bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S3 from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

High CDK7 protein expression is associated with poor prognosis in TNBC tissues
Figure S2 from Therapeutic Rationale to Target Highly Expressed CDK7 Conferring Poor Outcomes in Triple-Negative Breast Cancer
Authors: Li Bo , Ni Chonghaile Triona , Fan Yue , Madden Stephen F. , Klinger Rut , O'Connor Aisling E. , Walsh Louise , O'Hurley Gillian , Mallya Udupi Girish , Joseph Jesuchristopher , Tarrant Finbarr , Conroy Emer , Gaber Alexander , Chin Suet-Feung , Bardwell Helen A. , Provenzano Elena , Crown John , Dubois Thierry , Linn Sabine , Jirstrom Karin , Caldas Carlos , O'Connor Darran P. , Gallagher William M.
Published: March 2023

Antibody optimization for immunohistochemical assessment of CDK7
Supplementary Figure 5 from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

Evaluation of donor and host Tregs 14 days after ACT
Supplementary Figure 4 from T Cells Deficient in Diacylglycerol Kinase ζ Are Resistant to PD-1 Inhibition and Help Create Persistent Host Immunity to Leukemia
Authors: Jing Weiqing , Gershan Jill A. , Holzhauer Sandra , Weber James , Palen Katie , McOlash Laura , Pulakanti Kirthi , Wesley Erin , Rao Sridhar , Johnson Bryon D. , Riese Matthew J.
Published: March 2023

Evaluation of proliferation marker and PD-1 expression on adoptively transfered cells 14 days after transfer
Supplementary Materials and Methods from An Immunosuppressive Dendritic Cell Subset Accumulates at Secondary Sites and Promotes Metastasis in Pancreatic Cancer
Authors: Kenkel Justin A. , Tseng William W. , Davidson Matthew G. , Tolentino Lorna L. , Choi Okmi , Bhattacharya Nupur , Seeley E. Scott , Winer Daniel A. , Reticker-Flynn Nathan E. , Engleman Edgar G.
Published: March 2023

Supplementary Materials and Methods
Supplemental materials and methods and figure legends from The SWI/SNF Complex Protein Snr1 Is a Tumor Suppressor in Drosophila Imaginal Tissues
Authors: Xie Gengqiang , Chen Hanqing , Jia Dongyu , Shu Zhiqiang , Palmer William Hunt , Huang Yi-Chun , Zeng Xiankun , Hou Steven X. , Jiao Renjie , Deng Wu-Min
Published: March 2023

Legends and methods.
Figure S9 from Combination Therapy with Bispecific Antibodies and PD-1 Blockade Enhances the Antitumor Potency of T Cells
Authors: Chang Chien-Hsing , Wang Yang , Li Rongxiu , Rossi Diane L. , Liu Donglin , Rossi Edmund A. , Cardillo Thomas M. , Goldenberg David M.
Published: March 2023

. Effect of cPD-1 and T cells purified from PBMCs on single spheroids of MDA-MB-231 stimulated (A) or not (B) with IFN-gamma in the presence and absence of (E1)-3s
Supplementary Table 4 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Frequency of mutations observed at different mononucleotide repeat sites.
Supplementary Figures 1-19, supplementary methods and extended literature evaluation of the candidate genes from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Authors: Kondelin Johanna , Gylfe Alexandra E. , Lundgren Sofie , Tanskanen Tomas , Hamberg Jiri , Aavikko Mervi , Palin Kimmo , Ristolainen Heikki , Katainen Riku , Kaasinen Eevi , Taipale Minna , Taipale Jussi , Renkonen-Sinisalo Laura , Järvinen Heikki , Böhm Jan , Mecklin Jukka-Pekka , Vahteristo Pia , Tuupanen Sari , Aaltonen Lauri A. , Pitkänen Esa
Published: March 2023

Figures describing the following; length distribution of somatic insertions and deletions in the exome sequencing data, coverage of mononucleotide microsatellite sites in both exome and MiSeq sequencing data, mutation frequencies at mononucleotide microsatellite sites in the exome sequencing data, number of somatic deletions and insertions in the exome sequencing data, model p-values, expected -log10(p) values, mutation frequency, significance and normalized allelic fraction (NAF) of the top genes, overlap between validation sets 1,2, and 3, and mapped base pairs in the MiSeq sequencing data as well as the supplementary methods and extended literature evaluation of the candidate genes.
Supplementary Table 2 from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains Supplementary Table 2. Supplementary Table 2 shows that the proliferative capacity of PD-1 expressing CD8, CD4, and FoxP3+ TILs are decreased compared to non-PD-1 expressing TILs in OTSCC.
Supplementary Table 1 from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains Supplementary Table 1. Supplementary Table 1 shows the immunohistochemical staining for PD-L1, PD-1, CD4, and CD8 in the samples analyzed in the manuscript.
Supplementary Figures 3-9 from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains Supplementary Figures 3-9. Supplementary Figure 3. Representative multi-color immunofluorescence staining shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 4. Representative multi-color immunofluorescence staining of a PD-L1 negative tumor shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 5. CD4+ T cells show markedly more specific PD-L1 localization in OTSCC tumors compared to CD8+ T cells. Supplementary Figure 6. Representative multi-color immunofluorescence staining of an OTSCC tumor shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 7. Higher magnification multi-color immunofluorescence staining of a representative OTSCC tumor stained with PD-L1, PD-1, CD4, and CD8. Supplementary Figure 8. Diffuse tumoral PD-L1 staining shows low infiltration of CD4+ and CD8+ T cells. Supplementary Figure 9. Representative multi-color immunofluorescence staining of FoxP3, PD1, and Ki67 in OTSCC.
Supplementary Figure Legends from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains the figure legends for supplementary figures 1-9. Supplementary Figure 1. Staining pattern of tumoral PD-L1 staining. Supplementary Figure 2. Tumoral PD-L1 staining in association with PD-1, CD8, and CD4 TILs. Supplementary Figure 3. Representative multi-color immunofluorescence staining shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 4. Representative multi-color immunofluorescence staining of a PD-L1 negative tumor shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 5. CD4+ T cells show markedly more specific PD-L1 localization in OTSCC tumors compared to CD8+ T cells. Supplementary Figure 6. Representative multi-color immunofluorescence staining of an OTSCC tumor shows that PD-1+CD4+ T cells demonstrate greater PD-1 expression than PD1+CD8+ T cells. Supplementary Figure 7. Higher magnification multi-color immunofluorescence staining of a representative OTSCC tumor stained with PD-L1, PD-1, CD4, and CD8. Supplementary Figure 8. Diffuse tumoral PD-L1 staining shows low infiltration of CD4+ and CD8+ T cells. Supplementary Figure 9. Representative multi-color immunofluorescence staining of FoxP3, PD1, and Ki67 in OTSCC.
Supplementary Figure 2 from PD-1 Expression in Head and Neck Squamous Cell Carcinomas Derives Primarily from Functionally Anergic CD4+ TILs in the Presence of PD-L1+ TAMs
Authors: Mattox Austin K. , Lee Jina , Westra William H. , Pierce Robert H. , Ghossein Ronald , Faquin William C. , Diefenbach Thomas J. , Morris Luc G. , Lin Derrick T. , Wirth Lori J. , Lefranc-Torres Armida , Ishida Eiichi , Chakravarty Patrick D. , Johnson Lauren , Zeng Yang C. , Chen Huabiao , Poznansky Mark C. , Iyengar Neil M. , Pai Sara I.
Published: March 2023

This file contains Supplementary Figure 2. Supplementary Figure 2 shows tumoral PD-L1 staining in association with PD-1, CD8, and CD4 TILs.
Supplementary Table 2 from PRMT1-Mediated Translation Regulation Is a Crucial Vulnerability of Cancer
Authors: Hsu Jessie Hao-Ru , Hubbell-Engler Benjamin , Adelmant Guillaume , Huang Jialiang , Joyce Cailin E. , Vazquez Francisca , Weir Barbara A. , Montgomery Philip , Tsherniak Aviad , Giacomelli Andrew O. , Perry Jennifer A. , Trowbridge Jennifer , Fujiwara Yuko , Cowley Glenn S. , Xie Huafeng , Kim Woojin , Novina Carl D. , Hahn William C. , Marto Jarrod A. , Orkin Stuart H.
Published: March 2023

GSEA analysis of differentially expressed genes in the control versus Prmt1 KO mOS at the transcript level using GO gene sets.
Supplementary Materials and Methods from PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma
Authors: Tsubota Shoma , Kishida Satoshi , Shimamura Teppei , Ohira Miki , Yamashita Satoshi , Cao Dongliang , Kiyonari Shinichi , Ushijima Toshikazu , Kadomatsu Kenji
Published: March 2023

This file contains additional details of materials and methods used in this study including medium preparation, H&E staining, immunofluorescence analysis of frozen sections, immunohistochemistry on paraffin sections, in situ hybridization, western blotting, qPCR, microarray analysis, array CGH, MBD-seq, ChIP-seq, immunoprecipitation, overexpression of MYCN, knockdown of Ezh2, Ezh2 inhibitor treatment, and statistical analysis.
Figure S3 from Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer
Authors: Gulbahce Natali , Magbanua Mark Jesus M. , Chin Robert , Agarwal Misha R. , Luo Xuhao , Liu Jia , Hayden Daniel M. , Mao Qing , Ciotlos Serban , Li Zhenyu , Chen Yanxiang , Chen Xingpeng , Li Yuxiang , Zhang Rebecca Yu , Lee Katharine , Tearle Rick , Park Emily , Drmanac Snezana , Rugo Hope S. , Park John W. , Drmanac Radoje , Peters Brock A.
Published: March 2023

Mutational spectrum of CTCs. The percent of particular base changes (labeled on the right of the figure) for different sets of mutations from CTCs, NA12877, and breast cancer from TCGA (BRCA) data are shown. Founder mutations and mutations found in 5 cells have a pattern very similar to that seen in breast cancer.
Supplementary Tables S1-6 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Supplementary tables detailing qRT-PCR primer sequences (S1), IHC antibodies (S2), and parameters for histological stain quantification (S3-6) described in methods.
Supplementary Figures S5-7 from Sleeping Beauty Insertional Mutagenesis in Mice Identifies Drivers of Steatosis-Associated Hepatic Tumors
Authors: Tschida Barbara R. , Temiz Nuri A. , Kuka Timothy P. , Lee Lindsey A. , Riordan Jesse D. , Tierrablanca Carlos A. , Hullsiek Robert , Wagner Sandra , Hudson Wendy A. , Linden Michael A. , Amin Khalid , Beckmann Pauline J. , Heuer Rachel A. , Sarver Aaron L. , Yang Ju Dong , Roberts Lewis R. , Nadeau Joseph H. , Dupuy Adam J. , Keng Vincent W. , Largaespada David A.
Published: March 2023

Oncoprints showing steatosis-associated CIS gene amplifications, deep deletions, and mutations occurring in at least 5% of all(S5), steatosis-associated(S6), and alcohol-associated(S7) TCGA HCC cases
Movie S1 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

T-DM1 internalization in live cells.
Figure S1 from Resistance to the Antibody–Drug Conjugate T-DM1 Is Based in a Reduction in Lysosomal Proteolytic Activity
Authors: Ríos-Luci Carla , García-Alonso Sara , Díaz-Rodríguez Elena , Nadal-Serrano Mercedes , Arribas Joaquín , Ocaña Alberto , Pandiella Atanasio
Published: March 2023

Gene expression analysis of ABC transporters in T-DM1 resistant clones.
Supplementary Table 2 from Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency
Authors: Davies Helen , Morganella Sandro , Purdie Colin A. , Jang Se Jin , Borgen Elin , Russnes Hege , Glodzik Dominik , Zou Xueqing , Viari Alain , Richardson Andrea L. , Børresen-Dale Anne-Lise , Thompson Alastair , Eyfjord Jorunn E. , Kong Gu , Stratton Michael R. , Nik-Zainal Serena
Published: March 2023

Details of 11 MMR deficient breast cancers.
Supplementary Figure 4 from Anti-Jagged Immunotherapy Inhibits MDSCs and Overcomes Tumor-Induced Tolerance
Authors: Sierra Rosa A. , Trillo-Tinoco Jimena , Mohamed Eslam , Yu Lolie , Achyut Bhagelu R. , Arbab Ali , Bradford Jennifer W. , Osborne Barbara A. , Miele Lucio , Rodriguez Paulo C.
Published: March 2023

Figure shows that anti-Jagged induces immunogenic antigen-presenting cells that do not resemble MDSC-LC.
Supplementary Figure 1 from Anti-Jagged Immunotherapy Inhibits MDSCs and Overcomes Tumor-Induced Tolerance
Authors: Sierra Rosa A. , Trillo-Tinoco Jimena , Mohamed Eslam , Yu Lolie , Achyut Bhagelu R. , Arbab Ali , Bradford Jennifer W. , Osborne Barbara A. , Miele Lucio , Rodriguez Paulo C.
Published: March 2023

This file contains a figure showing the expression of CD31 in tumors from mice treated with anti-Jagged, compared to controls treated with an isotype
Supplemental Table 2: Predicted gene targets of the 16 differentially expressed miRNAs from An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia
Authors: Viswanathan Vignesh , Damle Shirish , Zhang Tao , Opdenaker Lynn , Modarai Shirin , Accerbi Monica , Schmidt Skye , Green Pamela , Galileo Deni , Palazzo Juan , Fields Jeremy , Haghighat Sepehr , Rigoutsos Isidore , Gonye Greg , Boman Bruce M.
Published: March 2023

* List gives the number of target gene transcripts that are hit by one or more of the miRNAs in order of decreasing number of miRNAs hitting them. **List gives the number of target gene transcripts that are hit by those miRNAs that are over-expressed in the crypt bottom in addition to hsa-mir-25 and hsa-mir-007
Supplemental Table 1: differentially expressed miRNAs in CRC vs normal tissue from An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia
Authors: Viswanathan Vignesh , Damle Shirish , Zhang Tao , Opdenaker Lynn , Modarai Shirin , Accerbi Monica , Schmidt Skye , Green Pamela , Galileo Deni , Palazzo Juan , Fields Jeremy , Haghighat Sepehr , Rigoutsos Isidore , Gonye Greg , Boman Bruce M.
Published: March 2023

List of 83 miRNAs which were differentially expressed in CRC vs normal colon.
Supplemental Figure 4 from Cyclin D1 Restrains Oncogene-Induced Autophagy by Regulating the AMPK–LKB1 Signaling Axis
Authors: Casimiro Mathew C. , Di Sante Gabriele , Di Rocco Agnese , Loro Emanuele , Pupo Claudia , Pestell Timothy G. , Bisetto Sara , Velasco-Velázquez Marco A. , Jiao Xuanmao , Li Zhiping , Kusminski Christine M. , Seifert Erin L. , Wang Chenguang , Ly Daniel , Zheng Bin , Shen Che-Hung , Scherer Philipp E. , Pestell Richard G.
Published: March 2023

Endogenous cyclin D1 restraint of mitochondrial mass is cell cycle independent.
Supplemental Figure 1 from Cyclin D1 Restrains Oncogene-Induced Autophagy by Regulating the AMPK–LKB1 Signaling Axis
Authors: Casimiro Mathew C. , Di Sante Gabriele , Di Rocco Agnese , Loro Emanuele , Pupo Claudia , Pestell Timothy G. , Bisetto Sara , Velasco-Velázquez Marco A. , Jiao Xuanmao , Li Zhiping , Kusminski Christine M. , Seifert Erin L. , Wang Chenguang , Ly Daniel , Zheng Bin , Shen Che-Hung , Scherer Philipp E. , Pestell Richard G.
Published: March 2023

Cyclin D1 reduces cellular ATP and sensitizes cells to glucose concentration in MEF.
Supplementary Table 1 from NFκB Promotes Ovarian Tumorigenesis via Classical Pathways That Support Proliferative Cancer Cells and Alternative Pathways That Support ALDH+ Cancer Stem–like Cells
Authors: House Carrie D. , Jordan Elizabeth , Hernandez Lidia , Ozaki Michelle , James Jana M. , Kim Marianne , Kruhlak Michael J. , Batchelor Eric , Elloumi Fathi , Cam Margaret C. , Annunziata Christina M.
Published: March 2023

Ovarian cancer cell line characteristics are listed with respect to source, tissue site, p53 mutation status, and histology at diagnosis.
Marchan Supplementary Table 7 from Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma
Authors: Marchan Rosemarie , Büttner Bettina , Lambert Jörg , Edlund Karolina , Glaeser Iris , Blaszkewicz Meinolf , Leonhardt Gregor , Marienhoff Lisa , Kaszta Darius , Anft Moritz , Watzl Carsten , Madjar Katrin , Grinberg Marianna , Rempel Eugen , Hergenröder Roland , Selinski Silvia , Rahnenführer Jörg , Lesjak Michaela S. , Stewart Joanna D. , Cadenas Cristina , Hengstler Jan G.
Published: March 2023

Lists of overlapping up- and downregulated probe sets and genes that were differentially expressed after GPAM knockdown with both oligos were compared to those differentially expressed after the knockdown of EDI3.
Supplementary Materials and Methods and References from Human Pluripotent Stem Cell–Derived TSC2-Haploinsufficient Smooth Muscle Cells Recapitulate Features of Lymphangioleiomyomatosis
Authors: Julian Lisa M. , Delaney Sean P. , Wang Ying , Goldberg Alexander A. , Doré Carole , Yockell-Lelièvre Julien , Tam Roger Y. , Giannikou Krinio , McMurray Fiona , Shoichet Molly S. , Harper Mary-Ellen , Henske Elizabeth P. , Kwiatkowski David J. , Darling Thomas N. , Moss Joel , Kristof Arnold S. , Stanford William L.
Published: March 2023

This file contains descriptions of materials and methods used in this study pertaining to cell and tissue staining, Western blot and mRNA analysis, and cell size and genotyping analyses. Corresponding references are also included.
Supplementary Figure 13 from Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer
Authors: Jaeger Samira , Igea Ana , Arroyo Rodrigo , Alcalde Victor , Canovas Begoña , Orozco Modesto , Nebreda Angel R. , Aloy Patrick
Published: March 2023

Distribution of DCI values (DCI20 to DCI80) ranging from 20 to 80% of proliferation inhibition (IC20 to IC80) for DC01 to DC10.
Supplementary Figure S5 from NEMO, a Transcriptional Target of Estrogen and Progesterone, Is Linked to Tumor Suppressor PML in Breast Cancer
Authors: Elsarraj Hanan S. , Valdez Kelli E. , Hong Yan , Grimm Sandra L. , Ricci Lawrence R. , Fan Fang , Tawfik Ossama , May Lisa , Cusick Therese , Inciardi Marc , Redick Mark , Gatewood Jason , Winblad Onalisa , Hilsenbeck Susan , Edwards Dean P. , Hagan Christy R. , Godwin Andrew K. , Fabian Carol , Behbod Fariba
Published: March 2023

Kaplan-Meier (KM) relapse-free and overall survival curves of breast cancer patients based on their expression levels of IKBKG, and PML.
Supplementary Figure S3 from NEMO, a Transcriptional Target of Estrogen and Progesterone, Is Linked to Tumor Suppressor PML in Breast Cancer
Authors: Elsarraj Hanan S. , Valdez Kelli E. , Hong Yan , Grimm Sandra L. , Ricci Lawrence R. , Fan Fang , Tawfik Ossama , May Lisa , Cusick Therese , Inciardi Marc , Redick Mark , Gatewood Jason , Winblad Onalisa , Hilsenbeck Susan , Edwards Dean P. , Hagan Christy R. , Godwin Andrew K. , Fabian Carol , Behbod Fariba
Published: March 2023

NEMO KD results in increased cell survival and proliferation in MCF7 cells in vitro.
Figure S4 from Astrocytes Promote Medulloblastoma Progression through Hedgehog Secretion
Authors: Liu Yongqiang , Yuelling Larra W. , Wang Yuan , Du Fang , Gordon Renata E. , O'Brien Jenny A. , Ng Jessica M.Y. , Robins Shannon , Lee Eric H. , Liu Hailong , Curran Tom , Yang Zeng-Jie
Published: March 2023

Nestin expression was not induced in Ptch1-deficient GNPs after Gli1 overexpression
Figure S3 from Astrocytes Promote Medulloblastoma Progression through Hedgehog Secretion
Authors: Liu Yongqiang , Yuelling Larra W. , Wang Yuan , Du Fang , Gordon Renata E. , O'Brien Jenny A. , Ng Jessica M.Y. , Robins Shannon , Lee Eric H. , Liu Hailong , Curran Tom , Yang Zeng-Jie
Published: March 2023

Apoptosis in MB slice culture
Figure S4 from Secretory Autophagy in Cancer-Associated Fibroblasts Promotes Head and Neck Cancer Progression and Offers a Novel Therapeutic Target
Authors: New Jacob , Arnold Levi , Ananth Megha , Alvi Sameer , Thornton Mackenzie , Werner Lauryn , Tawfik Ossama , Dai Hongying , Shnayder Yelizaveta , Kakarala Kiran , Tsue Terance T. , Girod Douglas A. , Ding Wen-Xing , Anant Shrikant , Thomas Sufi Mary
Published: March 2023

bFGF treatment increases autophagy regulated secreted factors
Supplementary Table S3 from Huwe1 Sustains Normal Ovarian Epithelial Cell Transformation and Tumor Growth through the Histone H1.3-H19 Cascade
Authors: Yang Dong , Sun Bin , Zhang Xiaohong , Cheng Daomei , Yu Xiaoping , Yan Lanzhen , Li Lei , An Sanqi , Jiang Hua , Lasorella Anna , Iavarone Antonio , Zhang Shu , Zou Fangdong , Zhao Xudong
Published: March 2023

Supplementary Table S3 The gene list with significant difference
Supplementary Table S1 from Huwe1 Sustains Normal Ovarian Epithelial Cell Transformation and Tumor Growth through the Histone H1.3-H19 Cascade
Authors: Yang Dong , Sun Bin , Zhang Xiaohong , Cheng Daomei , Yu Xiaoping , Yan Lanzhen , Li Lei , An Sanqi , Jiang Hua , Lasorella Anna , Iavarone Antonio , Zhang Shu , Zou Fangdong , Zhao Xudong
Published: March 2023

Supplementary Table S1 Primers used in this study for real-time PCR
Supplementary Figure S2 from Differential PI3Kδ Signaling in CD4+ T-cell Subsets Enables Selective Targeting of T Regulatory Cells to Enhance Cancer Immunotherapy
Authors: Ahmad Shamim , Abu-Eid Rasha , Shrimali Rajeev , Webb Mason , Verma Vivek , Doroodchi Atbin , Berrong Zuzana , Samara Raed , Rodriguez Paulo C. , Mkrtichyan Mikayel , Khleif Samir N.
Published: March 2023

Flow cytometry gating strategy for pAkt (S473) and pS6 (pS244) and proliferation determination.
Supplement Materials and Methods from Differential PI3Kδ Signaling in CD4+ T-cell Subsets Enables Selective Targeting of T Regulatory Cells to Enhance Cancer Immunotherapy
Authors: Ahmad Shamim , Abu-Eid Rasha , Shrimali Rajeev , Webb Mason , Verma Vivek , Doroodchi Atbin , Berrong Zuzana , Samara Raed , Rodriguez Paulo C. , Mkrtichyan Mikayel , Khleif Samir N.
Published: March 2023

Supplement Methods
Supplementary Materials and Methods from Dual Roles for Regulatory T-cell Depletion and Costimulatory Signaling in Agonistic GITR Targeting for Tumor Immunotherapy
Authors: Mahne Ashley E. , Mauze Smita , Joyce-Shaikh Barbara , Xia Jane , Bowman Edward P. , Beebe Amy M. , Cua Daniel J. , Jain Renu
Published: March 2023

Supplementary Materials and Methods include Treg lineage tracing data in B16 melanoma tumor model and binding, pharmacokinetics characterization and agonist signaling activity data for mDTA-1 Fc mutant antibody.
Supplementary Table S6 from Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment
Authors: Varn Frederick S. , Wang Yue , Mullins David W. , Fiering Steven , Cheng Chao
Published: March 2023

Correlations between TCGA mutation load and infiltration score.
Supplementary Materials and Methods and Supplementary Figure Legends from Cancer Stem Cells Regulate Cancer-Associated Fibroblasts via Activation of Hedgehog Signaling in Mammary Gland Tumors
Authors: Valenti Giovanni , Quinn Hazel M. , Heynen Guus J.J.E. , Lan Linxiang , Holland Jane D. , Vogel Regina , Wulf-Goldenberg Annika , Birchmeier Walter
Published: March 2023

Supplementary Materials and Methods and Supplementary Figure Legends
Supplemental figure 7 from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

The treatment effect of YAP/TAZ inhibitor on an EC animal model
Supplemental figure 5 from YAP/TAZ-Mediated Upregulation of GAB2 Leads to Increased Sensitivity to Growth Factor–Induced Activation of the PI3K Pathway
Authors: Wang Chao , Gu Chao , Jeong Kang Jin , Zhang Dong , Guo Wei , Lu Yiling , Ju Zhenlin , Panupinthu Nattapon , Yang Ji Yeon , Gagea Mihai (Mike) , Ng Patrick Kwok Shing , Zhang Fan , Mills Gordon B.
Published: March 2023

The effects of YAP/TAZ on biological behavior of EC cells
Supplementary Table 1 from Bone Metastasis of Prostate Cancer Can Be Therapeutically Targeted at the TBX2–WNT Signaling Axis
Authors: Nandana Srinivas , Tripathi Manisha , Duan Peng , Chu Chia-Yi , Mishra Rajeev , Liu Chunyan , Jin Renjie , Yamashita Hironobu , Zayzafoon Majd , Bhowmick Neil A. , Zhau Haiyen E. , Matusik Robert J. , Chung Leland W.K.
Published: March 2023

Cancer Outlier Profile Analysis (COPA) in Oncomine 4.4 showing TBX2 over-expression in PCa microarray data sets
Supplementary Figure Legends from Anti-Folate Receptor-α IgE but not IgG Recruits Macrophages to Attack Tumors via TNFα/MCP-1 Signaling
Authors: Josephs Debra H. , Bax Heather J. , Dodev Tihomir , Georgouli Mirella , Nakamura Mano , Pellizzari Giulia , Saul Louise , Karagiannis Panagiotis , Cheung Anthony , Herraiz Cecilia , Ilieva Kristina M. , Correa Isabel , Fittall Matthew , Crescioli Silvia , Gazinska Patrycja , Woodman Natalie , Mele Silvia , Chiaruttini Giulia , Gilbert Amy E. , Koers Alexander , Bracher Marguerite , Selkirk Christopher , Lentfer Heike , Barton Claire , Lever Elliott , Muirhead Gareth , Tsoka Sophia , Canevari Silvana , Figini Mariangela , Montes Ana , Downes Noel , Dombrowicz David , Corrigan Christopher J. , Beavil Andrew J. , Nestle Frank O. , Jones Paul S. , Gould Hannah J. , Sanz-Moreno Victoria , Blower Philip J. , Spicer James F. , Karagiannis Sophia N.
Published: March 2023

Legends for Supplementary Figures S1-S4
Figure S7 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

Representative Images of ISH and IHC with different intensity.
Figure S2 from Gastric Cancer Cell Proliferation and Survival Is Enabled by a Cyclophilin B/STAT3/miR-520d-5p Signaling Feedback Loop
Authors: Li Ting , Guo Hanqing , Zhao Xiaodi , Jin Jiang , Zhang Lifeng , Li Hong , Lu Yuanyuan , Nie Yongzhan , Wu Kaichun , Shi Yongquan , Fan Daiming
Published: March 2023

CypB regulates GC growth through activation of STAT3.
Supplementary Figure S5andS6 from H3B-6527 Is a Potent and Selective Inhibitor of FGFR4 in FGF19-Driven Hepatocellular Carcinoma
Authors: Joshi Jaya Julie , Coffey Heather , Corcoran Erik , Tsai Jennifer , Huang Chia-Ling , Ichikawa Kana , Prajapati Sudeep , Hao Ming-Hong , Bailey Suzanna , Wu Jeremy , Rimkunas Victoria , Karr Craig , Subramanian Vanitha , Kumar Pavan , MacKenzie Crystal , Hurley Raelene , Satoh Takashi , Yu Kun , Park Eunice , Rioux Nathalie , Kim Amy , Lai Weidong G. , Yu Lihua , Zhu Ping , Buonamici Silvia , Larsen Nicholas , Fekkes Peter , Wang John , Warmuth Markus , Reynolds Dominic J. , Smith Peter G. , Selvaraj Anand
Published: March 2023

Body weight data of H3B-6527 as single agent and in combination
Supplemental Figure 1 from Armed Oncolytic Adenovirus–Expressing PD-L1 Mini-Body Enhances Antitumor Effects of Chimeric Antigen Receptor T Cells in Solid Tumors
Authors: Tanoue Kiyonori , Rosewell Shaw Amanda , Watanabe Norihiro , Porter Caroline , Rana Bhakti , Gottschalk Stephen , Brenner Malcolm , Suzuki Masataka
Published: March 2023

Cancer cells express HER2 and PD-L1 expression is induced in the presence of recombinant IFNï�§, and HER2.CAR T-cells express PD-1 in the presence of target cells.
Supplementary Materials and Methods from CYP27A1 Loss Dysregulates Cholesterol Homeostasis in Prostate Cancer
Authors: Alfaqih Mahmoud A. , Nelson Erik R. , Liu Wen , Safi Rachid , Jasper Jeffery S. , Macias Everardo , Geradts Joseph , Thompson J. Will , Dubois Laura G. , Freeman Michael R. , Chang Ching-yi , Chi Jen-Tsan , McDonnell Donald P. , Freedland Stephen J.
Published: March 2023

Reagents and cell culture conditions. Methods for bioinformatics analysis, CYP27A1 IHC, caspase assays and 27HC measurements.
Supplementary Table 2 from EZH2 Modifies Sunitinib Resistance in Renal Cell Carcinoma by Kinome Reprogramming
Authors: Adelaiye-Ogala Remi , Budka Justin , Damayanti Nur P. , Arrington Justine , Ferris Mary , Hsu Chuan-Chih , Chintala Sreenivasulu , Orillion Ashley , Miles Kiersten Marie , Shen Li , Elbanna May , Ciamporcero Eric , Arisa Sreevani , Pettazzoni Piergiorgio , Draetta Giulio F. , Seshadri Mukund , Hancock Bradley , Radovich Milan , Kota Janaiah , Buck Michael , Keilhack Heike , McCarthy Brian P. , Persohn Scott A. , Territo Paul R. , Zang Yong , Irudayaraj Joseph , Tao W. Andy , Hollenhorst Peter , Pili Roberto
Published: March 2023

Gene list for Fig.5B, C, D
Supplementary Figures 1 through 3 and Supplementary Table 1 from IL6 Signaling in Peripheral Blood T Cells Predicts Clinical Outcome in Breast Cancer
Authors: Wang Lei , Miyahira Andrea K. , Simons Diana L. , Lu Xuyang , Chang Andrew Y. , Wang Carrie , Suni Maria A. , Maino Vernon C. , Dirbas Frederick M. , Yim John , Waisman James , Lee Peter P.
Published: March 2023

Fig S1: Similar level of total STAT1/3 and similar level of basal pSTAT1/3 were found in CD4 naïve T cells from healthy donors and BC patients, suggesting that the observed defective IL-6 signaling responses were not caused by lower level of total STAT1/3 or basal pSTAT1/3 in BC patients. Fig S2: Among relapsed BC patients, similar IL-6 signaling responses were found at diagnosis and at relapsed, indicating that impaired IL-6 signaling responses persistent through progression. In relapsed patients who went on to achieve remission, there was a trend towards higher IL-6 signaling in some patients. Fig S3: Lower IL-6 signaling response in peripheral CD4+ naïve T cells from melanoma (Mel), gastrointestinal (GI) and lung cancer (LC) patients. Table S1: No significant associations were found between IL-6 signaling response and clinicopathologic characteristics (age, tumor grade, T status or subtype) of BC patients.
Table S1 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

Correlation between elevated gene expression and diminished patient survival
Figure S5 from Protein Acyltransferase DHHC3 Regulates Breast Tumor Growth, Oxidative Stress, and Senescence
Authors: Sharma Chandan , Wang Hong-Xing , Li Qinglin , Knoblich Konstantin , Reisenbichler Emily S. , Richardson Andrea L. , Hemler Martin E.
Published: March 2023

This figure shows a schematic of DHHC3 reconstitution lentiviral vectors, DHHC3 expression in stably infected MDA-MB-231 cells, and an overview of effects of DHHC3 ablation.
Supplementary Table S1 from Long Noncoding RNA LINC00092 Acts in Cancer-Associated Fibroblasts to Drive Glycolysis and Progression of Ovarian Cancer
Authors: Zhao Linjie , Ji Gaili , Le Xiaobing , Wang Chenlu , Xu Lian , Feng Min , Zhang Yaguang , Yang Huiliang , Xuan Yu , Yang Yanfei , Lei Lingzi , Yang Qilian , Lau Wayne Bond , Lau Bonnie , Chen Yi , Deng Xiangbing , Yao Shaohua , Yi Tao , Zhao Xia , Wei Yuquan , Zhou Shengtao
Published: March 2023

Antibody information.
Supplementary Fig 5 from Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia
Authors: Ding Ling-Wen , Sun Qiao-Yang , Tan Kar-Tong , Chien Wenwen , Thippeswamy Anand Mayakonda , Eng Juh Yeoh Allen , Kawamata Norihiko , Nagata Yasunobu , Xiao Jin-Fen , Loh Xin-Yi , Lin De-Chen , Garg Manoj , Jiang Yan-Yi , Xu Liang , Lim Su-Lin , Liu Li-Zhen , Madan Vikas , Sanada Masashi , Fernández Lucia Torres , Preethi Hema , Lill Michael , Kantarjian Hagop M. , Kornblau Steven M. , Miyano Satoru , Liang Der-Cherng , Ogawa Seishi , Shih Lee-Yung , Yang Henry , Koeffler H. Phillip
Published: March 2023

Supplementary Fig. 5. Kaplan-Meier analysis of the survival of patients with different mutations.
Supplementary Fig 2 from Mutational Landscape of Pediatric Acute Lymphoblastic Leukemia
Authors: Ding Ling-Wen , Sun Qiao-Yang , Tan Kar-Tong , Chien Wenwen , Thippeswamy Anand Mayakonda , Eng Juh Yeoh Allen , Kawamata Norihiko , Nagata Yasunobu , Xiao Jin-Fen , Loh Xin-Yi , Lin De-Chen , Garg Manoj , Jiang Yan-Yi , Xu Liang , Lim Su-Lin , Liu Li-Zhen , Madan Vikas , Sanada Masashi , Fernández Lucia Torres , Preethi Hema , Lill Michael , Kantarjian Hagop M. , Kornblau Steven M. , Miyano Satoru , Liang Der-Cherng , Ogawa Seishi , Shih Lee-Yung , Yang Henry , Koeffler H. Phillip
Published: March 2023

Supplementary Fig. 2. Mutations found in the ASXL family of genes.
Supplementary Video S1 from A Novel Mouse Model to Study Image-Guided, Radiation-Induced Intestinal Injury and Preclinical Screening of Radioprotectors
Authors: Verginadis Ioannis I. , Kanade Rahul , Bell Brett , Koduri Sravya , Ben-Josef Edgar , Koumenis Constantinos
Published: March 2023

Supplementary Video
Supplementary Methods & Figure Legends from A Novel Mouse Model to Study Image-Guided, Radiation-Induced Intestinal Injury and Preclinical Screening of Radioprotectors
Authors: Verginadis Ioannis I. , Kanade Rahul , Bell Brett , Koduri Sravya , Ben-Josef Edgar , Koumenis Constantinos
Published: March 2023

Supplementary Methods & Figure legends
Supplementary Fig. 3 from A Novel Mouse Model to Study Image-Guided, Radiation-Induced Intestinal Injury and Preclinical Screening of Radioprotectors
Authors: Verginadis Ioannis I. , Kanade Rahul , Bell Brett , Koduri Sravya , Ben-Josef Edgar , Koumenis Constantinos
Published: March 2023

Supplementary Fig. 3 - Localized DNA damage caused by a single dose of 12 Gy after targeting radiation to the radiopaque marker.
Supplementary Table S3 from Constitutive NOTCH3 Signaling Promotes the Growth of Basal Breast Cancers
Authors: Choy Lisa , Hagenbeek Thijs J. , Solon Margaret , French Dorothy , Finkle David , Shelton Amy , Venook Rayna , Brauer Matthew J. , Siebel Christian W.
Published: March 2023

Gene lists related to Fig. 6D. X axis = anti-N3.A13 vs. anti-gD, Y axis = Jag1 vs. Fc.
Supplementary Figure Legends from Constitutive NOTCH3 Signaling Promotes the Growth of Basal Breast Cancers
Authors: Choy Lisa , Hagenbeek Thijs J. , Solon Margaret , French Dorothy , Finkle David , Shelton Amy , Venook Rayna , Brauer Matthew J. , Siebel Christian W.
Published: March 2023

Legends for figures.
Supplementray Table and Figures from The NCX1/TRPC6 Complex Mediates TGFβ-Driven Migration and Invasion of Human Hepatocellular Carcinoma Cells
Authors: Xu Jingyu , Yang Yuan , Xie Rui , Liu Jilong , Nie Xubiao , An Jiaxing , Wen Guorong , Liu Xuemei , Jin Hai , Tuo Biguang
Published: March 2023

Supplementary Table for PCR primers used in this study and all supplementary Figures in this study and their Figure Legends
Figure S7-S8 from New Generation Nanomedicines Constructed from Self-Assembling Small-Molecule Prodrugs Alleviate Cancer Drug Toxicity
Authors: Wang Hangxiang , Lu Zhongjie , Wang Lijiang , Guo Tingting , Wu Jiaping , Wan Jianqin , Zhou Liqian , Li Hui , Li Zhen , Jiang Donghai , Song Penghong , Xie Haiyang , Zhou Lin , Xu Xiao , Zheng Shusen
Published: March 2023

Antitumor efficacy assessed in MDA-MB-231 and DU145 tumor-bearing mouse models
Supplementary Tables from Wnt5a Drives an Invasive Phenotype in Human Glioblastoma Stem-like Cells
Authors: Binda Elena , Visioli Alberto , Giani Fabrizio , Trivieri Nadia , Palumbo Orazio , Restelli Silvia , Dezi Fabio , Mazza Tommaso , Fusilli Caterina , Legnani Federico , Carella Massimo , Di Meco Francesco , Duggal Rohit , Vescovi Angelo L.
Published: March 2023

Table S1: Molecular Classification of Low-Grade and Anaplastic Gliomas; Table S2: WNT5A and FRIZZLED5 gene copy number in glioma tissues and hGBM TPCs; Table S3: Ingenuity analysis of the LVWnt5a classical TPCs genes demonstrating the associated cancer genes and molecular and cellular functions (5% FDR); Table S4: Ingenuity analysis of the LVWnt5a U87 and U87 vector genes demonstrating the associated cancer genes and molecular and cellular functions related to Cellular Movement (5% FDR); Table S5: Ingenuity Analysis of the Wnt5a^high Genes Demonstrating The Associated Cancer Genes Molecular and Cellular Function (5% FDR).
Supplementary Data from Selective Reversible Inhibition of Autophagy in Hypoxic Breast Cancer Cells Promotes Pulmonary Metastasis
Authors: Dower Christopher M. , Bhat Neema , Wang Edward W. , Wang Hong-Gang
Published: March 2023

Supplementary materials, methods and figure legends
Supplemental Figure 1 from Selective Reversible Inhibition of Autophagy in Hypoxic Breast Cancer Cells Promotes Pulmonary Metastasis
Authors: Dower Christopher M. , Bhat Neema , Wang Edward W. , Wang Hong-Gang
Published: March 2023

Schematic representation and immunoblot assessment of HRE-dnULK1
Figure S2 from Type I IFN Receptor Signaling Controls IL7-Dependent Accumulation and Activity of Protumoral IL17A-Producing γδT Cells in Breast Cancer
Authors: Patin Emmanuel C. , Soulard Daphnée , Fleury Sébastien , Hassane Maya , Dombrowicz David , Faveeuw Christelle , Trottein François , Paget Christophe
Published: March 2023

gamma/delta T cells represent the major source of IL-17A in AT3 breast cancer tumors
Table S5 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

Proteomics and phosphoproteomics data analyses II
Table S1 from Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Authors: Niklasson Mia , Maddalo Gianluca , Sramkova Zuzana , Mutlu Ercan , Wee Shimei , Sekyrova Petra , Schmidt Linnéa , Fritz Nicolas , Dehnisch Ivar , Kyriatzis Gregorios , Krafcikova Michaela , Carson Brittany B. , Feenstra Jennifer M. , Marinescu Voichita D. , Segerman Anna , Haraldsson Martin , Gustavsson Anna-Lena , Hammarström Lars G.J. , Jenmalm Jensen Annika , Uhrbom Lene , Altelaar A.F. Maarten , Linnarsson Sten , Uhlén Per , Trantirek Lukas , Vincent C. Theresa , Nelander Sven , Enger Per Øyvind , Andäng Michael
Published: March 2023

Small molecule screen data
Table S2 from Genes Predisposed to DNA Hypermethylation during Acquired Resistance to Chemotherapy Are Identified in Ovarian Tumors by Bivalent Chromatin Domains at Initial Diagnosis
Authors: Curry Edward , Zeller Constanze , Masrour Nahal , Patten Darren K. , Gallon John , Wilhelm-Benartzi Charlotte S. , Ghaem-Maghami Sadaf , Bowtell David D. , Brown Robert
Published: March 2023

genes with evidence for poised promoter chromatin states in multiple primary high-grade serous ovarian tumours, but not in normal ovarian surface or fallopian epithelia
Table S3 from Antitumor Properties of RAF709, a Highly Selective and Potent Inhibitor of RAF Kinase Dimers, in Tumors Driven by Mutant RAS or BRAF
Authors: Shao Wenlin , Mishina Yuji M. , Feng Yun , Caponigro Giordano , Cooke Vesselina G. , Rivera Stacy , Wang Yingyun , Shen Fang , Korn Joshua M. , Mathews Griner Lesley A. , Nishiguchi Gisele , Rico Alice , Tellew John , Haling Jacob R. , Aversa Robert , Polyakov Valery , Zang Richard , Hekmat-Nejad Mohammad , Amiri Payman , Singh Mallika , Keen Nicholas , Dillon Michael P. , Lees Emma , Ramurthy Savithri , Sellers William R. , Stuart Darrin D.
Published: March 2023

KiNative assay results for RAF709
Supplemental legends from Antitumor Properties of RAF709, a Highly Selective and Potent Inhibitor of RAF Kinase Dimers, in Tumors Driven by Mutant RAS or BRAF
Authors: Shao Wenlin , Mishina Yuji M. , Feng Yun , Caponigro Giordano , Cooke Vesselina G. , Rivera Stacy , Wang Yingyun , Shen Fang , Korn Joshua M. , Mathews Griner Lesley A. , Nishiguchi Gisele , Rico Alice , Tellew John , Haling Jacob R. , Aversa Robert , Polyakov Valery , Zang Richard , Hekmat-Nejad Mohammad , Amiri Payman , Singh Mallika , Keen Nicholas , Dillon Michael P. , Lees Emma , Ramurthy Savithri , Sellers William R. , Stuart Darrin D.
Published: March 2023

Legends for supplemental figures and tables
Supplemental Table S2 from Tight Junction Protein Claudin-2 Promotes Self-Renewal of Human Colorectal Cancer Stem-like Cells
Authors: Paquet-Fifield Sophie , Koh Shir Lin , Cheng Lesley , Beyit Laura M. , Shembrey Carolyn , Mølck Christina , Behrenbruch Corina , Papin Marina , Gironella Meritxell , Guelfi Sophie , Nasr Ramona , Grillet Fanny , Prudhomme Michel , Bourgaux Jean-Francois , Castells Antoni , Pascussi Jean-Marc , Heriot Alexander G. , Puisieux Alain , Davis Melissa J. , Pannequin Julie , Hill Andrew F. , Sloan Erica K. , Hollande Frédéric
Published: March 2023

This table contains the de-identified clinical data on all patients from the Tissue microarray used in Figure 1 and S1.
Supplementary Material 3 from Cross-Talk between Receptor Tyrosine Kinases AXL and ERBB3 Regulates Invadopodia Formation in Melanoma Cells
Authors: Revach Or-Yam , Sandler Oded , Samuels Yardena , Geiger Benjamin
Published: March 2023

Statistics for gene expression analysis (Figure 6A). In the first tab, significant levels of ERRB3 and AXL expression against all 6 genes (AXL, ERBB3, MITF3 and the 3 targets) in each cluster. In the second tab, significant levels of differences in invadopodia genes between Clusters 1 and 2, as well as the delta median of expression for each gene. In the third tab, significant levels of the differences in TK genes between Clusters 1 and 2, as well as the delta median of expression for each gene.
Supplementary Data from Hemap: An Interactive Online Resource for Characterizing Molecular Phenotypes across Hematologic Malignancies
Authors: Pölönen Petri , Mehtonen Juha , Lin Jake , Liuksiala Thomas , Häyrynen Sergei , Teppo Susanna , Mäkinen Artturi , Kumar Ashwini , Malani Disha , Pohjolainen Virva , Porkka Kimmo , Heckman Caroline A. , May Patrick , Hautamäki Ville , Granberg Kirsi J. , Lohi Olli , Nykter Matti , Heinäniemi Merja
Published: March 2023

Supplementary Data includes Methods and Figures and Legends for Supplementary tables. Fig. S1: Sample-level quality control and pre-processing; Fig. S2: Two-dimensional representations of sample distances; Fig S3: Known vulnerabilities confirmed by Hemap; Fig. S4: Evaluation of drug screening results and confirmation using hemap data; Fig. S5: Candidate immunotherapy targets in pre-B-ALL
FigureS1 from Inhibition of Nr4a Receptors Enhances Antitumor Immunity by Breaking Treg-Mediated Immune Tolerance
Authors: Hibino Sana , Chikuma Shunsuke , Kondo Taisuke , Ito Minako , Nakatsukasa Hiroko , Omata-Mise Setsuko , Yoshimura Akihiko
Published: March 2023

Expression of Nr4a factors in human Treg cells
Supplementary Figures from Multiparametric MRI and Coregistered Histology Identify Tumor Habitats in Breast Cancer Mouse Models
Authors: Jardim-Perassi Bruna V. , Huang Suning , Dominguez-Viqueira William , Poleszczuk Jan , Budzevich Mikalai M. , Abdalah Mahmoud A. , Pillai Smitha R. , Ruiz Epifanio , Bui Marilyn M. , Zuccari Debora A.P.C. , Gillies Robert J. , Martinez Gary V.
Published: March 2023

SF1: Pimonidazole and carbonic anhydrase IX (CA-IX) staining patterns in 4T1 and MDA-MB-231 breast tumors; SF2: Breast tumor stained with hematoxylin & eosin (H&E), showing different stages of necrosis; SF3: Representative examples of the corresponding habitat maps from MRI and histology for the 4T1 and MDA-MB-231 tumor samples; SF4: Histograms showing the pixels values distribution of Area under the curve (AUC), slope and time to max (TTM) from DCE-MRI in each cluster of representative MRI habitat maps for 4T1 and MDA-MB-231 tumor samples; SF5: Representative examples showing that the DCE-MRI maps have visual similarity with pimonidazole staining in breast samples. SF6: Representative examples of MRI habitat maps, which were created by clustering five MRI-parameters [T2-map, T2*-map, Slope, Area under the curve (AUC) and time to max (TTM)] using a Gaussian Mixture Model (GMM) Expectation-Maximization algorithm. SF7: Comparison of mean values of each parameter from habitat maps generated by clustering five MRI-parameters [T2-map, T2*-map, Slope, Area under the curve (AUC) and time to max (TTM)]; SF8: Histograms showing the distribution of the Apparent diffusion coefficient (ADC) values in the cluster classified as non-viable tumor cells in the MRI habitat map. SF9: Representative images of the immunohistochemistry for perilipin-1 in breast tumor samples.