bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data from ZDHHC2-mediated AGK palmitoylation activates AKT/mTOR signaling to reduce sunitinib sensitivity in renal cell carcinoma
Authors: Sun Yan , Zhu Liang , Liu Pian , Zhang Huan , Guo Feng , Jin Xin
Published: September 2024

Supplementary Data
Supplementary Fig 8 from Ubiquitin ligases Siah1a/2 control alveolar macrophage functions to limit carcinogen-induced lung adenocarcinoma
Authors: Scortegagna Marzia , Du Yuanning , Bradley Linda M. , Wang Kun , Molinolo Alfredo , Ruppin Eytan , Murad Rabi , Ronai Ze'ev A.
Published: September 2024

Supp Fig 8
Supplementary Fig 2 from Ubiquitin ligases Siah1a/2 control alveolar macrophage functions to limit carcinogen-induced lung adenocarcinoma
Authors: Scortegagna Marzia , Du Yuanning , Bradley Linda M. , Wang Kun , Molinolo Alfredo , Ruppin Eytan , Murad Rabi , Ronai Ze'ev A.
Published: September 2024

Sup Fig 2
Table S2 from Proteomic profiling of extracellular matrix components from patient metastases identifies consistently elevated proteins for developing nanobodies that target primary tumors and metastases
Authors: Jailkhani Noor , Clauser Karl R. , Mak Howard H. , Rickelt Steffen , Tian Chenxi , Whittaker Charles A. , Tanabe Kenneth K. , Purdy Stephen R. , Carr Steven A. , Hynes Richard O.
Published: September 2024

Supplementary Table S2
Supplementary Table 2 from N6-methyladenosine promotes translation of VEGFA to accelerate angiogenesis in lung cancer
Authors: Zhang Haisheng , Zhou Jiawang , Li Jiexin , Wang Zhaotong , Chen Zhuojia , Lv Ziyan , Ge Lichen , Xie Guoyou , Deng Guoming , Rui Yalan , Huang Hongbing , Chen Likun , Wang Hongsheng
Published: September 2024

Table S2
Supplementary Data from Tumor-derived Small Extracellular Vesicles Inhibit the Efficacy of CAR T Cells against Solid Tumors
Authors: Zhong Wenqun , Xiao Zebin , Qin Zhiyuan , Yang Jingbo , Wen Yi , Yu Ziyan , Li Yumei , Sheppard Neil C. , Fuchs Serge Y. , Xu Xiaowei , Herlyn Meenhard , June Carl H. , Pure Ellen , Guo Wei
Published: September 2024

Supplementary Figures and Figure Legends
Supplementary Table 2 from CellMinerCDB: NCATS is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations
Authors: Reinhold William C. , Wilson Kelli , Elloumi Fathi , Bradwell Katie R. , Ceribelli Michele , Varma Sudhir , Wang Yanghsin , Duveau Damien , Menon Nikhil , Trepel Jane , Zhang Xiaohu , Klumpp-Thomas Carleen , Michael Samuel , Shinn Paul , Luna Augustin , Thomas Craig , Pommier Yves
Published: September 2024

Tissues of origin
Supplementary Figure 1 from CellMinerCDB: NCATS is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations
Authors: Reinhold William C. , Wilson Kelli , Elloumi Fathi , Bradwell Katie R. , Ceribelli Michele , Varma Sudhir , Wang Yanghsin , Duveau Damien , Menon Nikhil , Trepel Jane , Zhang Xiaohu , Klumpp-Thomas Carleen , Michael Samuel , Shinn Paul , Luna Augustin , Thomas Craig , Pommier Yves
Published: September 2024

BAX versus SN38
Supplemental Figure 2 from CellMinerCDB: NCATS is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations
Authors: Reinhold William C. , Wilson Kelli , Elloumi Fathi , Bradwell Katie R. , Ceribelli Michele , Varma Sudhir , Wang Yanghsin , Duveau Damien , Menon Nikhil , Trepel Jane , Zhang Xiaohu , Klumpp-Thomas Carleen , Michael Samuel , Shinn Paul , Luna Augustin , Thomas Craig , Pommier Yves
Published: September 2024

BRAF versus dabrafenib
Table S1 from TGF-β antagonizes IFN-γ-mediated adaptive immune evasion via activation of the AKT-Smad3-SHP1 axis in lung adenocarcinoma
Authors: Ye Fan , Cai Zihao , Wang Boyu , Zeng Chenxi , Xi Yu , Hu Shaojie , Qu Rirong , Yuan Zhiwei , Yue Jiaqi , Tian Yitao , Wang Xue , Fu Xiangning , Li Lequn
Published: September 2024

Table S1
Supplementary Data from TGF-β antagonizes IFN-γ-mediated adaptive immune evasion via activation of the AKT-Smad3-SHP1 axis in lung adenocarcinoma
Authors: Ye Fan , Cai Zihao , Wang Boyu , Zeng Chenxi , Xi Yu , Hu Shaojie , Qu Rirong , Yuan Zhiwei , Yue Jiaqi , Tian Yitao , Wang Xue , Fu Xiangning , Li Lequn
Published: September 2024

Table S2
Supplementary Data from Attenuation of sialylation augments antitumor immunity and improves response to immunotherapy in ovarian cancer
Authors: Cao Kankan , Zhang Guodong , Yang Moran , Wang Yiying , He Mengdi , Zhang Chen , Huang Yan , Lu Jiaqi , Liu Haiou
Published: September 2024

Materials and Methods；
Supplementary Figure S1 to S14 for multiple supplementary figures
Supplementary Figure Legends from Retinol saturase mediates retinoid metabolism to impair a ferroptosis defense system in cancer cells
Authors: Bi Guoshu , Liang Jiaqi , Shan Guangyao , Bian Yunyi , Chen Zhencong , Huang Yiwei , Lu Tao , Li Ming , Besskaya Valeria , Zhao Mengnan , Fan Hong , Wang Qun , Gan Boyi , Zhan Cheng
Published: September 2024

The legends for supplementary figure 1-7.
Supplementary Figure 6 from Retinol saturase mediates retinoid metabolism to impair a ferroptosis defense system in cancer cells
Authors: Bi Guoshu , Liang Jiaqi , Shan Guangyao , Bian Yunyi , Chen Zhencong , Huang Yiwei , Lu Tao , Li Ming , Besskaya Valeria , Zhao Mengnan , Fan Hong , Wang Qun , Gan Boyi , Zhan Cheng
Published: September 2024

RETSAT-RAR pathway promotes ferroptosis by activating SCD-mediated MUFA generation.
Supplementary Figure 3 from Retinol saturase mediates retinoid metabolism to impair a ferroptosis defense system in cancer cells
Authors: Bi Guoshu , Liang Jiaqi , Shan Guangyao , Bian Yunyi , Chen Zhencong , Huang Yiwei , Lu Tao , Li Ming , Besskaya Valeria , Zhao Mengnan , Fan Hong , Wang Qun , Gan Boyi , Zhan Cheng
Published: September 2024

RETSAT does not interfere with known ferroptosis regulators.
Supplementary Figure 2 from Retinol saturase mediates retinoid metabolism to impair a ferroptosis defense system in cancer cells
Authors: Bi Guoshu , Liang Jiaqi , Shan Guangyao , Bian Yunyi , Chen Zhencong , Huang Yiwei , Lu Tao , Li Ming , Besskaya Valeria , Zhao Mengnan , Fan Hong , Wang Qun , Gan Boyi , Zhan Cheng
Published: September 2024

RETSAT is a pro-ferroptosis gene.
Table S1 from Ccr2+ monocyte-derived macrophages influence trajectories of acquired therapy resistance in Braf-mutant melanoma
Authors: Kim Dahihm , An Luye , Moon Jiwon , Maymi Viviana I. , McGurk Alexander I. , Rudd Brian D. , Fowell Deborah , White Andrew C.
Published: September 2024

Antibodies used for immunostaining and flow cytometry
Figure S4 from Ccr2+ monocyte-derived macrophages influence trajectories of acquired therapy resistance in Braf-mutant melanoma
Authors: Kim Dahihm , An Luye , Moon Jiwon , Maymi Viviana I. , McGurk Alexander I. , Rudd Brian D. , Fowell Deborah , White Andrew C.
Published: September 2024

Different resistance phenotypes observed with and without Ccr2+ macrophages.
Supplementary Fig. S2 from The mTOR Signaling Pathway Interacts with the ER Stress Response and the Unfolded Protein Response in Cancer
Authors: Mafi Sahar , Ahmadi Elham , Meehan Eileen , Chiari Conner , Mansoori Behzad , Sadeghi Hossein , Milani Sahar , Jafarinia Morteza , Taeb Shahram , Mafakheri Bashmagh Bayan , Mansoorian Seyed Mohammad Ali. , Soltani-Zangbar Mohammad Sadegh , Wang Kepeng , Rostamzadeh Davoud
Published: September 2024

Supplementary Fig. S2. Endoplasmic reticulum stress and unfolded protein response in normal physiology and cancer
Tumor cells frequently encounter endogenous and exogenous stresses that influence protein folding in the ER, including hypoxia, inflammation, nutrient deprivation, altered glycolysis, DNA damage, genomic instability, oncogene activation, and proteasome dysfunction, can cause excessive accumulation of misfolded or unfolded proteins within the ER lumen, a condition termed "ER stress." As a response to prolonged ER stress conditions, the ER responds to the ER stress by activating intracellular signal transduction pathways, collectively referred to as the UPR, to restore-ER homeostasis (protective effect) or activate cell death (cytotoxic effect). The UPR signaling cascade comprises three parallel pathways that employ unique signal transduction mechanisms and are initiated by activating three conserved ER-stress sensors: IRE1, ATF6, and PERK. Furthermore, in mammals and under resting conditions, the critical ER-resident chaperone, GRP78/BiP, prevents the activation and blocks the downstream signaling of UPR by binding to the N-terminal side of stress sensor proteins, IRE-1, PERK, and ATF6 and maintains these sensors in an inactive state. When ER stress is triggered, and the ER luminal load of unfolded or misfolded proteins increases, the GRP78/BiP dissociates, activating IRE1, PERK, and ATF6 signaling cascades, leading to the activation of these UPR signaling pathways. Upon activation, the UPR can regulate many cellular events of tumor cells, including autophagy, ER biogenesis, cell survival, metastasis, angiogenesis, migration and invasion, chemoresistance, glycolysis, and proliferation.
ER, Endoplasmic reticulum; UPR, unfolded protein response; PREK, protein kinase R (PKR) like endoplasmic reticulum kinase; ATF, activating transcription factor; IRE1, inositol requiring enzyme 1; GRP78, 78-kDa glucose-regulated protein/immunoglobulin-binding protein; CHOP, C/EBP homologous protein; AMPK, AMP-activated protein kinase; XBP-1, X-box binding protein 1; Dr5, death receptor 5; GADD34, growth arrest and DNA damage-inducible protein 34; ERO1α, ER oxidoreductin 1; GCN2, general control non-derepressible 2.
Figure S4 from Metformin reprograms tryptophan metabolism to stimulate CD8+ T cell function in colorectal cancer
Authors: Huang Xiaowen , Sun Tiantian , Wang Jilin , Hong Xialu , Chen Huimin , Yan Tingting , Zhou Chengbei , Sun Danfeng , Yang Chen , Yu TaChung , Su Wenyu , Du Wan , Xiong Hua
Published: September 2024

Figure S4 is the validation of SLC7A5 knockdown at protein level.
Figure S3 from Metformin reprograms tryptophan metabolism to stimulate CD8+ T cell function in colorectal cancer
Authors: Huang Xiaowen , Sun Tiantian , Wang Jilin , Hong Xialu , Chen Huimin , Yan Tingting , Zhou Chengbei , Sun Danfeng , Yang Chen , Yu TaChung , Su Wenyu , Du Wan , Xiong Hua
Published: September 2024

Figure S3 describes that lack of tryptophan impairs the function of CD8+T cells.
Supplementary Data from The HDAC2-SP1 axis orchestrates pro-tumor macrophage polarization
Authors: Zheng Xiang , Sarode Poonam , Weigert Andreas , Turkowski Kati , Chelladurai Prakash , Günther Stefan , Kuenne Carsten , Winter Hauke , Stenzinger Albrecht , Reu Simone , Grimminger Friedrich , Stiewe Thorsten , Seeger Werner , Pullamsetti Soni Savai. , Savai Rajkumar
Published: September 2024

Supplementary Data with figires_tables
Supplementary Data from Periostin+ stromal cells guide lymphovascular invasion by cancer cells
Authors: Null Jamie L. , Kim Dae Joong , McCann James V. , Pramoonjago Patcharin , Fox Jay W. , Zeng Jianhao , Kumar Pankaj , Edatt Lincy , Pecot Chad V. , Dudley Andrew C.
Published: September 2024

Data supplement
Supplementary File 7 from Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway
Authors: Ludwig Michael P. , Galbraith Matthew D. , Eduthan Neetha Paul. , Hill Amanda A. , Clay Michael R. , Moreno Tellez Cristiam , Wilky Breelyn A. , Elias Anthony , Espinosa Joaquín Maximiliano. , Sullivan Kelly D.
Published: September 2024

Western blots.
Supplementary File 4 from Proteasome Inhibition Sensitizes Liposarcoma to MDM2 Inhibition with Nutlin-3 by Activating the ATF4/CHOP Stress Response Pathway
Authors: Ludwig Michael P. , Galbraith Matthew D. , Eduthan Neetha Paul. , Hill Amanda A. , Clay Michael R. , Moreno Tellez Cristiam , Wilky Breelyn A. , Elias Anthony , Espinosa Joaquín Maximiliano. , Sullivan Kelly D.
Published: September 2024

Genome-wide CRISPR Nutlin-3 Sensitizing Gene screen data.
Supplementary Table 2 from Targeting CD44 variant 5 with an antibody-drug conjugate is an effective therapeutic strategy for intrahepatic cholangiocarcinoma
Authors: Bei Yuncheng , He Jian , Dong Xuhui , Wang Yuxin , Wang Sijie , Guo Wan , Cai Chengjie , Xu Zhiye , Wei Jia , Liu Baorui , Zhang Nan , Shen Pingping
Published: September 2024

amino acid sequences of mAbs in this study
Movie S4 from Inter- and intra-metastatic heterogeneity shapes adaptive therapy cycling dynamics
Authors: Gallaher Jill , Strobl Maximilian , West Jeffrey , Gatenby Robert , Zhang Jingsong , Robertson-Tessi Mark , Anderson Alexander R.A.
Published: September 2024

Movies corresponding to simulation examples in Figure 6, comparing continuous and adaptive therapy for simulations with intermetastasis and intrametastasis heterogeneity.
Supplementary Data from PP2Ac Deficiency Enhances Tumor Immunogenicity by Activating STING-Type I Interferon Signaling in Glioblastoma
Authors: Mondal Isha , Das Oishika , Sun Raymond , Gao Jian , Yu Bohyeon , Diaz Aaron , Behnan Jinan , Dubey Abhishek , Meng Zhipeng , Eskandar Emad , Xu Beisi , Lu Rongze Olivia. , Ho Winson S.
Published: September 2024

Cluster defining genes from scRNAseq data
Supplementary figure legends from BRCA1 Insufficiency Induces a Hypersialylated Acidic Tumor Microenvironment that Promotes Metastasis and Immunotherapy Resistance
Authors: Shu Xiaodong , Li Jianjie , Chan Un In , Su Sek Man , Shi Changxiang , Zhang Xin , An Tingting , Xu Jun , Mo Lihua , Liu Jianlin , Wang Yuqing , Li Xiaoling , Deng Min , Lei Josh Haipeng , Wang Chunfei , Tian Hao , Sun Heng , Shim Joong Sup , Zhang Xuanjun , Dai Yunlu , Yao Zhicheng , Kuang Xiaying , Lin Ying , Deng Chu-Xia , Xu Xiaoling
Published: September 2024

supp. figure legends S1-S7
Figure S5 from BRCA1 Insufficiency Induces a Hypersialylated Acidic Tumor Microenvironment that Promotes Metastasis and Immunotherapy Resistance
Authors: Shu Xiaodong , Li Jianjie , Chan Un In , Su Sek Man , Shi Changxiang , Zhang Xin , An Tingting , Xu Jun , Mo Lihua , Liu Jianlin , Wang Yuqing , Li Xiaoling , Deng Min , Lei Josh Haipeng , Wang Chunfei , Tian Hao , Sun Heng , Shim Joong Sup , Zhang Xuanjun , Dai Yunlu , Yao Zhicheng , Kuang Xiaying , Lin Ying , Deng Chu-Xia , Xu Xiaoling
Published: September 2024

Original picture
Figure S1 from BRCA1 Insufficiency Induces a Hypersialylated Acidic Tumor Microenvironment that Promotes Metastasis and Immunotherapy Resistance
Authors: Shu Xiaodong , Li Jianjie , Chan Un In , Su Sek Man , Shi Changxiang , Zhang Xin , An Tingting , Xu Jun , Mo Lihua , Liu Jianlin , Wang Yuqing , Li Xiaoling , Deng Min , Lei Josh Haipeng , Wang Chunfei , Tian Hao , Sun Heng , Shim Joong Sup , Zhang Xuanjun , Dai Yunlu , Yao Zhicheng , Kuang Xiaying , Lin Ying , Deng Chu-Xia , Xu Xiaoling
Published: September 2024

Original picture
Table S3 from Elevated Mast Cell Abundance is Associated with Enrichment of CCR2+ Cytotoxic T cells and Favorable Prognosis in Lung Adenocarcinoma
Authors: Fan Fanfan , Gao Jian , Zhao Yue , Wang Jun , Meng Lu , Ma Jiaqiang , Li Teng , Han Han , Lai Jinglei , Gao Zhendong , Li Xiongfei , Guo Ran , Cao Zhiwei , Zhang Yang , Zhang Xiaoming , Chen Haiquan
Published: September 2024

Table S3
Figure S9 from Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci
Authors: Kanholm Tomas , Rentia Uzma , Hadley Melissa , Karlow Jennifer A. , Cox Olivia L. , Diab Noor , Bendall Matthew L. , Dawson Tyson , McDonald James I. , Xie Wenbing , Crandall Keith A. , Burns Kathleen H. , Baylin Stephen B. , Easwaran Hariharan , Chiappinelli Katherine B.
Published: September 2024

Supplemental Figure 9
Table S3 from Breast cancer mutations HER2 V777L and PIK3CA H1047R activate the p21-CDK4/6 –Cyclin D1 axis driving tumorigenesis and drug resistance.
Authors: Cheng Xiaoqing , Sun Yirui , Highkin Maureen , Vemalapally Nagalaxmi , Jin Xiaohua , Zhou Brandon , Prior Julie L. , Tipton Ashley R. , Li Shunqiang , Iliuk Anton , Achilefu Samuel , Hagemann Ian S. , Edwards John R. , Bose Ron
Published: September 2024

Phosphoproteins in Volcano Plot
Supplementary Figures from Deficiency of the Polycomb protein RYBP and TET methylcytosine oxidases promotes extensive CpG island hypermethylation and malignant transformation
Authors: Cui Wei , Huang Zhijun , Jin Seung-Gi , Johnson Jennifer , Lau Kin H. , Hostetter Galen , Pfeifer Gerd P.
Published: September 2024

Supplementary Figures S1 to S11
Table S1 from Oxidative phosphorylation fueled by fatty acid oxidation sensitizes leukemic stem cells to cold
Authors: Griessinger Emmanuel , Pereira-Martins Diego , Nebout Marielle , Bosc Claudie , Saland Estelle , Boet Emeline , Sahal Ambrine , Chiche Johanna , Debayle Delphine , Fleuriot Lucile , Pruis Maurien , Mansat-De Mas Veronique , Vergez Francois , Récher Christian , Huls Gerwin , Sarry Jean-Emmanuel , Schuringa Jan Jacob , Peyron Jean-François
Published: September 2024

AML_Patient_Clinical features
Supplementary Data from Characterizing evolutionary dynamics reveals strategies to exhaust the spectrum of subclonal resistance in EGFR-mutant lung cancer
Authors: Müller Nina , Lorenz Carina , Ostendorp Jenny , Heisel Felix S. , Friese Ulrich P. , Cartolano Maria , Plenker Dennis , Tumbrink Hannah L. , Heimsoeth Alena , Baedeker Philipp , Ortiz-Cuaran Sandra , Weiss Jonathan , Büttner Reinhard , Peifer Martin , Thomas Roman K. , Sos Martin L. , Berg Johannes , Brägelmann Johannes
Published: September 2024

Supplementary Note covering the mathematical modelling
Supplementary Figure 4. from The genomic and epigenomic landscape of double-negative metastatic prostate cancer
Authors: Lundberg Arian , Zhang Meng , Aggarwal Rahul , Li Haolong , Zhang Li , Foye Adam , Sjöström Martin , Chou Jonathan , Chang Kevin , Moreno-Rodriguez Thaidy , Shrestha Raunak , Baskin Avi , Zhu Xiaolin , Weinstein Alana S. , Younger Noah , Alumkal Joshi J. , Beer Tomasz M. , Chi Kim N. , Evans Christopher P. , Gleave Martin , Lara Primo N. , Reiter Rob E. , Rettig Matthew B. , Witte Owen N. , Wyatt Alexander W. , Feng Felix Y. , Small Eric J. , Quigley David A.
Published: September 2024

Gene Ontology (GO) with Biological processes (BP) on the genes uniquely up- or down-regulated within each subtype
Supplementary Figure 3. from The genomic and epigenomic landscape of double-negative metastatic prostate cancer
Authors: Lundberg Arian , Zhang Meng , Aggarwal Rahul , Li Haolong , Zhang Li , Foye Adam , Sjöström Martin , Chou Jonathan , Chang Kevin , Moreno-Rodriguez Thaidy , Shrestha Raunak , Baskin Avi , Zhu Xiaolin , Weinstein Alana S. , Younger Noah , Alumkal Joshi J. , Beer Tomasz M. , Chi Kim N. , Evans Christopher P. , Gleave Martin , Lara Primo N. , Reiter Rob E. , Rettig Matthew B. , Witte Owen N. , Wyatt Alexander W. , Feng Felix Y. , Small Eric J. , Quigley David A.
Published: September 2024

Volcano plots representing the differentially expressed (DE) genes in the mCRPC subtypes compared to AR+/NE- tumors
Supplementary Figure 2 from PTEN loss confers resistance to anti-PD-1 therapy in non-small cell lung cancer by increasing tumor infiltration of regulatory T cells
Authors: Exposito Francisco , Redrado Miriam , Houry Maeva , Hastings Katherine , Molero-Abraham Magdalena , Lozano Teresa , Solórzano José Luis. , Sanz-Ortega Julian , Adradas Vera , Amat Ramon , Redin Esther , Leon Sergio , Legarra Naroa , Garcia Javier , Serrano Diego , Valencia Karmele , Robles-Oteiza Camila , Foggetti Giorgia , Otegui Nerea , Felip Enriqueta , Lasarte Juan J. , Paz-Ares Luis , Zugazagoitia Jon , Politi Katerina , Montuenga Luis , Calvo Alfonso
Published: September 2024

Supplementary Figure 2
Supplementary Figure 1 from PTEN loss confers resistance to anti-PD-1 therapy in non-small cell lung cancer by increasing tumor infiltration of regulatory T cells
Authors: Exposito Francisco , Redrado Miriam , Houry Maeva , Hastings Katherine , Molero-Abraham Magdalena , Lozano Teresa , Solórzano José Luis. , Sanz-Ortega Julian , Adradas Vera , Amat Ramon , Redin Esther , Leon Sergio , Legarra Naroa , Garcia Javier , Serrano Diego , Valencia Karmele , Robles-Oteiza Camila , Foggetti Giorgia , Otegui Nerea , Felip Enriqueta , Lasarte Juan J. , Paz-Ares Luis , Zugazagoitia Jon , Politi Katerina , Montuenga Luis , Calvo Alfonso
Published: September 2024

Supplementary Figure 1
Supplementary Figures from Targeting KDM2A Enhances T Cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma
Authors: Chen Chen , Shin June Ho. , Fang Zhuoqing , Brennan Kevin , Horowitz Nina B. , Pfaff Kathleen L. , Welsh Emma L. , Rodig Scott J. , Gevaert Olivier , Gozani Or , Uppaluri Ravindra , Sunwoo John B.
Published: September 2024

Supplemental figures
Supplementary Data 4 from Targeting KDM2A Enhances T Cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma
Authors: Chen Chen , Shin June Ho. , Fang Zhuoqing , Brennan Kevin , Horowitz Nina B. , Pfaff Kathleen L. , Welsh Emma L. , Rodig Scott J. , Gevaert Olivier , Gozani Or , Uppaluri Ravindra , Sunwoo John B.
Published: September 2024

raw cell counts from organoid staining
Supplementary Data 3 from Targeting KDM2A Enhances T Cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma
Authors: Chen Chen , Shin June Ho. , Fang Zhuoqing , Brennan Kevin , Horowitz Nina B. , Pfaff Kathleen L. , Welsh Emma L. , Rodig Scott J. , Gevaert Olivier , Gozani Or , Uppaluri Ravindra , Sunwoo John B.
Published: September 2024

Western_imageJ data
Supplementary Data 2 from Targeting KDM2A Enhances T Cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma
Authors: Chen Chen , Shin June Ho. , Fang Zhuoqing , Brennan Kevin , Horowitz Nina B. , Pfaff Kathleen L. , Welsh Emma L. , Rodig Scott J. , Gevaert Olivier , Gozani Or , Uppaluri Ravindra , Sunwoo John B.
Published: September 2024

Western blots
Supplementary Data from Nanoparticle-based combination therapy enhances fulvestrant efficacy and overcomes tumor resistance in ER-positive breast cancer
Authors: Li Bozhao , Qi Feilong , Zhu Fei , Lu Zefang , Wang Meiqi , Chu Tianjiao , Wu Suying , Wei Jingyan , Song Zhenchuan , Sukumar Saraswati , Zhang Cheng , Xu Jiangfei , Li Suping , Nie Guangjun
Published: September 2024

Supporting information for manuscript
Supplementary Figures 1-4 and Tables 1-2 from Targeting CaMKK2 inhibits actin cytoskeletal assembly to suppress cancer metastasis
Authors: Mukherjee Debarati , Previs Rebecca A. , Haines Corinne , Al Abo Muthana , Juras Patrick K. , Strickland Kyle C. , Chakraborty Binita , Artham Sandeep , Whitaker Regina S. , Hebert Katherine , Fontenot Jake , Patierno Steven R. , Freedman Jennifer A. , Lau Frank H. , Burow Matthew E. , Chang Ching-Yi , McDonnell Donald P.
Published: September 2024

Contains Supplementary Figures 1-4, Supplementary Tables 1-2 and legends for Supplementary Videos 1-4
Table S4 from Mesenchymal-like tumor cells and myofibroblastic cancer-associated fibroblasts are associated with progression and immunotherapy response of clear-cell renal cell carcinoma
Authors: Davidson Guillaume , Helleux Alexandra , Vano Yann A. , Lindner Véronique , Fattori Antonin , Cerciat Marie , Elaidi Reza Thierry. , Verkarre Virginie , Sun Cheng-Ming , Chevreau Christine , Bennamoun Mostefa , Lang Hervé , Tricard Thibault , Fridman Wolf Herman. , Sautes-Fridman Catherine , Su Xiaoping , Plassard Damien , Keime Celine , Thibault-Carpentier Christelle , Barthélémy Philippe , Oudard Stéphane Marie. , Davidson Irwin , Malouf Gabriel G.
Published: September 2024

Deconvolution of cell types in BIONIKK cohort.
Supplementary Data from Dual inhibition of KRASG12D and pan-ERBB is synergistic in pancreatic ductal adenocarcinoma
Authors: Gulay Kevin Christian Montecillo. , Zhang Xinlian , Pantazopoulou Vasiliki , Patel Jay , Esparza Edgar , Pran Babu Deepa Sheik. , Ogawa Satoshi , Weitz Jonathan , Ng Isabella , Mose Evangeline S. , Pu Minya , Engle Dannielle D. , Lowy Andrew M. , Tiriac Hervé
Published: September 2024

Supplemental Figure and Table Legends
Supplemental Figures from Dual inhibition of KRASG12D and pan-ERBB is synergistic in pancreatic ductal adenocarcinoma
Authors: Gulay Kevin Christian Montecillo. , Zhang Xinlian , Pantazopoulou Vasiliki , Patel Jay , Esparza Edgar , Pran Babu Deepa Sheik. , Ogawa Satoshi , Weitz Jonathan , Ng Isabella , Mose Evangeline S. , Pu Minya , Engle Dannielle D. , Lowy Andrew M. , Tiriac Hervé
Published: September 2024

Figure S1 - S12
Figure S5 from ESRRB inhibits the TGF-β signaling pathway to drive cell proliferation in cervical cancer
Authors: Li Qin-Shu , Zheng Peng-Sheng
Published: September 2024

Fig. S5 describes supplementary data related to ESRRB transactivated SMAD7 and MYC transactivated ESRRB; survival curves of CDKN1A,CCNA2, MYC.
Table S7 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Table S7
Table S6 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Table S6
Table S3 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Table S3
Figure S8 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S8
Figure S4 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S4
Figure S1 from Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer
Authors: Chen Zhihang , Zhang Guopei , Ren Xiaoxue , Yao Zhijia , Zhou Qian , Ren Xuxin , Chen Shuling , Xu Lixia , Sun Kaiyu , Zeng Qianwen , Kuang Ming , Kuang Dong-Ming , Peng Sui
Published: September 2024

Figure S1
Table S8 from CD25high Effector Regulatory T Cells Hamper Responses to PD-1 Blockade in Triple-Negative Breast Cancer
Authors: Fattori Stéphane , Le Roy Aude , Houacine Jemila , Robert Lucie , Abes Riad , Gorvel Laurent , Granjeaud Samuel , Rouvière Marie-Sarah , Ben Amara Amira , Boucherit Nicolas , Tarpin Carole , Pakradouni Jihane , Charafe-Jauffret Emmanuelle , Houvenaeghel Gilles , Lambaudie Eric , Bertucci Francois , Rochigneux Philippe , Gonçalves Anthony , Foussat Arnaud , Chrétien Anne-Sophie , Olive Daniel
Published: September 2024

Differentially expressed genes between pre-αPD-1 Tregs versus post-αPD-1 Tregs, related to Figure 4
Table S4 from CD25high Effector Regulatory T Cells Hamper Responses to PD-1 Blockade in Triple-Negative Breast Cancer
Authors: Fattori Stéphane , Le Roy Aude , Houacine Jemila , Robert Lucie , Abes Riad , Gorvel Laurent , Granjeaud Samuel , Rouvière Marie-Sarah , Ben Amara Amira , Boucherit Nicolas , Tarpin Carole , Pakradouni Jihane , Charafe-Jauffret Emmanuelle , Houvenaeghel Gilles , Lambaudie Eric , Bertucci Francois , Rochigneux Philippe , Gonçalves Anthony , Foussat Arnaud , Chrétien Anne-Sophie , Olive Daniel
Published: September 2024

Inferred pseudotime gene features, related to Figure 1
Supplementary Data from Oncogenic ASPM is a regulatory hub of developmental and stemness signaling in cancers
Authors: Tsai Kelvin K. , Bae Byoung-Il , Hsu Chung-Chi , Cheng Li-Hsin , Shaked Yuval
Published: September 2024

This file contains Supplementary Figures 1-5, Supplementary Tables 1-2, and Supplementary Materials and Methods.
Supplementary Figure Legends from Galectin-1 mediates chronic STING activation in tumors to promote metastasis through MDSC recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette. , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh-Thu
Published: September 2024

sh-RNA knockdown sequences used in the study
Supplementary Figure 5 from Galectin-1 mediates chronic STING activation in tumors to promote metastasis through MDSC recruitment
Authors: Nambiar Dhanya K. , Viswanathan Vignesh , Cao Hongbin , Zhang Weiruo , Guan Li , Chamoli Manish , Holmes Brittany , Kong Christina , Hildebrand Rachel , Koong Amanda Jeanette. , von Eyben Rie , Plevritis Sylvia , Li Lingyin , Giaccia Amato , Engleman Edgar , Le Quynh-Thu
Published: September 2024

A. Quantification of phospho-p65 (NF-kb) staining in MOC2 and mEERL WT/KO-Gal1 tumors (N=5 tumors, 3 random microscopic fields per tumor). B. Quantitation of STING mRNA levels in MOC2 and mEERL WT/KO-Gal1 cell lines. C. Immunoblot showing degradation kinetics of STING in LLC and FaDU WT/KD-Gal1 cells at 1, 2, 4h post cycloheximide treatment. D. Magnified images showing co-localization of STING and LAMP1 in MOC2 WT/KO-Gal1 cells. E. Representative images showing low and high IHC staining of STING in oral cavity cancer (Left) and the distribution of negative and positive STING staining in 83 oral cavity cancers on the TMA. F. Kaplan Meier curve showing progression-free survival (calculated as the time from the surgery date until death or progression) of patients based on Gal1 and STING expression in the tumor.
Table S3 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Table S3 shows clinical characteristics of feces providers for fecal microbiota transplantation.
Supplementary figure legend from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Supplementary figure legend
Figure S4 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Figure S4 shows intra-tumoral bacteria identified in patients with ESCC.
Figure S3 from Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma
Authors: Wu Hong , Leng Xuefeng , Liu Qianshi , Mao Tianqin , Jiang Tao , Liu Yiqiang , Li Feifei , Cao Chenhui , Fan Jun , Chen Liang , Chen Yaqi , Yao Quan , Lu Shun , Liang Renchuan , Hu Lanlin , Liu Mingxin , Wan Yejian , Li Zhaoshen , Peng Jun , Luo Qiyu , Zhou Hang , Yin Jun , Xu Ke , Lan Mei , Peng Xinhao , Lan Haitao , Li Gang , Han Yongtao , Zhang Xia , Xiao Zhi-Xiong Jim. , Lang Jinyi , Wang Guihua , Xu Chuan
Published: September 2024

Figure S3 shows bacterial components differed between the NACI responders and non-responders of ESCC patients.
Supplementary Fig. S8 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S8. Comprehensive analysis of fulvestrant and birinapant treatment in HR+ breast cancer cell.
Supplementary Fig. S5 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S5. Analysis of the impact of the ER axis on the response to IFNg stimulation in HR+ breast cancer cells.
Supplementary Fig. S4 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S4. Schematic of flow cytometry experiments and differential impact of IFNg stimulation on HR+ breast cancer cells.
Supplementary Fig. S2 from Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer
Authors: Hermida-Prado Francisco , Xie Yingtian , Sherman Shira , Nagy Zsuzsanna , Russo Douglas , Akhshi Tara , Chu Zhengtao , Feit Avery , Campisi Marco , Chen Minyue , Nardone Agostina , Guarducci Cristina , Lim Klothilda , Font-Tello Alba , Lee Irene , García-Pedrero Juana , Canadas Israel , Agudo Judith , Huang Ying , Sella Tal , Jin Qingchun , Tayob Nabihah , Mittendorf Elizabeth A. , Tolaney Sara M. , Qiu Xintao , Long Henry , Symmans William F. , Lin Jia-Ren , Santagata Sandro , Bedrosian Isabelle , Yardley Denise A. , Mayer Ingrid A. , Richardson Edward T. , Oliveira Giacomo , Wu Catherine J. , Schuster Eugene F. , Dowsett Mitch , Welm Alana L. , Barbie David , Metzger Otto , Jeselsohn Rinath
Published: September 2024

Supplementary Fig. S2. Comprehensive analysis of protein expression changes before and after endocrine treatment
Table S4 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S4
Table S2 from LncRNA AGPG confers endocrine resistance in breast cancer by promoting E2F1 activity
Authors: Yu Shiyi , Wang Ying , Gong Xue , Fan Zhehao , Wang Zheng , Liang Zhengyan , Wu Rui , Cao Binjie , Wang Ning , Bi Caili , Lv Dan , Sun Haibo
Published: September 2024

Table S2
Supplementary Figures from GTP cyclohydrolase drives breast cancer development and promotes EMT in an enzyme-independent manner
Authors: Wang Zijing , Zhang Nan , Zhang Miao , Jiang Yao , Ng Aik Seng , Bridges Esther , Zhang Wei , Zeng Xin , Luo Qi , Liang Jiabien , Gyorffy Balázs , Hublitz Philip , Liang Zhu , Fischer Roman , Kerr David , Harris Adrian L. , Cai Shijie
Published: September 2024

Supplementary Figures S1-S11
Supplementary Data from GTP cyclohydrolase drives breast cancer development and promotes EMT in an enzyme-independent manner
Authors: Wang Zijing , Zhang Nan , Zhang Miao , Jiang Yao , Ng Aik Seng , Bridges Esther , Zhang Wei , Zeng Xin , Luo Qi , Liang Jiabien , Gyorffy Balázs , Hublitz Philip , Liang Zhu , Fischer Roman , Kerr David , Harris Adrian L. , Cai Shijie
Published: September 2024

Tables and figure legends
Supplementary Figure S6 from Radiation therapy-induced neurocognitive impairment is driven by heightened apoptotic priming in early life and prevented by blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: September 2024

Supplementary Figure S6
Supplementary Figure S2 from Radiation therapy-induced neurocognitive impairment is driven by heightened apoptotic priming in early life and prevented by blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: September 2024

Supplementary Figure S2
Supplementary Figure S1 from Radiation therapy-induced neurocognitive impairment is driven by heightened apoptotic priming in early life and prevented by blocking BAX
Authors: Singh Rumani , Yu Stacey , Osman Marwa , Inde Zintis , Fraser Cameron , Cleveland Abigail H. , Almanzar Nicole , Lim Chuan Bian , Joshi Gaurav N. , Spetz Johan , Qin Xingping , Toprani Sneh M. , Nagel Zachary , Hocking Matthew C. , Cormack Robert A. , Yock Torunn I. , Miller Jeffrey W. , Yuan Zhi-Min , Gershon Timothy , Sarosiek Kristopher A.
Published: September 2024

Supplementary Figure S1
Supplementary Fig. 9 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

Single molecule in situ hybridization for circSLC8A1 in prostate adenocarcinoma. Brightfield microscopy image at 200X magnification of DESMIN immunohistochemical staining (left panel). Brightfield and fluorescent microscopy images of circSLC8A1 at 200X magnification. A signal from circSLC8A1 can be observed in muscle cells, whereas the cancer cells were negative (right panel).
Supplementary Fig. 7 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

Single molecule in situ hybridization for circITGA7 and circHIPK3 in colon adenocarcinoma and adjacent normal tissues. A, B. Brightfield and fluorescent microscopy images at 200X magnification. A strong signal from circITGA7 can be observed in muscle cells, whereas the epithelium, tumor stroma, and cancer cells were negative
(A). A signal from circHIPK3 can be observed in the epithelium, tumor stroma, muscle, and cancer cells (B).
Supplementary Fig. 5 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

Analysis of Ki67 staining on colon adenocarcinoma and adjacent normal tissue sections.
Representative Ki67 staining from tumor (left) and adjacent normal (right) tissues from the five patients’
samples subjected to the analysis. Positive staining is visible as brown color. In the tumor tissues, Ki67 is clearly present in the cancer cells and in some cells in the tumor stroma. In the normal tissue sections, the
positive staining is found at the bottom of the crypts in the epithelium whereas no staining is detected in the mucosa and muscle sub-compartments.
Supplementary Fig. 2 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

Tissue markers specificity. Normalized NanoString counts from specific tissue markers used for sub-compartment purity assessment after laser capture microdissection. KRT8, CDX2 and SATB2 are epithelial markers. VIM is an activated stromal marker and ACTA2 and DES are muscle cell markers. Parametric t-tests were performed to compute the p-values using the values from the cancer cells as reference. The box represents the interquartile range (Q1 and Q3), the median is marked with a horizontal line, and whiskers represent minimum and maximum values.
Supplementary Fig. 10 from Spatial profiling of circular RNAs in cancer reveals high expression in muscle and stromal cells
Authors: García-Rodríguez Juan L. , Korsgaard Ulrik , Ahmadov Ulvi , Jarlstad Olesen Morten T. , Dietrich Kim-Gwendolyn , Hansen Emma B. , Vissing Stine M. , Ulhøi Benedicte P. , Dyrskjøt Lars , Sørensen Karina D. , Kjems Jørgen , Hager Henrik , Kristensen Lasse S.
Published: September 2024

Muscle and epithelial marker correlations to circSLC8A1 in prostate cancer patients. Scatter plots comparing the normalized expression levels of circSLC8A1 with levels of the muscle-specific marker, DES, ACTA2
and the epithelial markers KLK3, NKX3.1, and KRT8 for each of the 172 prostatic tumor tissue samples. Linear regression was performed to assess potential correlation and the Pearson correlation coefficient (R).
Type refers to tissue sample type, where 0 stands for Adjacent normal, 1 stands for localized prostate cancer
and 2 stands for Primary tumor sample from patient with metastatic prostate cancer.
Supplementary Tables from Bi-allelic Dicer1 mutations in the gynecologic tract of mice drive lineage-specific development of DICER1 syndrome-associated cancer
Authors: Wang Yemin , Chen Shary Yuting , Ta Monica , Senz Janine , Tao Lan Valerie. , Thornton Shelby , Tamvada Nirupama , Yang Winnie , Moscovitz Yana , Li Eunice , Guo Jingjie , Shen Cindy , Douglas J. Maxwell , El-Naggar Amal M. , Kommoss Felix K. F. , Underhill T. Michael , Singh Naveena , Gilks C. Blake , Morin Gregg B. , Huntsman David G.
Published: September 2024

Table S1-S6
Figure S7 from Targeting the immunoglobulin IGSF9 enhances anti-tumor T cell activity and sensitivity to anti-PD-1 immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: September 2024

Anti-IGSF9 reversed the inhibition of T cells mediated by IGSF9-ECD.
Figure S2 from Targeting the immunoglobulin IGSF9 enhances anti-tumor T cell activity and sensitivity to anti-PD-1 immunotherapy
Authors: Liu Yifan , Wang Hongying , Zhao Xinyu , Zhang Jiashen , Zhao Zhiling , Lian Xia , Zhang Juan , Kong Feng , Hu Tao , Wang Ting , Li Xiaohua , Wang Lei , Wang Dapeng , Li Chunling , Luan Huiwen , Liu Xiaoli , Wang Chunyan , Jiang Yun , Li Xiaomin , Li Fangmin , Ji Shuhao , Wang Yaopeng , Li Zunling
Published: September 2024

IGSF9 expression was detected in normal tissue array.
Table S1 from Breast cancer-secreted factors promote lung metastasis by signaling systemically to induce a fibrotic pre-metastatic niche
Authors: Cohen Noam , Mundhe Dhanashree , Deasy Sarah K. , Adler Omer , Ershaid Nour , Shami Tamar , Levi-Galibov Oshrat , Wassermann Rina , Scherz-Shouval Ruth , Erez Neta
Published: September 2024

Supplementary Table 1 showing list of proteins detected in protein array
Figure S1 from Breast cancer-secreted factors promote lung metastasis by signaling systemically to induce a fibrotic pre-metastatic niche
Authors: Cohen Noam , Mundhe Dhanashree , Deasy Sarah K. , Adler Omer , Ershaid Nour , Shami Tamar , Levi-Galibov Oshrat , Wassermann Rina , Scherz-Shouval Ruth , Erez Neta
Published: September 2024

Supplementary data to Figure 1
Tables S4-S6 from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Table S4: Top 10 expressed lncRNAs across TARGET cancers and GTEx tissues, Table S5: Tissue specificity index (tau score) annotation per gene, Table S6: Validation of tissue specific lncRNAs based on tau score analysis in alternate NBL datasets
Tables S15-S17 from Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: September 2024

Table S15: Data integration using multi-dimensional analysis to prioritize functional lncRNAs in each cancer, Table S16: Prioritized lncRNAs and predicted lncRNA target genes and pathways in NBL, Table S17: GSEA Analysis: MSigDB Hallmarks enriched across genes impacted by siTBX2-AS1 or siTBX2 treatment in NLF