifically in MADM tumors not in GL261; ST4: The mutational and expression status of 162 epigenome-associated genes in LGGs and GBMs; ST5: Significantly upregulated and downregulated genes by Ezh2 depletion; ST6: Representative genes with H3K4me3 alone, H3K27me3 alone or bivalent modifications in Ezh2 wild-type P8 precancerous cells and Ezh2 wild-type MADM tumor cells (top 50 genes with highest relative value); ST7: Gene ontology of upregulated genes by Ezh2 depletion.
Supplementary Materials and Methods from Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas
Authors: Ohka Fumiharu , Shinjo Keiko , Deguchi Shoichi , Matsui Yusuke , Okuno Yusuke , Katsushima Keisuke , Suzuki Miho , Kato Akira , Ogiso Noboru , Yamamichi Akane , Aoki Kosuke , Suzuki Hiromichi , Sato Shinya , Arul Rayan Nirmala , Prabhakar Shyam , Göke Jonathan , Shimamura Teppei , Maruyama Reo , Takahashi Satoru , Suzumura Akio , Kimura Hiroshi , Wakabayashi Toshihiko , Zong Hui , Natsume Atsushi , Kondo Yutaka
Published: April 2023

This file explains the additional details of Materials and Methods
Supplementary Experimental Procedures from Hepatic Endothelial Notch Activation Protects against Liver Metastasis by Regulating Endothelial-Tumor Cell Adhesion Independent of Angiocrine Signaling
Authors: Wohlfeil Sebastian A. , Häfele Verena , Dietsch Bianca , Schledzewski Kai , Winkler Manuel , Zierow Johanna , Leibing Thomas , Mohammadi Mona Malek , Heineke Joerg , Sticht Carsten , Olsavszky Victor , Koch Philipp-Sebastian , Géraud Cyrill , Goerdt Sergij
Published: April 2023

Additional information about the following materials and methods are enclosed here: Animal experiments, bioluminescence imaging, blood parameters, embryo and organ preparation, routine and immuno histology, microarray analysis, RNA in situ hybridization, image acquisition and processing, confocal microscopy, LSEC isolation, details of antibodies and qRT-PCR analysis.
Supplementary Figures from MUC1-C Integrates Chromatin Remodeling and PARP1 Activity in the DNA Damage Response of Triple-Negative Breast Cancer Cells
Authors: Yamamoto Masaaki , Jin Caining , Hata Tsuyoshi , Yasumizu Yota , Zhang Yan , Hong Deli , Maeda Takahiro , Miyo Masaaki , Hiraki Masayuki , Suzuki Yozo , Hinohara Kunihiko , Rajabi Hasan , Kufe Donald
Published: April 2023

Supplementary Figures S1-S11
Figure S2 from Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance
Authors: Dalin Simona , Sullivan Mark R. , Lau Allison N. , Grauman-Boss Beatrice , Mueller Helen S. , Kreidl Emanuel , Fenoglio Silvia , Luengo Alba , Lees Jacqueline A. , Vander Heiden Matthew G. , Lauffenburger Douglas A. , Hemann Michael T.
Published: April 2023

Fig. S2. N-acetyl alanine does not protect from gemcitabine toxicity and nucleoside levels in PDAC cells are not effected by treatment with gemcitabine or conditioned media (A) Dose response curves with N-acetyl-alanine without (solid lines) or with (dashed lines) 0.025 uM gemcitabine. The viability after treatment with PSC2 CM is also shown. Data show three biological replicates +/- SEM. (B-E) Absolute quantification of the indicated species in within PDAC cells after the indicated treatment. Data show 3 biological replicates +/- SEM.
Supplementary Table S2 from Collagen Remodeling in the Hypoxic Tumor-Mesothelial Niche Promotes Ovarian Cancer Metastasis
Authors: Natarajan Suchitra , Foreman Kaitlyn M. , Soriano Michaela I. , Rossen Ninna S. , Shehade Hussein , Fregoso Daniel R. , Eggold Joshua T. , Krishnan Venkatesh , Dorigo Oliver , Krieg Adam J. , Heilshorn Sarah C. , Sinha Subarna , Fuh Katherine C. , Rankin Erinn B.
Published: April 2023

Supplementary Table S2 shows the list of overlapping genes between the metastatic and hypoxic gene signatures. Suppl. to Fig 1.
Supplementary Data from FBXW7 Triggers Degradation of KMT2D to Favor Growth of Diffuse Large B-cell Lymphoma Cells
Authors: Saffie Rizwan , Zhou Nan , Rolland Delphine , Önder Özlem , Basrur Venkatesha , Campbell Sydney , Wellen Kathryn E. , Elenitoba-Johnson Kojo S.J. , Capell Brian C. , Busino Luca
Published: April 2023

Supplementary Data (Fig. S1- S6)
Supplementary Table S1-S5 from Targeted Metabolomics Identifies the Cytochrome P450 Monooxygenase Eicosanoid Pathway as a Novel Therapeutic Target of Colon Tumorigenesis
Authors: Wang Weicang , Yang Jun , Edin Matthew L. , Wang Yuxin , Luo Ying , Wan Debin , Yang Haixia , Song Chun-Qing , Xue Wen , Sanidad Katherine Z. , Song Mingyue , Bisbee Heather A. , Bradbury Jennifer A. , Nan Guanjun , Zhang Jianan , Shih Pei-an Betty , Lee Kin Sing Stephen , Minter Lisa M. , Kim Daeyoung , Xiao Hang , Liu Jun-Yan , Hammock Bruce D. , Zeldin Darryl C. , Zhang Guodong
Published: April 2023

ST1: Composition of the modified AIN-93G diet used in the animal experiment; ST2: Sequences of primers in qRT-PCR; ST3: Concentrations of lipid mediators in the plasma of control mice (not treated with AOM/DSS) and colon cancer mice (treated with AOM/DSS); ST4: Concentrations of lipid mediators in the colon of control mice (not treated with AOM/DSS) and colon cancer mice (treated with AOM/DSS); ST5: Concentrations of lipid mediators in the colon of AOM/DSS-treated Cyp2c+/+ and Cyp2c+/- mice.
Supplementary Table S1 from HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases
Authors: Kogler Melanie , Tortola Luigi , Negri Gian Luca , Leopoldi Alexandra , El-Naggar Amal M. , Mereiter Stefan , Gomez-Diaz Carlos , Nitsch Roberto , Tortora Davide , Kavirayani Anoop M. , Gapp Bianca V. , Rao Shuan , Uribesalgo Iris , Hoffmann David , Cikes Domagoj , Novatchkova Maria , Williams David A. , Trent Jeffrey M. , Ikeda Fumiyo , Daugaard Mads , Hagelkruys Astrid , Sorensen Poul H. , Penninger Josef M.
Published: April 2023

HACE1 mutational landscape in human cancer.
Supplement methods from EIF3H Orchestrates Hippo Pathway–Mediated Oncogenesis via Catalytic Control of YAP Stability
Authors: Zhou Zhuan , Zhou Honghong , Ponzoni Luca , Luo Aiping , Zhu Rui , He Mingjing , Huang Yi , Guan Kun-Liang , Bahar Ivet , Liu Zhihua , Wan Yong
Published: April 2023

Supplement methods
Supplementary Figure Legends from Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma
Authors: Wang Jun , Merino Diana M. , Light Nicholas , Murphy Brian L. , Wang Yong-Dong , Guo Xiaohui , Hodges Andrew P. , Chau Lianne Q. , Liu Kun-Wei , Dhall Girish , Asgharzadeh Shahab , Kiehna Erin N. , Shirey Ryan J. , Janda Kim D. , Taylor Michael D. , Malkin David , Ellison David W. , VandenBerg Scott R. , Eberhart Charles G. , Sears Rosalie C. , Roussel Martine F. , Gilbertson Richard J. , Wechsler-Reya Robert J.
Published: April 2023

Supplementary Figure Legends
Supplementary methods from Disruption of Endolysosomal RAB5/7 Efficiently Eliminates Colorectal Cancer Stem Cells
Authors: Takeda Mitsunobu , Koseki Jun , Takahashi Hidekazu , Miyoshi Norikatsu , Nishida Naohiro , Nishimura Junichi , Hata Taishi , Matsuda Chu , Mizushima Tsunekazu , Yamamoto Hirofumi , Ishii Hideshi , Doki Yuichiro , Mori Masaki , Haraguchi Naotsugu
Published: April 2023

Supplementary methods
Supplementary Data Fig. 7 from Negative Regulation of p53-Induced Senescence by N-WASP Is Crucial for DMBA/TPA-Induced Skin Tumor Formation
Authors: Li Hui , Petersen Simon , Garcia Mariscal Alberto , Brakebusch Cord
Published: April 2023

N-WASP regulation of p53 dependent senescence in keratinocytes
Supplementary Data Fig. 5 from Negative Regulation of p53-Induced Senescence by N-WASP Is Crucial for DMBA/TPA-Induced Skin Tumor Formation
Authors: Li Hui , Petersen Simon , Garcia Mariscal Alberto , Brakebusch Cord
Published: April 2023

Complete p53 knockout rescues senescen induced by N-WASP knockout
Supplementary Data from Targeted Inhibition of the E3 Ligase SCFSkp2/Cks1 Has Antitumor Activity in RB1-Deficient Human and Mouse Small-Cell Lung Cancer
Authors: Zhao Hongling , Iqbal Niloy J. , Sukrithan Vineeth , Nicholas Cari , Xue Yingjiao , Yu Cindy , Locker Joseph , Zou Juntao , Schwartz Edward L. , Zhu Liang
Published: April 2023

Figure S1. Longitudinal micro CT images of Rb1lox/loxTrp53lox/lox (RP) mice lungs. Figure S2. Lung and liver tumors in RP mice. Figure S3. Comparison of orthotopic and autochthonous RP lung tumors. Figure S4. Pevonedistat inhibits proliferation and induces cell death in SCLC organoids. Figure S5. Neuroendocrine markers in tumors in vivo.
Supplementary Video from Blockade of a Laminin-411–Notch Axis with CRISPR/Cas9 or a Nanobioconjugate Inhibits Glioblastoma Growth through Tumor-Microenvironment Cross-talk
Authors: Sun Tao , Patil Rameshwar , Galstyan Anna , Klymyshyn Dmytro , Ding Hui , Chesnokova Alexandra , Cavenee Webster K. , Furnari Frank B. , Ljubimov Vladimir A. , Shatalova Ekaterina S. , Wagner Shawn , Li Debiao , Mamelak Adam N. , Bannykh Serguei I. , Patil Chirag G. , Rudnick Jeremy D. , Hu Jethro , Grodzinski Zachary B. , Rekechenetskiy Arthur , Falahatian Vida , Lyubimov Alexander V. , Chen Yongmei L. , Leoh Lai S. , Daniels-Wells Tracy R. , Penichet Manuel L. , Holler Eggehard , Ljubimov Alexander V. , Black Keith L. , Ljubimova Julia Y.
Published: April 2023

Video schematically shows the mechanism of glioblastoma treatment by laminin-411 inhibiting nanobioconjugate
Legends to Supplementary Data from Negative Regulation of p53-Induced Senescence by N-WASP Is Crucial for DMBA/TPA-Induced Skin Tumor Formation
Authors: Li Hui , Petersen Simon , Garcia Mariscal Alberto , Brakebusch Cord
Published: April 2023

Legends to Supplementary Data
Supplementary Figure Legends from H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death
Authors: Zhang Yilei , Shi Jiejun , Liu Xiaoguang , Xiao Zhenna , Lei Guang , Lee Hyemin , Koppula Pranavi , Cheng Weijie , Mao Chao , Zhuang Li , Ma Li , Li Wei , Gan Boyi
Published: April 2023

Supplementary Figure and Table Legends
Supplementary Figure 1-8 from H2A Monoubiquitination Links Glucose Availability to Epigenetic Regulation of the Endoplasmic Reticulum Stress Response and Cancer Cell Death
Authors: Zhang Yilei , Shi Jiejun , Liu Xiaoguang , Xiao Zhenna , Lei Guang , Lee Hyemin , Koppula Pranavi , Cheng Weijie , Mao Chao , Zhuang Li , Ma Li , Li Wei , Gan Boyi
Published: April 2023

Including Supplementary Figures 1-8. Supplementary Figure 1 shows working model for different energy stress inducers. Supplementary Figures 2-7 are additional data corresponding to Figures 2-7 in the manuscript. Supplementary Figure 8 showing proposed working model from this study.
Supplementary Data 5 from Blockade of a Laminin-411–Notch Axis with CRISPR/Cas9 or a Nanobioconjugate Inhibits Glioblastoma Growth through Tumor-Microenvironment Cross-talk
Authors: Sun Tao , Patil Rameshwar , Galstyan Anna , Klymyshyn Dmytro , Ding Hui , Chesnokova Alexandra , Cavenee Webster K. , Furnari Frank B. , Ljubimov Vladimir A. , Shatalova Ekaterina S. , Wagner Shawn , Li Debiao , Mamelak Adam N. , Bannykh Serguei I. , Patil Chirag G. , Rudnick Jeremy D. , Hu Jethro , Grodzinski Zachary B. , Rekechenetskiy Arthur , Falahatian Vida , Lyubimov Alexander V. , Chen Yongmei L. , Leoh Lai S. , Daniels-Wells Tracy R. , Penichet Manuel L. , Holler Eggehard , Ljubimov Alexander V. , Black Keith L. , Ljubimova Julia Y.
Published: April 2023

Figure S5. Binding of the nanobioconjugates to U87MG studied by flow cytometry is inhibited by human soluble TfR. This shows that the chimeric anti-human TfR antibody as part of nanobioconjugate fully retained its activity
Supplementary Data from Heparanase and Chemotherapy Synergize to Drive Macrophage Activation and Enhance Tumor Growth
Authors: Bhattacharya Udayan , Gutter-Kapon Lilach , Kan Tal , Boyango Ilanit , Barash Uri , Yang Shi-Ming , Liu JingJing , Gross-Cohen Miriam , Sanderson Ralph D. , Shaked Yuval , Ilan Neta , Vlodavsky Israel
Published: April 2023

Suppl. Figure legends Suppl. Fig. 1. The structure of H1001, a small molecule heparanase inhibitor. H1001 inhibit heparanase activity inside and outside the cell, and attenuates cellular invasion Suppl. Fig. 2. Medium conditioned by PCT-treated macrophages promote cell migration; Matrigel containing PCT-treated macrophages recruits far more host macrophages into the plug. Suppl. Fig. 3. Injecting LLC cells with PCT-treated macrophages modestly increase tumor growth in WT C57Bl/6 mice Suppl. Fig. 4. Differential cytokine induction in WT vs KO macrophages is not mediated by TLR2 and TLR4 or MLL1-4, SET1A or RBBP5 Suppl. Fig. 5. Cytokine induction by PCT is attenuated by OICR-9429, a WDR5 inhibitor Suppl. Fig. 6. WDR5 silencing attenuates while WDR5 over expression promote cytokine induction. Cytokine induction by PCT is attenuated by CCG-203971, a MKL1 inhibitor Suppl. Fig. 7. PCT enhances the phosphorylation of JNK in WT but not KO macrophages, and cytokine induction by PCT is attenuated by inhibitor of JNK Suppl. Table 1. Mouse primers sets utilized in this study Suppl. Table 2. Antibodies utilized for FACS analyses
Supplementary Figures 1-4 and extended methods from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus
Authors: Buckley Melissa A. , Woods Nicholas T. , Tyrer Jonathan P. , Mendoza-Fandiño Gustavo , Lawrenson Kate , Hazelett Dennis J. , Najafabadi Hamed S. , Gjyshi Anxhela , Carvalho Renato S. , Lyra Paulo C. , Coetzee Simon G. , Shen Howard C. , Yang Ally W. , Earp Madalene A. , Yoder Sean J. , Risch Harvey , Chenevix-Trench Georgia , Ramus Susan J. , Phelan Catherine M. , Coetzee Gerhard A. , Noushmehr Houtan , Hughes Timothy R. , Sellers Thomas A. , Goode Ellen L. , Pharoah Paul D. , Gayther Simon A. , Monteiro Alvaro N.A.
Published: April 2023

This file contains: Supplementary Figure 1 (Related to Figure 2): Haplotype frequency for tiles Enhancer Scanning times with multiple SNPs. Supplementary Figure 2 (Related to Figure 3): Conservation and S/MAR predicted sequences at the locus. Supplementary Figure 3: Study overview and Overlap between the set of 134 SNPs obtained through the LD-guided analysis and the set of 40 SNPs obtained through the fine mapping-guided approach. Supplementary Figure 4 (Related to Figure 5): BNC2 binds to its own promoter. Extended data and detailed methods (including QC metrics) for BNC2 ChIP-Seq.
Supplementary Data 5 from Inhibition of NF-κB–Dependent Signaling Enhances Sensitivity and Overcomes Resistance to BET Inhibition in Uveal Melanoma
Authors: Ambrosini Grazia , Do Catherine , Tycko Benjamin , Realubit Ronald B. , Karan Charles , Musi Elgilda , Carvajal Richard D. , Chua Vivian , Aplin Andrew E. , Schwartz Gary K.
Published: April 2023

BETi-resistant cutaneous and uveal melanoma cells have different gene expression profiles
Supplementary Data 4 from Overexpression of RUNX3 Represses RUNX1 to Drive Transformation of Myelodysplastic Syndrome
Authors: Yokomizo-Nakano Takako , Kubota Sho , Bai Jie , Hamashima Ai , Morii Mariko , Sun Yuqi , Katagiri Seiichiro , Iimori Mihoko , Kanai Akinori , Tanaka Daiki , Oshima Motohiko , Harada Yuka , Ohyashiki Kazuma , Iwama Atsushi , Harada Hironori , Osato Motomi , Sashida Goro
Published: April 2023

Motif enrichment analysis
Video 2 from esiCancer: Evolutionary In Silico Cancer Simulator
Authors: Minussi Darlan Conterno , Henz Bernardo , dos Santos Oliveira Mariana , Filippi-Chiela Eduardo C. , Oliveira Manuel M. , Lenz Guido
Published: April 2023

This video describes how to use esiCancer.
Supplementary Data from A Feedback Loop between Hypoxia and Matrix Stress Relaxation Increases Oxygen-Axis Migration and Metastasis in Sarcoma
Authors: Lewis Daniel M. , Pruitt Hawley , Jain Nupur , Ciccaglione Mark , McCaffery J. Michael , Xia Zhiyong , Weber Kristy , Eisinger-Mathason T.S. Karin , Gerecht Sharon
Published: April 2023

This file contains additional data including material characterization, cell phenotype and migration, mechanotransduction pathway, proteases activity, tumor mechanics and human sarcoma cell migration.
Supplementary Data from YY1 Complex Promotes Quaking Expression via Super-Enhancer Binding during EMT of Hepatocellular Carcinoma
Authors: Han Jingxia , Meng Jing , Chen Shuang , Wang Xiaorui , Yin Shan , Zhang Qiang , Liu Huijuan , Qin Rong , Li Zhongwei , Zhong Weilong , Zhang Chao , Zhang Heng , Tang Yuanhao , Lin Tingting , Gao Wanfeng , Zhang Xiaoyun , Yang Lan , Liu Yanrong , Zhou Hong-gang , Sun Tao , Yang Cheng
Published: April 2023

Supplementary Data from YY1 Complex Promotes Quaking Expression via Super-Enhancer Binding during EMT of Hepatocellular Carcinoma
Supplementary Data from Retrodifferentiation of Human Tumor Hepatocytes to Stem Cells Leads to Metabolic Reprogramming and Chemoresistance
Authors: Fekir Karim , Dubois-Pot-Schneider Hélène , Désert Romain , Daniel Yoann , Glaise Denise , Rauch Claudine , Morel Fabrice , Fromenty Bernard , Musso Orlando , Cabillic Florian , Corlu Anne
Published: April 2023

Supplemental Table 2 provides the specific signatures defining the periportal, perivenous, extracellular matrix and stem HCC subclasses.
Supplementary Data from The EMT Transcription Factor ZEB2 Promotes Proliferation of Primary and Metastatic Melanoma While Suppressing an Invasive, Mesenchymal-Like Phenotype
Authors: Vandamme Niels , Denecker Geertrui , Bruneel Kenneth , Blancke Gillian , Akay Özden , Taminau Joachim , De Coninck Jordy , De Smedt Eva , Skrypek Nicolas , Van Loocke Wouter , Wouters Jasper , Nittner David , Köhler Corinna , Darling Douglas S. , Cheng Phil F. , Raaijmakers Marieke I.G. , Levesque Mitchell P. , Mallya Udupi Girish , Rafferty Mairin , Balint Balazs , Gallagher William M. , Brochez Lieve , Huylebroeck Danny , Haigh Jody J. , Andries Vanessa , Rambow Florian , Van Vlierberghe Pieter , Goossens Steven , van den Oord Joost J. , Marine Jean-Christophe , Berx Geert
Published: April 2023

Supplementary Figure legends for Figures 1-5.
Supplementary Table 1 from Phosphorylation of RAB7 by TBK1/IKKϵ Regulates Innate Immune Signaling in Triple-Negative Breast Cancer
Authors: Ritter Jessica L. , Zhu Zehua , Thai Tran C. , Mahadevan Navin R. , Mertins Philipp , Knelson Erik H. , Piel Brandon P. , Han Saemi , Jaffe Jacob D. , Carr Steven A. , Barbie David A. , Barbie Thanh U.
Published: April 2023

Phosphopeptides from cell based screen
Supplementary Data from Suppression of LIM Kinase 1 and LIM Kinase 2 Limits Glioblastoma Invasion
Authors: Chen Joseph , Ananthanarayanan Badriprasad , Springer Kelsey S. , Wolf Kayla J. , Sheyman Sharon M. , Tran Vivien D. , Kumar Sanjay
Published: April 2023

Supplemental Video 1. LIMK1/2 KD U373s exhibit abnormal actin turnover
Supplementary Data from Epigenetic Regulation of the PTEN–AKT–RAC1 Axis by G9a Is Critical for Tumor Growth in Alveolar Rhabdomyosarcoma
Authors: Bhat Akshay V. , Palanichamy Kala Monica , Rao Vinay Kumar , Pignata Luca , Lim Huey Jin , Suriyamurthy Sudha , Chang Kenneth T. , Lee Victor K. , Guccione Ernesto , Taneja Reshma
Published: April 2023

Supplementary Figure S1. Inhibition of G9a activity reduces colony formation. Supplementary Figure S2. Inhibition of G9a expression or activity in RH30 cells impacts proliferation, differentiation and motility Supplementary Figure S3. Inhibition of G9a expression or activity in RH41 cells impacts proliferation, differentiation and motility Supplementary Figure S4. Validation of transcriptome analysis with G9a knockdown cells Supplementary Figure S5. Validation of ChIP-Seq analysis by CHIP-PCR Supplementary Figure S6. Inhibition of RAC1 activity reduces proliferation, migration and invasion Supplementary Table 1. Nanostring PanCancer pathway analysis in siG9a cells
Supplementary Table S2 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Table S2 shows the double-stranded shRNAs targeting selected up-regulated genes and siRNA for PNO1.
Supplementary Figure S2 from EBF1-Mediated Upregulation of Ribosome Assembly Factor PNO1 Contributes to Cancer Progression by Negatively Regulating the p53 Signaling Pathway
Authors: Shen Aling , Chen Youqin , Liu Liya , Huang Yue , Chen Hongwei , Qi Fei , Lin Jiumao , Shen Zhiqing , Wu Xiangyan , Wu Meizhu , Li Qiongyu , Qiu Liman , Yu Na , Sferra Thomas J. , Peng Jun
Published: April 2023

Figure S2 indicates that higher PNO1 mRNA levels are associated with poorer overall survival, relapse-free survival and shorter time of first progression of patients with breast or lung cancer. PNO1 knockdown decreased cell viability and cell survival of lung and breast cancer cells.
Supplementary Data Table S8 from Loss of FOXP3 and TSC1 Accelerates Prostate Cancer Progression through Synergistic Transcriptional and Posttranslational Regulation of c-MYC
Authors: Wu Lianpin , Yi Baozhu , Wei Shi , Rao Dapeng , He Youhua , Naik Gurudatta , Bae Sejong , Liu Xiaoguang M. , Yang Wei-Hsiung , Sonpavde Guru , Liu Runhua , Wang Lizhong
Published: April 2023

Supplementary Data Table S8: Original data for the gene copy differences of candidate genes between nFOXP3+ and FOXP3- human prostate tumors in Supplementary Figure S1B.
Figure S1 from GARP Dampens Cancer Immunity by Sustaining Function and Accumulation of Regulatory T Cells in the Colon
Authors: Salem Mohammad , Wallace Caroline , Velegraki Maria , Li Anqi , Ansa-Addo Ephraim , Metelli Alessandra , Kwon Hyunwoo , Riesenberg Brian , Wu Bill , Zhang Yongliang , Guglietta Silvia , Sun Shaoli , Liu Bei , Li Zihai
Published: April 2023

Activated Treg cells express GARP
Supplementary Figure 3 from CoA Synthase (COASY) Mediates Radiation Resistance via PI3K Signaling in Rectal Cancer
Authors: Ferrandon Sylvain , DeVecchio Jennifer , Duraes Leonardo , Chouhan Hanumant , Karagkounis Georgios , Davenport Jacqueline , Orloff Matthew , Liska David , Kalady Matthew F.
Published: April 2023

Characterization of multiple COASY level cell lines.
Supplementary Table 4 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Supplementary Table 4
Supplementary Methods from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Supplementary Methods
Supplementary Data from The Interaction of Platelets with Colorectal Cancer Cells Inhibits Tumor Growth but Promotes Metastasis
Authors: Plantureux Léa , Mège Diane , Crescence Lydie , Carminita Estelle , Robert Stéphane , Cointe Sylvie , Brouilly Nicolas , Ezzedine Walid , Dignat-George Françoise , Dubois Christophe , Panicot-Dubois Laurence
Published: April 2023

Supplemental methods concerning the antibodies and reagents used, the preparation of platelets, the purification of monocytes, the knock-down of Cdh6, the flow cytometry experiments, the immunohistochemistry, the measure of the TF and TFPI activity, the aggregation of platelets, the RT-PCR, the western-blotting, the gene expression analysis and the methods used to detect macrophages and performed the experimental metastasis model. This file contains also the legend for the supplemental Fig 1 to 4.
Supplementary Figure 6 from Hispanic/Latino Patients with Gastric Adenocarcinoma Have Distinct Molecular Profiles Including a High Rate of Germline CDH1 Variants
Authors: Wang Sam C. , Yeu Yunku , Hammer Suntrea T.G. , Xiao Shu , Zhu Min , Hong Changjin , Clemenceau Jean R. , Yoon Lynn Y. , Nassour Ibrahim , Shen Jeanne , Agarwal Deepak , Reznik Scott I. , Mansour John C. , Yopp Adam C. , Zhu Hao , Hwang Tae Hyun , Porembka Matthew R.
Published: April 2023

Immunofluorescence staining for E-cadherin in Chinese hamster ovary cells overexpressing wild-type (WT) CDH1, A286G, or G1849A variants, all of which have wild-type membranous localization. Scale bar = 10 μm.
Supplementary Data File S3 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

Annotated Matlab output for OpenArray{trade mark, serif} and CFX gene expression analysis and signature development via singular value decomposition and bagged decision tree ensemble including raw figures from manuscript to correlate with associated code.
Supplementary Figures from Extracellular ATP and Purinergic P2Y2 Receptor Signaling Promote Liver Tumorigenesis in Mice by Exacerbating DNA Damage
Authors: Schulien Isabel , Hockenjos Birgit , van Marck Veerle , Ayata C. Korcan , Follo Marie , Thimme Robert , Hasselblatt Peter
Published: April 2023

Suppl. Figures
Supplementary Data File 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

NCBI GEO formatted submission for OpenArray{trade mark, serif} RT-qPCR data including: ID_REF, Gene Symbol, Reference/Target use, Catalog Number, Assay Type, Gene Name, Alias, RefSeq Accession Number, GenBank mRNA Numbers, Target Species, Amplicon Length, Platform, Raw Non-Normalized Cq, Reference Gene Normalized Î"Cq and Î"Î"Cq Fold Changes.