bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure Legends, Supplementary Tables 1 and 2 and Supplementary Materials and Methods from Chemoresistance in Pancreatic Cancer Is Driven by Stroma-Derived Insulin-Like Growth Factors
Authors: Ireland Lucy , Santos Almudena , Ahmed Muhammad S. , Rainer Carolyn , Nielsen Sebastian R. , Quaranta Valeria , Weyer-Czernilofsky Ulrike , Engle Danielle D. , Perez-Mancera Pedro A. , Coupland Sarah E. , Taktak Azzam , Bogenrieder Thomas , Tuveson David A. , Campbell Fiona , Schmid Michael C. , Mielgo Ainhoa
Published: April 2023

Supplementary Figure legends. Table S1. Clinical information from 40 consented PDA patient samples. Table S2. Clinical information from 16 consented PDA patient samples. Supplementary Materials and Methods.
Supplemental Table 1 from SMAC Mimetic Birinapant plus Radiation Eradicates Human Head and Neck Cancers with Genomic Amplifications of Cell Death Genes FADD and BIRC2
Authors: Eytan Danielle F. , Snow Grace E. , Carlson Sophie , Derakhshan Adeeb , Saleh Anthony , Schiltz Stephen , Cheng Hui , Mohan Suresh , Cornelius Shaleeka , Coupar Jamie , Sowers Anastasia L. , Hernandez Lidia , Mitchell James B. , Annunziata Christina M. , Chen Zhong , Van Waes Carter
Published: April 2023

HNSCC cell lines
Raw data for Supplementary Table 1 and 2 from p62/SQSTM1 Cooperates with Hyperactive mTORC1 to Regulate Glutathione Production, Maintain Mitochondrial Integrity, and Promote Tumorigenesis
Authors: Lam Hilaire C. , Baglini Christian V. , Lope Alicia Llorente , Parkhitko Andrey A. , Liu Heng-Jia , Alesi Nicola , Malinowska Izabela A. , Ebrahimi-Fakhari Darius , Saffari Afshin , Yu Jane J. , Pereira Ana , Khabibullin Damir , Ogorek Barbara , Nijmeh Julie , Kavanagh Taylor , Handen Adam , Chan Stephen Y. , Asara John M. , Oldham William M. , Diaz-Meco Maria T. , Moscat Jorge , Sahin Mustafa , Priolo Carmen , Henske Elizabeth P.
Published: April 2023

Raw data and bioinformatic analysis of metabolomics and ion torrent expression profiling
Supplementary Table 2 from A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma
Authors: Kaufman Jacob M. , Yamada Tadaaki , Park Kyungho , Timmers Cynthia D. , Amann Joseph M. , Carbone David P.
Published: April 2023

Mutational information for cell lines
Supplementary Figures and Tables from IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity
Authors: Chiang Sarah , Weigelt Britta , Wen Huei-Chi , Pareja Fresia , Raghavendra Ashwini , Martelotto Luciano G. , Burke Kathleen A. , Basili Thais , Li Anqi , Geyer Felipe C. , Piscuoglio Salvatore , Ng Charlotte K.Y. , Jungbluth Achim A. , Balss Jörg , Pusch Stefan , Baker Gabrielle M. , Cole Kimberly S. , von Deimling Andreas , Batten Julie M. , Marotti Jonathan D. , Soh Hwei-Choo , McCalip Benjamin L. , Serrano Jonathan , Lim Raymond S. , Siziopikou Kalliopi P. , Lu Song , Liu Xiaolong , Hammour Tarek , Brogi Edi , Snuderl Matija , Iafrate A. John , Reis-Filho Jorge S. , Schnitt Stuart J.
Published: April 2023

Document containing figures illustrating results of Sanger sequencing, DNA methylation profiling of SPCRPs, the analysis of IDH2 expression in non-malignant breast epithelial cells and its downstream effects, and tables describing the antibodies used for immunohistochemical analysis, the alterations surveyed by the SNaPshot genotyping assay, Sanger sequencing primers, and statistics and results of the massively parallel sequencing analyses.
Supplementary Material and Methods from Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry
Authors: Abbassi-Ghadi Nima , Golf Ottmar , Kumar Sacheen , Antonowicz Stefan , McKenzie James S. , Huang Juzheng , Strittmatter Nicole , Kudo Hiromi , Jones Emrys A. , Veselkov Kirill , Goldin Robert , Takats Zoltan , Hanna George B.
Published: April 2023

Full methodological details of data analysis with respect to: tissue specific mass spectra extraction; data pre-processing (mass range selection, peak alignment, normalization, de-noising, data averaging); multivariate statistical models; glycerophospholipid annotation and individual glycerophospholipid comparison between tissue types.
Supplementary Figure Legends from Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry
Authors: Abbassi-Ghadi Nima , Golf Ottmar , Kumar Sacheen , Antonowicz Stefan , McKenzie James S. , Huang Juzheng , Strittmatter Nicole , Kudo Hiromi , Jones Emrys A. , Veselkov Kirill , Goldin Robert , Takats Zoltan , Hanna George B.
Published: April 2023

Supplementary Figure Legends
Figure S4: Evaluation of AR variant binding to known AREs and Snail promoters from Disrupting Androgen Receptor Signaling Induces Snail-Mediated Epithelial–Mesenchymal Plasticity in Prostate Cancer
Authors: Miao Lu , Yang Lin , Li Rui , Rodrigues Daniel N. , Crespo Mateus , Hsieh Jer-Tsong , Tilley Wayne D. , de Bono Johann , Selth Luke A. , Raj Ganesh V.
Published: April 2023

A) Validation of consititutive ARv567es binding to FASN and TSC2 AR binding sites in R1-D567 cells by ChIP-PCR; Examination of ARv567es binding events at putative AR binding sites within SNAI1 promoter region in R1-D567 by ChIP-PCR. Data from three independent experiments mean{plus minus}SD; *, p<0.05 as determined by t-test. B) DHT was not able to suppress Snail expression in R1-D567 cells.
Figure S2: Effect of treatment protocol on migration in PC3 and PC-3(AR)2 cells from Disrupting Androgen Receptor Signaling Induces Snail-Mediated Epithelial–Mesenchymal Plasticity in Prostate Cancer
Authors: Miao Lu , Yang Lin , Li Rui , Rodrigues Daniel N. , Crespo Mateus , Hsieh Jer-Tsong , Tilley Wayne D. , de Bono Johann , Selth Luke A. , Raj Ganesh V.
Published: April 2023

PC3 and PC-3(AR)2 cells were subjected to the treatment protocol (Fig.1A). After 6 days of treatment, the monolayer surface was scratched carefully and washed. Wound healing at 24 hours under normal growth media conditions was quantitated. Data are expressed as percentage of wound healing (WH %) calculated by dividing migrated distance by scratched distance.
Supplemental Figures 1 through 14 from A Hyaluronidase-Responsive Nanoparticle-Based Drug Delivery System for Targeting Colon Cancer Cells
Authors: Zhang Mingzhen , Xu Changlong , Wen Liuqing , Han Moon Kwon , Xiao Bo , Zhou Jun , Zhang Yuchen , Zhang Zhan , Viennois Emilie , Merlin Didier
Published: April 2023

Adsorption/desorption isotherms and pore size distributions of MSN-NH2 (S1). FITR spectra of MSN-NH2 and MSN-destriobiotin (S2). DLS and TEM characterizations of MSN-HA/Dox (S3). Figures of MSN-HA loaded with rhodamine B (S4). Release profiles of Dox in MSN-HA/Dox under neutral buffer (pH 7.0) (S5). The co-localization of MSN-HA/rhodamine B with the endocytosis marker (S6). In vitro compatibilities investigated by MTT and ATPlite assays (S7). In vivo biocompatibility evaluation of MSN-HA (S8). Fluorescence images of Colon-26 and HT-29 cells incubated with Dox and MSN-HA/Dox (S9). MSN-HA/Dox induced apoptosis in vitro (S10). Interaction of MSN-HA with proteins and blood cells (S11). Immunological analysis of MSN-HA and MSN-HA/Dox (S12). Histological analysis of tumor tissues (S13). Times-dependent biodistribution of MSN-HA (S14).
Supplementary Table S1 from Preclinical Efficacy of the Auristatin-Based Antibody–Drug Conjugate BAY 1187982 for the Treatment of FGFR2-Positive Solid Tumors
Authors: Sommer Anette , Kopitz Charlotte , Schatz Christoph A. , Nising Carl F. , Mahlert Christoph , Lerchen Hans-Georg , Stelte-Ludwig Beatrix , Hammer Stefanie , Greven Simone , Schuhmacher Joachim , Braun Manuela , Zierz Ruprecht , Wittemer-Rump Sabine , Harrenga Axel , Dittmer Frank , Reetz Frank , Apeler Heiner , Jautelat Rolf , Huynh Hung , Ziegelbauer Karl , Kreft Bertolt
Published: April 2023

The expression of FGFR2 on tumor cell surface and half maximal inhibitory concentration of cell viability for FGFR2-ADC BAY 1187982 and control ADC.
Supplementary Materials and Methods from An Integrated Nanotechnology-Enabled Transbronchial Image-Guided Intervention Strategy for Peripheral Lung Cancer
Authors: Jin Cheng S. , Wada Hironobu , Anayama Takashi , McVeigh Patrick Z. , Hu Hsin Pei , Hirohashi Kentaro , Nakajima Takahiro , Kato Tatsuya , Keshavjee Shaf , Hwang David , Wilson Brian C. , Zheng Gang , Yasufuku Kazuhiro
Published: April 2023

Description of additional methods and procedures used in the study.
Supplementary Figures from Personalized Management of Pancreatic Ductal Adenocarcinoma Patients through Computational Modeling
Authors: Yamamoto Kimiyo N. , Yachida Shinichi , Nakamura Akira , Niida Atsushi , Oshima Minoru , De Subhajyoti , Rosati Lauren M. , Herman Joseph M. , Iacobuzio-Donahue Christine A. , Haeno Hiroshi
Published: April 2023

'Supplementary Figures. Fig. S1. Immunohistochemical labeling of CDKN2A, TP53, and SMAD4 from PDAC patients in Japan cohort. Fig. S2. Study design. Fig. S3. The combination of gene alterations in Japan cohort. Fig. S4. CTx improves survival outcomes. Fig. S5. Effects of treatments and immunosuppression on OS in cases with resectable and unresectable diseases. Fig. S6. Effects of treatments and immunosuppression on OS in cases with one, two, and more than two genetic alterations. Fig. S7. Effects of treatments and immunosuppression on OS in cases with oligometastatic (PToligo) and widely metastatic diseases (PTwidely). Fig. S8. Effects of treatments and immunosuppression on OS in cases in T1 and other stages. Fig. S9. Prediction of future progression patterns - PToligo or PTwidely by the number of primary, ALTkras, and ALTmulti cells. Fig. S10. Prediction of future progression patterns - PToligo or PTwidely by the number of ALTtwo cells. Fig. S11. Beneficial effect of adjuvant CRTx on OS in ALT-two throughout the size range at diagnosis. Fig. S12. Beneficial effect of adjuvant CRTx on OS in all cases diagnosed at less than 1-cm in diameter. Fig. S13. Beneficial effect of neoadjuvant CRTx on OS. Fig. S14. Beneficial effect of salvage therapy to isolated recurrence on OS in ALT-two throughout the size range at diagnosis. Fig. S15. Beneficial effect of salvage therapy on OS in all cases diagnosed at less than 1-cm in diameter. Fig. S16. The feasibility of our model validated by clinical data from literatures. Fig. S17. The impact of threshold of ALTtwo cells on selecting potential responders to adjuvant CRTx. Fig. S18. The impact of threshold of ALTtwo cells on selecting potential responders to surgical intervention to the initial recurrence. Fig. S19. The impact of threshold of ALTtwo cells on selecting potential responders to salvage CRTx to the initial recurrence.'
Supplementary Table 4- Orthotopic tumor incidence of Zeb1 knockdown cells from Inflammation Triggers Zeb1-Dependent Escape from Tumor Latency
Authors: De Cock Jasmine M. , Shibue Tsukasa , Dongre Anushka , Keckesova Zuzana , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

Summary of tumor incidences at limiting dilutions for D2A1-d + Zeb1 knockdown cells
Supplementary Figure 1- Extended characterization of D2A1-d and parental D2A1 from Inflammation Triggers Zeb1-Dependent Escape from Tumor Latency
Authors: De Cock Jasmine M. , Shibue Tsukasa , Dongre Anushka , Keckesova Zuzana , Reinhardt Ferenc , Weinberg Robert A.
Published: April 2023

In vivo and in vitro growth curves of D2A1-d and parental D2A1 cells
Supplementary Figure S3 from Metastatic Progression of Prostate Cancer Is Mediated by Autonomous Binding of Galectin-4-O-Glycan to Cancer Cells
Authors: Tsai Chin-Hsien , Tzeng Sheue-Fen , Chao Tai-Kuang , Tsai Chia-Yun , Yang Yu-Chih , Lee Ming-Ting , Hwang Jiuan-Jiuan , Chou Yu-Ching , Tsai Mong-Hsun , Cha Tai-Lung , Hsiao Pei-Wen
Published: April 2023

Role of C1GALT1 in the phosphorylation of RTKs and downstream effectors mediated by galectin-4, EGF, and heregulin.
Supplementary Table 2 and Supplemental Figures from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations
Authors: Fehringer Gordon , Kraft Peter , Pharoah Paul D. , Eeles Rosalind A. , Chatterjee Nilanjan , Schumacher Fredrick R. , Schildkraut Joellen M. , Lindström Sara , Brennan Paul , Bickeböller Heike , Houlston Richard S. , Landi Maria Teresa , Caporaso Neil , Risch Angela , Amin Al Olama Ali , Berndt Sonja I. , Giovannucci Edward L. , Grönberg Henrik , Kote-Jarai Zsofia , Ma Jing , Muir Kenneth , Stampfer Meir J. , Stevens Victoria L. , Wiklund Fredrik , Willett Walter C. , Goode Ellen L. , Permuth Jennifer B. , Risch Harvey A. , Reid Brett M. , Bezieau Stephane , Brenner Hermann , Chan Andrew T. , Chang-Claude Jenny , Hudson Thomas J. , Kocarnik Jonathan K. , Newcomb Polly A. , Schoen Robert E. , Slattery Martha L. , White Emily , Adank Muriel A. , Ahsan Habibul , Aittomäki Kristiina , Baglietto Laura , Blomquist Carl , Canzian Federico , Czene Kamila , dos-Santos-Silva Isabel , Eliassen A. Heather , Figueroa Jonine D. , Flesch-Janys Dieter , Fletcher Olivia , Garcia-Closas Montserrat , Gaudet Mia M. , Johnson Nichola , Hall Per , Hazra Aditi , Hein Rebecca , Hofman Albert , Hopper John L. , Irwanto Astrid , Johansson Mattias , Kaaks Rudolf , Kibriya Muhammad G. , Lichtner Peter , Liu Jianjun , Lund Eiliv , Makalic Enes , Meindl Alfons , Müller-Myhsok Bertram , Muranen Taru A. , Nevanlinna Heli , Peeters Petra H. , Peto Julian , Prentice Ross L. , Rahman Nazneen , Sanchez Maria Jose , Schmidt Daniel F. , Schmutzler Rita K. , Southey Melissa C. , Tamimi Rulla , Travis Ruth C. , Turnbull Clare , Uitterlinden Andre G. , Wang Zhaoming , Whittemore Alice S. , Yang Xiaohong R. , Zheng Wei , Buchanan Daniel D. , Casey Graham , Conti David V. , Edlund Christopher K. , Gallinger Steven , Haile Robert W. , Jenkins Mark , Le Marchand Loïc , Li Li , Lindor Noralene M. , Schmit Stephanie L. , Thibodeau Stephen N. , Woods Michael O. , Rafnar Thorunn , Gudmundsson Julius , Stacey Simon N. , Stefansson Kari , Sulem Patrick , Chen Y. Ann , Tyrer Jonathan P. , Christiani David C. , Wei Yongyue , Shen Hongbing , Hu Zhibin , Shu Xiao-Ou , Shiraishi Kouya , Takahashi Atsushi , Bossé Yohan , Obeidat Ma'en , Nickle David , Timens Wim , Freedman Matthew L. , Li Qiyuan , Seminara Daniela , Chanock Stephen J. , Gong Jian , Peters Ulrike , Gruber Stephen B. , Amos Christopher I. , Sellers Thomas A. , Easton Douglas F. , Hunter David J. , Haiman Christopher A. , Henderson Brian E. , Hung Rayjean J.
Published: April 2023

Table S2: Odds ratio and 95% confidence limits for cancers associated with variants with pleiotropic associations. Figure S1: Flowchart showing analysis steps. Figure S2. Manhattan plots by chromosome for individual cancer sites. Figure S3. Results for rs11571833. Figure S4: Conditional QQ-plots.
Supplementary Material: Funding, Acknowledgements, Consortia, and Bioinformatics Tools Funding sources from Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations
Authors: Fehringer Gordon , Kraft Peter , Pharoah Paul D. , Eeles Rosalind A. , Chatterjee Nilanjan , Schumacher Fredrick R. , Schildkraut Joellen M. , Lindström Sara , Brennan Paul , Bickeböller Heike , Houlston Richard S. , Landi Maria Teresa , Caporaso Neil , Risch Angela , Amin Al Olama Ali , Berndt Sonja I. , Giovannucci Edward L. , Grönberg Henrik , Kote-Jarai Zsofia , Ma Jing , Muir Kenneth , Stampfer Meir J. , Stevens Victoria L. , Wiklund Fredrik , Willett Walter C. , Goode Ellen L. , Permuth Jennifer B. , Risch Harvey A. , Reid Brett M. , Bezieau Stephane , Brenner Hermann , Chan Andrew T. , Chang-Claude Jenny , Hudson Thomas J. , Kocarnik Jonathan K. , Newcomb Polly A. , Schoen Robert E. , Slattery Martha L. , White Emily , Adank Muriel A. , Ahsan Habibul , Aittomäki Kristiina , Baglietto Laura , Blomquist Carl , Canzian Federico , Czene Kamila , dos-Santos-Silva Isabel , Eliassen A. Heather , Figueroa Jonine D. , Flesch-Janys Dieter , Fletcher Olivia , Garcia-Closas Montserrat , Gaudet Mia M. , Johnson Nichola , Hall Per , Hazra Aditi , Hein Rebecca , Hofman Albert , Hopper John L. , Irwanto Astrid , Johansson Mattias , Kaaks Rudolf , Kibriya Muhammad G. , Lichtner Peter , Liu Jianjun , Lund Eiliv , Makalic Enes , Meindl Alfons , Müller-Myhsok Bertram , Muranen Taru A. , Nevanlinna Heli , Peeters Petra H. , Peto Julian , Prentice Ross L. , Rahman Nazneen , Sanchez Maria Jose , Schmidt Daniel F. , Schmutzler Rita K. , Southey Melissa C. , Tamimi Rulla , Travis Ruth C. , Turnbull Clare , Uitterlinden Andre G. , Wang Zhaoming , Whittemore Alice S. , Yang Xiaohong R. , Zheng Wei , Buchanan Daniel D. , Casey Graham , Conti David V. , Edlund Christopher K. , Gallinger Steven , Haile Robert W. , Jenkins Mark , Le Marchand Loïc , Li Li , Lindor Noralene M. , Schmit Stephanie L. , Thibodeau Stephen N. , Woods Michael O. , Rafnar Thorunn , Gudmundsson Julius , Stacey Simon N. , Stefansson Kari , Sulem Patrick , Chen Y. Ann , Tyrer Jonathan P. , Christiani David C. , Wei Yongyue , Shen Hongbing , Hu Zhibin , Shu Xiao-Ou , Shiraishi Kouya , Takahashi Atsushi , Bossé Yohan , Obeidat Ma'en , Nickle David , Timens Wim , Freedman Matthew L. , Li Qiyuan , Seminara Daniela , Chanock Stephen J. , Gong Jian , Peters Ulrike , Gruber Stephen B. , Amos Christopher I. , Sellers Thomas A. , Easton Douglas F. , Hunter David J. , Haiman Christopher A. , Henderson Brian E. , Hung Rayjean J.
Published: April 2023

Funding sources, acknowledgements, consortia involved in study and bioinformatics tools used
Supplementary figure 6 from Differential Effects of IL6 and Activin A in the Development of Cancer-Associated Cachexia
Authors: Chen Justin L. , Walton Kelly L. , Qian Hongwei , Colgan Timothy D. , Hagg Adam , Watt Matthew J. , Harrison Craig A. , Gregorevic Paul
Published: April 2023

In mice injected with rAAV6:activin A and/or rAAV6:IL-6, the mRNA expression of E3 ubiquitin ligases was determined in quadriceps muscles. In addition, skeletal muscle, epididymal WAT and BAT depots were probed for IL-6 target genes or genes involved in lipolysis and browning.
Supplementary Figures S1 and S2 legends from A Cell-Penetrating Peptide Targeting AAC-11 Specifically Induces Cancer Cells Death
Authors: Jagot-Lacoussiere Léonard , Kotula Ewa , Villoutreix Bruno O. , Bruzzoni-Giovanelli Heriberto , Poyet Jean-Luc
Published: April 2023

This file contains Supplementary Figures S1 and S2 legends
Supplemental Materials & Methods from Impaired Planar Germ Cell Division in the Testis, Caused by Dissociation of RHAMM from the Spindle, Results in Hypofertility and Seminoma
Authors: Li Huaibiao , Frappart Lucien , Moll Jürgen , Winkler Anne , Kroll Torsten , Hamann Jana , Kufferath Iris , Groth Marco , Taudien Stefan , Schütte Moritz , Yaspo Marie-Laure , Heuer Heike , Lange Bodo M.H. , Platzer Matthias , Zatloukal Kurt , Herrlich Peter , Ploubidou Aspasia
Published: April 2023

Supplemental Materials & Methods and the references cited within.
Supplementary Table S3 from Recurrent PPP2R1A Mutations in Uterine Cancer Act through a Dominant-Negative Mechanism to Promote Malignant Cell Growth
Authors: Haesen Dorien , Abbasi Asbagh Layka , Derua Rita , Hubert Antoine , Schrauwen Stefanie , Hoorne Yana , Amant Frédéric , Waelkens Etienne , Sablina Anna , Janssens Veerle
Published: April 2023

Primary antibodies used in this study.
Supplemental Figure Legends from Stromal-Based Signatures for the Classification of Gastric Cancer
Authors: Uhlik Mark T. , Liu Jiangang , Falcon Beverly L. , Iyer Seema , Stewart Julie , Celikkaya Hilal , O'Mahony Marguerita , Sevinsky Christopher , Lowes Christina , Douglass Larry , Jeffries Cynthia , Bodenmiller Diane , Chintharlapalli Sudhakar , Fischl Anthony , Gerald Damien , Xue Qi , Lee Jee-yun , Santamaria-Pang Alberto , Al-Kofahi Yousef , Sui Yunxia , Desai Keyur , Doman Thompson , Aggarwal Amit , Carter Julia H. , Pytowski Bronislaw , Jaminet Shou-ching , Ginty Fiona , Nasir Aejaz , Nagy Janice A. , Dvorak Harold F. , Benjamin Laura E.
Published: April 2023

These are the figure legends for the supplemental figures and tables.
Supplementary Figure Legends from Recurrent PPP2R1A Mutations in Uterine Cancer Act through a Dominant-Negative Mechanism to Promote Malignant Cell Growth
Authors: Haesen Dorien , Abbasi Asbagh Layka , Derua Rita , Hubert Antoine , Schrauwen Stefanie , Hoorne Yana , Amant Frédéric , Waelkens Etienne , Sablina Anna , Janssens Veerle
Published: April 2023

Supplementary Figure Legends
Supplementary Table 1: Patient and Healthy volunteer's characteristics from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Baseline characteristics (Age, Sex, Tumor origin, K-Ras and B-Raf status, number of metastatic sites, LDH, PA and CEA) of metastatic colorectal cancer patients (mCRC) and healthy volunteers.
Supplementary Figure Legends from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Supplementary Figure 1: THelper gating strategy Flow cytometry gating strategy to identify memory CD4 T cell subpopulations through chemokine receptor expression. Supplementary Figure 2: MDSC gating strategy and IL-4Rα expression analysis. A. Flow cytometry gating strategy to identify MDSC subpopulations through CD33, Lin (=CD3, CD20, CD19 and CD56), HLA-DR, CD14 and CD15 marker expression. Pictures correspond to May-Grünwald Giemsa staining mMDSC and gMDSC isolated after cell sorting. B. As in A, we identify MDSC subpopulations, granulocytes and monocytes and we have analyzed IL-4Rα (CD124) expression in 3 mCRC patients. Supplementary Figure 3: Blood parameters in Healthy Volunteers versus mCRC patients Whole blood of Healthy volunteers and metastatic colorectal cancer patient (mCRC) was sample on EDTA-K2 tubes (BD Bioscience) and a complete blood count (CBC) was performed in Clinical Biology Unit (Centre George François Leclerc). Supplementary Figure 4: IFN-γ and IL-17A secretion by CCR6 and CXCR3 expressing CD4 T cells PBMCs of mCRC patients were stained after PMA/ionomycin/Brefeldin/Monensin stimulation (4 hrs) with anti-CD4, anti-CD45RA, anti-CCR6, anti-CXCR3, anti-IFN-γ and anti-IL-17A antibodies and analyzed by flow cytometry. The expression of IFN-γ and/or IL-17A on memory CD4 (CD45RA- CD4+) Th1 (CCR6- CXCR3+), Th17 (CCR6+ CXCR3-), Th17/Th1 (CCR6+ CXCR3+) and CCR6- CXCR3- cells is depicted. Supplementary Figure 5: Blood parameters in mCRC patients, D0 versus D15 Whole blood of metastatic colorectal cancer patient (mCRC) was sample before (D0) and after chemotherapy (D15) on EDAT-K2 tubes (BD Bioscience) and a complete blood count (CBC) was performed in Clinical Biology Unit (Centre George François Leclerc). Supplementary Figure 6: mRNA relative expression of genes involved in immunosuppression gMDSC and mMDSC were cell sorted from four mCRC patient blood. mRNA were extracted and the expression of Entpd1, Nt5e, Pdl1, Pdl2, Indo, Arg1 and Inos was determined using RT-qPCR. Supplementary Table 1: Patient and Healthy volunteer's characteristics Baseline characteristics (Age, Sex, Tumor origin, K-Ras and B-Raf status, number of metastatic sites, LDH, PA and CEA) of metastatic colorectal cancer patients (mCRC) and healthy volunteers. Supplementary Table 2: Human primer sequences used for RT-qPCR analysis List of primer used for mRNA relative expression in different myeloid subsets.
Table S4. Association of human-based TF scores with OS and RFS. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

Survival analysis for human-based TF scores on H&E stained sections by univariate and multivariate cox regressions. OS=overall survival; RFS=relapse-free survival; CI=95% confidence interval; TF (low/high): scores dichotomized at the median (categorical); TF (continuous): score as continuous variable.
Supplementary Figure 5: Blood parameters in mCRC patients, D0 versus D15 from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Whole blood of metastatic colorectal cancer patient (mCRC) was sample before (D0) and after chemotherapy (D15) on EDAT-K2 tubes (BD Bioscience) and a complete blood count (CBC) was performed in Clinical Biology Unit (Centre George François Leclerc).
Supplementary Figure 4: IFN-γ and IL-17A secretion by CCR6 and CXCR3 expressing CD4 T cells from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

PBMCs of mCRC patients were stained after PMA/ionomycin/Brefeldin/Monensin stimulation (4 hrs) with anti-CD4, anti-CD45RA, anti-CCR6, anti-CXCR3, anti-IFN-γ and anti-IL-17A antibodies and analyzed by flow cytometry. The expression of IFN-γ and/or IL-17A on memory CD4 (CD45RA- CD4+) Th1 (CCR6- CXCR3+), Th17 (CCR6+ CXCR3-), Th17/Th1 (CCR6+ CXCR3+) and CCR6- CXCR3- cells is depicted.
Table S1. Complete list of proteins identifications. from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

The list of proteins identified by mass spectrometry (n=2614) for 48 samples of the WS cohort.
Supplementary Figure 3: Blood parameters in Healthy Volunteers versus mCRC patients from Accumulation of MDSC and Th17 Cells in Patients with Metastatic Colorectal Cancer Predicts the Efficacy of a FOLFOX–Bevacizumab Drug Treatment Regimen
Authors: Limagne Emeric , Euvrard Romain , Thibaudin Marion , Rébé Cédric , Derangère Valentin , Chevriaux Angélique , Boidot Romain , Végran Frédérique , Bonnefoy Nathalie , Vincent Julie , Bengrine-Lefevre Leila , Ladoire Sylvain , Delmas Dominique , Apetoh Lionel , Ghiringhelli François
Published: April 2023

Whole blood of Healthy volunteers and metastatic colorectal cancer patient (mCRC) was sample on EDTA-K2 tubes (BD Bioscience) and a complete blood count (CBC) was performed in Clinical Biology Unit (Centre George François Leclerc).
PRoteomics IDEntifications database from Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness
Authors: Casanova Ruben , Xia Daniel , Rulle Undine , Nanni Paolo , Grossmann Jonas , Vrugt Bart , Wettstein Reto , Ballester-Ripoll Rafael , Astolfo Alberto , Weder Walter , Moch Holger , Stampanoni Marco , Beck Andrew H. , Soltermann Alex
Published: April 2023

The PRIDE (PRoteomics IDEntifications database) additional raw and search files of our experiment
Supplementary Figure 3 from Anticancer Effects of Targeting Hsp70 in Tumor Stromal Cells
Authors: Gabai Vladimir L. , Yaglom Julia A. , Wang Yongmei , Meng Le , Shao Hao , Kim Geunwon , Colvin Teresa , Gestwicki Jason , Sherman Michael Y.
Published: April 2023

Fig. S3. Cross section of tumor cell injection sites from WT and Hsp70KO mice.
Supplementary Figure 2 from Anticancer Effects of Targeting Hsp70 in Tumor Stromal Cells
Authors: Gabai Vladimir L. , Yaglom Julia A. , Wang Yongmei , Meng Le , Shao Hao , Kim Geunwon , Colvin Teresa , Gestwicki Jason , Sherman Michael Y.
Published: April 2023

Fig. S2. JG-98 suppresses expression of p38.
Supplementary Figure 1 from Anticancer Effects of Targeting Hsp70 in Tumor Stromal Cells
Authors: Gabai Vladimir L. , Yaglom Julia A. , Wang Yongmei , Meng Le , Shao Hao , Kim Geunwon , Colvin Teresa , Gestwicki Jason , Sherman Michael Y.
Published: April 2023

Fig. S1. JG-98 does not affect density of endothelial cells (CD31 staining) and fibroblasts (SMA, smooth muscle actin staining) in the tumor.
Supplemental Figure legends from Aberrant JMJD3 Expression Upregulates Slug to Promote Migration, Invasion, and Stem Cell–Like Behaviors in Hepatocellular Carcinoma
Authors: Tang Bo , Qi Guangying , Tang Fang , Yuan Shengguang , Wang Zhenran , Liang Xingsi , Li Bo , Yu Shuiping , Liu Jie , Huang Qi , Wei Yangchao , Zhai Run , Lei Biao , Yu Hongping , Tomlinson Stephen , He Songqing
Published: April 2023

This file contains 10 supplemental figures. Supplemental Figure 1. JMJD3 is highly expressed in HCC tissues and cancer cell lines. Supplemental Figure 2. JMJD3 promotes proliferative capacity of HCC cells both in vivo. Supplemental Figure 3. JMJD3 promotes proliferative, EMT, migratory, and invasive capacities of HCC cells. Supplemental Figure. 4 JMJD3 promotes emergence of stem cell-like behavior in HCC cells. Supplemental Figure. 5 JMJD3 promotes emergence of stem cell-like behavior in HCC cells. Supplemental Figure. 6 JMJD3 regulates slug expression need its demethylase activity. Supplemental Figure. 7 JMJD3 regulates slug expression through H3K27 trimethylation Supplemental Figure. 8 JMJD3 regulates slug expression through H3K27 trimethylation Supplemental Figure. 9 Slug is a mediator for JMJD3-induced migration, invasion and in vivo metastasis capacity in HCC cells. Supplemental Figure. 10 Slug is a mediator for JMJD3-induced stemness capacity in HCC cells.
Supplementary Table 4 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

Ingenuity Pathway Analysis of positive hits identifies enrichment of genes involved in the ubiquitin-proteasome pathway.
Supplementary Table 3 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

Results and analysis of a genome-wide functional genomic screen using the Sigma-Aldrich shRNA Human Genome Library consisting of 63,093 shRNAs targeting 11,748 human genes.
Supplementary Table 1 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

72 hour IC50 growth inhibition levels (Î¼M) of 23 compounds (labeled EWS-A through EWS-X) against five EWS cell lines and 11 non-EWS cell lines
Supplementary Table S2 from Predicting Responses to Neoadjuvant Chemotherapy in Breast Cancer: ACRIN 6691 Trial of Diffuse Optical Spectroscopic Imaging
Authors: Tromberg Bruce J. , Zhang Zheng , Leproux Anaïs , O'Sullivan Thomas D. , Cerussi Albert E. , Carpenter Philip M. , Mehta Rita S. , Roblyer Darren , Yang Wei , Paulsen Keith D. , Pogue Brian W. , Jiang Shudong , Kaufman Peter A. , Yodh Arjun G. , Chung So Hyun , Schnall Mitchell , Snyder Bradley S. , Hylton Nola , Boas David A. , Carp Stefan A. , Isakoff Steven J. , Mankoff David
Published: April 2023

Number of subjects with DOSI scans performed at each time-point.
Supplementary Figure 2 from Proteasome Addiction Defined in Ewing Sarcoma Is Effectively Targeted by a Novel Class of 19S Proteasome Inhibitors
Authors: Shukla Neerav , Somwar Romel , Smith Roger S. , Ambati Sri , Munoz Stanley , Merchant Melinda , D'Arcy Padraig , Wang Xin , Kobos Rachel , Antczak Christophe , Bhinder Bhavneet , Shum David , Radu Constantin , Yang Guangbin , Taylor Barry S. , Ng Charlotte K.Y. , Weigelt Britta , Khodos Inna , de Stanchina Elisa , Reis-Filho Jorge S. , Ouerfelli Ouathek , Linder Stig , Djaballah Hakim , Ladanyi Marc
Published: April 2023

Panel upper left: CHP100 cells exposed 3 hours to different concentrations of b-AP15. Extracts were labeled with HA-Ub-VS and subjected to western blot. Filters probed with HA antibody. Note the lack of inhibition of any of the DUBs labeled by HA-Ub-VS. Panel upper right: CHP100 cells exposed 3 hours to 1 uM b-AP15 Extracts were labeled with Ub-VS and subjected to western blot. Filters probed with USP14, UCHL5 or UCHL1 antibodies. b-AP15 treated extracts demonstrate inhibition of USP14, weak inhibition of UCHL5, and no inhibition of UCHL1. Middle Panels: Purified 26S proteasomes (5 nM) were treated with indicate concentrations for b-AP15 and DUB activity was determined by cleavage of Ub-AMC. Note the reduction in 26S associated proteasome activity following treatment with b-AP15. Lower Panels: Recombinant UCHL1 or UCHL3 was treated with b-AP15 and DUB activity was monitored using Ub-AMC cleavage as above. No inhibition of either UCHL1 or UCHL3 was observed.
Supplementary Figure 2 from Efficacy of Adoptive T-cell Therapy Is Improved by Treatment with the Antioxidant N-Acetyl Cysteine, Which Limits Activation-Induced T-cell Death
Authors: Scheffel Matthew J. , Scurti Gina , Simms Patricia , Garrett-Mayer Elizabeth , Mehrotra Shikhar , Nishimura Michael I. , Voelkel-Johnson Christina
Published: April 2023

Supplementary Figure 2. Pretreatment of T cells with N-acetyl cysteine prevent TCR restimulation induced ROS accumulation.
Supplementary Figure 1 from Efficacy of Adoptive T-cell Therapy Is Improved by Treatment with the Antioxidant N-Acetyl Cysteine, Which Limits Activation-Induced T-cell Death
Authors: Scheffel Matthew J. , Scurti Gina , Simms Patricia , Garrett-Mayer Elizabeth , Mehrotra Shikhar , Nishimura Michael I. , Voelkel-Johnson Christina
Published: April 2023

Supplementary Figure 1. The DNA damage pathway occurs in CD4+ TIL1383I TCR transduced cells upon antigen-specific TCR restimulation.
Supplementary Material and Methods from EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition
Authors: Hsu Ya-Ting , Osmulski Pawel , Wang Yao , Huang Yi-Wen , Liu Lu , Ruan Jianhua , Jin Victor X. , Kirma Nameer B. , Gaczynska Maria E. , Huang Tim Hui-Ming
Published: April 2023

Transgenic mice,Immunofluorescence staining and image quantification, Proliferation and migration assays, ChIP-seq and network-based pathway analysis, TCGA expression analysis, CRISPR/Cas9 genome-editing of EpCAM, Apoptosis assay, Nanomechanical imaging of cells with Atomic Force Microscopy (AFM), Probing of cell surface with molecular recognition AFM
Supplementary Figure from EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition
Authors: Hsu Ya-Ting , Osmulski Pawel , Wang Yao , Huang Yi-Wen , Liu Lu , Ruan Jianhua , Jin Victor X. , Kirma Nameer B. , Gaczynska Maria E. , Huang Tim Hui-Ming
Published: April 2023

Supplementary Figure S1 Expression of EpCAM, LEF1 in human endometrial cancer patients, cancer cell lines and mouse endometrial tissues. Supplementary Figure S2 Quantification of EpEX immunofluorescence staining and EGFR expression in endometrial cancer cell lines. Supplementary Figure S3 Summary of ChIP-seq of EpICD in RL95-2 cells. Supplementary Figure S4 Overview of ChIP-seq of LEF1 in RL95-2 cells. Supplementary Figure S5 Pathway enrichment analysis unique/shared TSS-bound genes in 12 and 24 hours EGF. Supplementary Figure S6 105 EpICD-LEF1-TSS gene expression profiles in UCEC (Uterine Corpus Endometrial Carcinoma) patients and normal control samples in TCGA cohort. Supplementary Figure S7 EpCAM-edited cells showed reduced EGF-stimulated gene activation. Supplementary Figure S8 RL95-2 cells showed no apoptosis and cytoskeleton content induced by EGF treatments in RL95-2 and EpCAM-edited clone. Supplementary Figure S9 EpCAM molecules were detected with recognition AFM only on cells expressing this protein.
Supplementary Materials from Mutational Landscape and Gene Expression Patterns in Adult Acute Myeloid Leukemias with Monosomy 7 as a Sole Abnormality
Authors: Eisfeld Ann-Kathrin , Kohlschmidt Jessica , Mrózek Krzysztof , Volinia Stefano , Blachly James S. , Nicolet Deedra , Oakes Christopher , Kroll Karl , Orwick Shelley , Carroll Andrew J. , Stone Richard M. , Byrd John C. , de la Chapelle Albert , Bloomfield Clara D.
Published: April 2023

Materials and Methods: Participating institutions. List of all institutions that participated in the study. Patients and treatments. Detailed information about patients included in the study and their treatments. Mutational profiling. Detailed information about the techniques used to perform the mutational profiling. Definition of clinical endpoints. Statistical definition of the used end point terms . Univariable outcome analysis. Listing of all parameters that were included in the univariable outcome analysis.
Supplemental Figure 1 from Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer
Authors: Cherkasova Elena , Scrivani Claire , Doh Susan , Weisman Quinn , Takahashi Yoshiyuki , Harashima Nanae , Yokoyama Hisayuki , Srinivasan Ramaprasad , Linehan W. Marston , Lerman Michael I. , Childs Richard W.
Published: April 2023

Example of gating strategy to identify peptide and tumor reactive T cells stimulated from healthy donors: analysis of TM1 peptide stimulated CTLs from donor 4 is shown.
Supplementary Table Legends from Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

This file contains the legends for Supplementary Tables 1 to 5.
Supplementary Table 2 from Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Statistical comparison of the DNF taxonomy against single datasets taxonomies, using one-sided superiority tests
Supplementary Tables 1 thruogh 8 and Supplementary Figures 1 through 4 from A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology
Authors: Mehta Sunali , Tsai Peter , Lasham Annette , Campbell Hamish , Reddel Roger , Braithwaite Antony , Print Cristin
Published: April 2023

Supplementary Table S1: Summary of the TCGA tumour sets for which RNAseq V2 RSEM normalised data was downloaded on 20th October 2015 and used for TP53 transcript expression analyses. Supplementary Table S2: Summary of QC for RNAseq and RNA expression using RNAseq for the nine human cell lines. Supplementary Table S3: UCSC and Locus Reference Genomic (LRG) IDs for canonical TP53 transcript variants. Supplementary Table S4: Primer sequences used for ddPCR and RT-qPCR. Supplementary Table S5: Read data for RNAseq RSEM Expected count, RNAseq Tuxedo-FPKM, RNAseq RSEM-FPKM, ddPCR and RT-qPCR. Supplementary Table S6: RNAseq reads containing both PCR primers Supplementary Table S7: RNAseq reads in 125nt specific regions in exon 4 and AluJB upstream and exon5/6 downstream of the 125nt unique to the 5'-UTR of delta133TP53 transcript subclass Supplementary Table S8: Mutations and sequencing errors do not significantly affect alignment of sequence reads to the TP53 locus Supplementary Figure S1: Shows examples of fluorescence amplitude by ddPCR Supplementary Figure S2: Dissociation curves for TP53 primer pairs by RT-qPCR Supplementary Figure S3: Sanger Sequencing of the amplicons for FL/delta40TP53_T1, FL/delta40TP53_T2, delta133TP53, TP53alpha and TP53beta Supplementary Figure S4: Relative abundance of TP53 transcript subclasses relative to FL/delta40TP53_T1.
Supplementary Table 1 from Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
Authors: El-Hachem Nehme , Gendoo Deena M.A. , Ghoraie Laleh Soltan , Safikhani Zhaleh , Smirnov Petr , Chung Christina , Deng Kenan , Fang Ailsa , Birkwood Erin , Ho Chantal , Isserlin Ruth , Bader Gary D. , Goldenberg Anna , Haibe-Kains Benjamin
Published: April 2023

Similarity Matrices of the DNF and single-layer taxonomies (based on the CTRPv2 drug sensitivity dataset).
Supplementary Table 2 from Activation of NOTCH Signaling by Tenascin-C Promotes Growth of Human Brain Tumor-Initiating Cells
Authors: Sarkar Susobhan , Mirzaei Reza , Zemp Franz J. , Wei Wu , Senger Donna L. , Robbins Stephen M. , Yong V. Wee
Published: April 2023

Supplementary data of microarray information contains results that support the tenascin C to notch pathway highlighted in this manuscript
Supplementary Table 1 from Incipient Melanoma Brain Metastases Instigate Astrogliosis and Neuroinflammation
Authors: Schwartz Hila , Blacher Eran , Amer Malak , Livneh Nir , Abramovitz Lilach , Klein Anat , Ben-Shushan Dikla , Soffer Shelly , Blazquez Raquel , Barrantes-Freer Alonso , Müller Meike , Müller-Decker Karin , Stein Reuven , Tsarfaty Galia , Satchi-Fainaro Ronit , Umansky Viktor , Pukrop Tobias , Erez Neta
Published: April 2023

Incidence of spontaneous brain macrometastases
Supplemental Tables 1 and 2 from BRD4 Regulates Breast Cancer Dissemination through Jagged1/Notch1 Signaling
Authors: Andrieu Guillaume , Tran Anna H. , Strissel Katherine J. , Denis Gerald V.
Published: April 2023

The Supplemental Table 1 lists the qPCR primers used in this study. The Supplemental Table 2 lists the ChIP primers used in this study.
Figure S1. Pan-BET protein inhibition does not affect cell proliferation or viability from BRD4 Regulates Breast Cancer Dissemination through Jagged1/Notch1 Signaling
Authors: Andrieu Guillaume , Tran Anna H. , Strissel Katherine J. , Denis Gerald V.
Published: April 2023

(A) MTT assay showing viability of MDA-MB-231, SUM149PT and MCF-7 cells treated either with 400 nM (R)-JQ1 (filled symbol) or (S)-JQ1 (open symbol) for the indicated times. Dots represent means {plus minus} SEM of three independent experiments. Statistical analysis was performed by using two-way ANOVA. (B) Dot plots of annexin V/propidium iodide co-staining of MDA-MB-231 and SUM149PT cells treated with either 400 nM (R)-JQ1 (upper panels) or (S)-JQ1 (lower panels) for 24h. Quadrant 1 (Q1): necrotic cells, Q2: late apoptotic cells, Q3: early apoptotic cells, Q4: viable cells. The percentage of cells in each quadrant is indicated. At least 20,000 cells were analyzed (n=3). Bottom panel: bars show means {plus minus} SEM of the percentage of annexin V-positive cells (n=3). Statistical analysis was performed by using Student's t test. (C) Cell cycle distribution of MDA-MB-231 and SUM149PT treated with 400 nM (R)-JQ1 (upper panels) or (S)-JQ1 (lower panels) for 24h. The percentage of cells in each phase is indicated. At least 10,000 cells were analyzed (n=3). Bottom panel: bars show means {plus minus} SEM of the percentage of cells in each phase of the cell cycle (n=3). Statistical analysis was performed by using two-way ANOVA.
Table S3 from Immune Gene Expression Is Associated with Genomic Aberrations in Breast Cancer
Authors: Safonov Anton , Jiang Tingting , Bianchini Giampaolo , Győrffy Balázs , Karn Thomas , Hatzis Christos , Pusztai Lajos
Published: April 2023

Candidate gene list of biological pathways related to antigen presentation, cytokines, chemokines, angiogenesis related signaling, the MAPK pathway, cell adhesion, and epithelial to mesenchymal transition.
Supplementary Figures S1-S6 from Immune Gene Expression Is Associated with Genomic Aberrations in Breast Cancer
Authors: Safonov Anton , Jiang Tingting , Bianchini Giampaolo , Győrffy Balázs , Karn Thomas , Hatzis Christos , Pusztai Lajos
Published: April 2023

Supplementary Figure S1. The expression distribution of each of the 13 immune metagenes is shown for the (A) ER positive, (B) TNBC and (C) HER2 positive cancers. Supplementary Figure S2. Correlation between the LCK metagene expression and infiltrating lymphocyte (TIL) count. Supplementary Figure S3. The distribution of genomic features and LCK metagene expression within breast cancer subtypes in the TCGA. Supplementary Figure S4. Correlations between 13 immune metagene expressions and 5 exome-wide genomic features including all breast cancers combined in TCGA. Supplementary Figure S5. Correlations between the LCK immune metagene expression and five different genomic features within each breast cancer subtype in the TCGA. Supplementary Figure S6. Distribution of genomic features and their correlation with an immune metagene in the breast cancer subtypes from TCGA data.
Supplementary Figures 1 through 4, Supplementary Table 1, and Supplementary Methods from Rapid Reprogramming of Primary Human Astrocytes into Potent Tumor-Initiating Cells with Defined Genetic Factors
Authors: Li Fang , Liu Xinjian , Sampson John H. , Bigner Darell D. , Li Chuan-Yuan
Published: April 2023

Supplementary Fig. S1. Supplementary Fig. 1 related to Fig.1 Transformation scheme and expression of external genes in transformed cells. Supplementary Fig. S2. Supplementary Fig. 2 related to Fig. 1. GEO analysis of gene expression patterns of transformed human astrocytes. Supplementary Fig. S3. Supplementary Fig. 3 related to Fig. 2. Chromosome aberration analysis and hTERT gene expression in transformed astrocytes. Supplementary Fig. S4. Supplementary Fig. S4 related to Fig. 4. In vivo growth of transformed astrocytes in nude mice. Supplementary Table S1. Source of antibodies used in the current study. Supplementary Methods. Additional details of experimental methods used in this study