bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Data Tables from Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations
Authors: Bianchi-Frias Daniella , Basom Ryan , Delrow Jeffrey J. , Coleman Ilsa M. , Dakhova Olga , Qu Xiaoyu , Fang Min , Franco Omar E. , Ericson Nolan G. , Bielas Jason H. , Hayward Simon W. , True Lawrence , Morrissey Colm , Brown Lisha , Bhowmick Neil A. , Rowley David , Ittmann Michael , Nelson Peter S.
Published: April 2023

Supplementary Data Tables
Supplementary Tables 1 and 2, Figures 1-9 from Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma
Authors: Walsh Alice M. , Kapoor Gurpreet S. , Buonato Janine M. , Mathew Lijoy K. , Bi Yingtao , Davuluri Ramana V. , Martinez-Lage Maria , Simon M. Celeste , O'Rourke Donald M. , Lazzara Matthew J.
Published: April 2023

Supplementary Tables 1 and 2, Figures 1-9. Supplemental Table 1. H-score analysis for SPRY2 staining in 10 EGFRvIII-negative and 10 EGFRvIII-positive tumors. Supplemental Table 2. Upregulated genes shared by human GBMs expressing EGFRvIII and 9L.EGFRvIII rat tumors compared to wild-type EGFR human GBMs or 9L.EV rat tumors. Supplemental Figure 1. SPRY2 is efficiently knocked down by shRNA expression in GBM cell lines. Supplemental Figure 2. SPRY2 knockdown by a second non-overlapping shRNA reduces cellular proliferation, and SPRY2 knockdown by transient siRNA transfection reduces colony formation in soft agar in EGFRvIII-expressing cells. Supplemental Figure 3. SPRY2 knockdown increases cellular sensitivity to EGFR and c-MET co-inhibition. Supplemental Figure 4. SPRY2 knockdown promotes response to EGFR and c-MET coinhibition in GSC cells. Supplemental Figure 5. p38 and JNK control anchorage-independent growth and response to EGFR and c-MET co-inhibition. Supplemental Figure 6. shRNA-mediated knockdown of MKP-1 or MKP-5 reduces MKP-1 or MKP-5 mRNA level. Supplemental Figure 7. SPRY2 protein expression in kidney and cerebellum sections by immunohistochemical analysis. Supplemental Figure 8. SPRY2 correlates well with ERK phosphorylation in a panel of GBM cell lines. Supplemental Figure 9. TCGA GBM dataset analysis reveals that SPRY2 expression is associated with reduced patient survival.
Supplementary Figure 4 from VDR Activity Is Differentially Affected by Hic-5 in Prostate Cancer and Stromal Cells
Authors: Solomon Joshua D. , Heitzer Marjet D. , Liu Teresa T. , Beumer Jan H. , Parise Robert A. , Normolle Daniel P. , Leach Damien A. , Buchanan Grant , DeFranco Donald B.
Published: April 2023

PDF file - 53K, Confidence Intervals for RT-qPCR.
Supplementary Figures S1-7 from Endophilin A2 Promotes TNBC Cell Invasion and Tumor Metastasis
Authors: Baldassarre Tomas , Watt Kathleen , Truesdell Peter , Meens Jalna , Schneider Mark M. , Sengupta Sandip K. , Craig Andrew W.
Published: April 2023

Supplementary Figures S1-7. Supplementary Figure S1. Endo II mRNA expression profiling in breast cancer cell lines arranged by molecular subtypes. Supplementary Figure S2. Endo II silencing causes defects in EGFR internalization. Supplementary Figure S3. Endo II silencing impairs ECM degradation in HCC 1806 cells. Supplementary Figure S4. Endo II promotes HCC 1806 tumor growth and metastasis in mice. Supplementary Figure S5. Assessing tumor mass and incidence of metastases in TNBC models. Supplementary Figure S6. Endo II promotes lung seeding efficiency of TNBC cells in mice. Supplementary Figure S7. Testing the specificity of Endo II IHC staining.
Supplementary Figure 2 from VDR Activity Is Differentially Affected by Hic-5 in Prostate Cancer and Stromal Cells
Authors: Solomon Joshua D. , Heitzer Marjet D. , Liu Teresa T. , Beumer Jan H. , Parise Robert A. , Normolle Daniel P. , Leach Damien A. , Buchanan Grant , DeFranco Donald B.
Published: April 2023

PDF file - 6K, Confidence Intervals RT-qPCR.
Supp. Fig. 6 from SOCS3 Modulates the Response to Enzalutamide and Is Regulated by Androgen Receptor Signaling and CpG Methylation in Prostate Cancer Cells
Authors: Handle Florian , Erb Holger H.H. , Luef Birgit , Hoefer Julia , Dietrich Dimo , Parson Walther , Kristiansen Glen , Santer Frédéric R. , Culig Zoran
Published: April 2023

Knock-down and overexpression of SOCS3 is sustained after 3 weeks of combined IL6 and Enzalutamide treatment. SOCS3 expression in LNCaP was modulated by lentiviral over-expression and knock-down with a pool of 3 individual shRNAs targeting SOCS3 and the effect on SOCS3 mRNA was determined by qPCR after 3 weeks of combined IL6 and enzalutamide treatment.
Supp. Fig. 3 from SOCS3 Modulates the Response to Enzalutamide and Is Regulated by Androgen Receptor Signaling and CpG Methylation in Prostate Cancer Cells
Authors: Handle Florian , Erb Holger H.H. , Luef Birgit , Hoefer Julia , Dietrich Dimo , Parson Walther , Kristiansen Glen , Santer Frédéric R. , Culig Zoran
Published: April 2023

Knock-down and overexpression efficiency of SOCS3 in LNCaP. SOCS3 expression in LNCaP was modulated by stable over-expression and knock-down with lentiviral vectors and the effect on SOCS3 mRNA was determined by qPCR after 72 hours of reatment with 5 ng/ml IL6.
Supplemental data from Transcription Factor KLF5 Binds a Cyclin E1 Polymorphic Intronic Enhancer to Confer Increased Bladder Cancer Risk
Authors: Pattison Jillian M. , Posternak Valeriya , Cole Michael D.
Published: April 2023

Figure legends for Supplemental Figures 1 and 2
Supplemental Figure 1 from Transcription Factor KLF5 Binds a Cyclin E1 Polymorphic Intronic Enhancer to Confer Increased Bladder Cancer Risk
Authors: Pattison Jillian M. , Posternak Valeriya , Cole Michael D.
Published: April 2023

S1. KLF5 binds the CCNE1 intronic region and contributes to CCNE1 expression in the J82 UBC cell line.
Supplementary Figure 6 from Aberrant Myosin 1b Expression Promotes Cell Migration and Lymph Node Metastasis of HNSCC
Authors: Ohmura Gaku , Tsujikawa Takahiro , Yaguchi Tomonori , Kawamura Naoshi , Mikami Shuji , Sugiyama Juri , Nakamura Kenta , Kobayashi Asuka , Iwata Takashi , Nakano Hiroshi , Shimada Taketoshi , Hisa Yasuo , Kawakami Yutaka
Published: April 2023

Myo1b regulates cell motility of human HNSCC not depending on the major EMT inducing transcription factors.
Supplementary Figure 4 from KLF4 Suppresses Tumor Formation in Genetic and Pharmacological Mouse Models of Colonic Tumorigenesis
Authors: Ghaleb Amr M. , Elkarim Enas A. , Bialkowska Agnieszka B. , Yang Vincent W.
Published: April 2023

Klf4Î”IS mice develop micro adenomas at an earlier time point (8 weeks) following AOM treatment.
Supplementary Figure 2 from KLF4 Suppresses Tumor Formation in Genetic and Pharmacological Mouse Models of Colonic Tumorigenesis
Authors: Ghaleb Amr M. , Elkarim Enas A. , Bialkowska Agnieszka B. , Yang Vincent W.
Published: April 2023

Klf4Î”IS/ApcMin/+ mice have stronger beta-catenin, Ki67 and cyclin D1 staining in the small intestine than Klf4fl/fl/ApcMin/+ mice.
Supplementary Figure 2 from Helicobacter pylori Induces a Novel NF-kB/LIN28A/let-7a/hTERT Axis to Promote Gastric Carcinogenesis
Authors: Shen Li , Zeng Jiping , Ma Lin , Li Shuyan , Chen Chunyan , Jia Jihui , Liang Xiuming
Published: April 2023

Figure S2. (a) hTERT and Lin28A expression were determined using western blot in hTERT depleted GC cells. (b) Co-expression of hTERT and Lin28A in GC cells.
Table S2 from Inhibition of the Cell Death Pathway in Nonalcoholic Steatohepatitis (NASH)-Related Hepatocarcinogenesis Is Associated with Histone H4 lysine 16 Deacetylation
Authors: de Conti Aline , Dreval Kostiantyn , Tryndyak Volodymyr , Orisakwe Orish E. , Ross Sharon A. , Beland Frederick A. , Pogribny Igor P.
Published: April 2023

List of differentially-expressed genes in the livers of STAM mice at 6, 12, and 20 weeks.
Supplementary Tables 2 and 3 from Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer—Evidence for a Relevant Model System and Urine-Based Diagnostic Test
Authors: Decker Brennan , Parker Heidi G. , Dhawan Deepika , Kwon Erika M. , Karlins Eric , Davis Brian W. , Ramos-Vara José A. , Bonney Patty L. , McNiel Elizabeth A. , Knapp Deborah W. , Ostrander Elaine A.
Published: April 2023

Supplementary Tables 2 and 3. Listing genotypes and clinical data.
Table S1 from Inhibition of the Cell Death Pathway in Nonalcoholic Steatohepatitis (NASH)-Related Hepatocarcinogenesis Is Associated with Histone H4 lysine 16 Deacetylation
Authors: de Conti Aline , Dreval Kostiantyn , Tryndyak Volodymyr , Orisakwe Orish E. , Ross Sharon A. , Beland Frederick A. , Pogribny Igor P.
Published: April 2023

List of primers and primary antibodies.
Figure S2 from Inhibition of the Cell Death Pathway in Nonalcoholic Steatohepatitis (NASH)-Related Hepatocarcinogenesis Is Associated with Histone H4 lysine 16 Deacetylation
Authors: de Conti Aline , Dreval Kostiantyn , Tryndyak Volodymyr , Orisakwe Orish E. , Ross Sharon A. , Beland Frederick A. , Pogribny Igor P.
Published: April 2023

Expression of cleaved caspase 3 and cleaved caspase 8 in the livers of control mice and STAM mice.
Supplementary Figure S3 from A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma
Authors: Hiemer Samantha E. , Zhang Liye , Kartha Vinay K. , Packer Trevor S. , Almershed Munirah , Noonan Vikki , Kukuruzinska Maria , Bais Manish V. , Monti Stefano , Varelas Xaralabos
Published: April 2023

Supplementary Figure S3. Gene set enrichment analysis of the YAP/TAZ-activated genes.
Supplemental Figure Legend from USP22 Interacts with PALB2 and Promotes Chemotherapy Resistance via Homologous Recombination of DNA Double-Strand Breaks
Authors: Nardi Isaac K. , Stark Jeremy M. , Larsen Adrien , Salgia Ravi , Raz Dan J.
Published: April 2023

Supplemental Figure Legend
Supplementary Figure 6 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT
Authors: Yang-Hartwich Yang , Tedja Roslyn , Roberts Cai M. , Goodner-Bingham Jamie , Cardenas Carlos , Gurea Marta , Sumi Natalia J. , Alvero Ayesha B. , Glackin Carlotta A. , Mor Gil
Published: April 2023

The effects of Î"b-Twist1 overexpression on spheroids formation and migration. (A) Representative images of spheroid forming assay. (B) Representative images of the migrated cells in migration assay. (C) Quantification of the migrated cells.*P< 0.05 compared to control group.
Supplementary Figure 2 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT
Authors: Yang-Hartwich Yang , Tedja Roslyn , Roberts Cai M. , Goodner-Bingham Jamie , Cardenas Carlos , Gurea Marta , Sumi Natalia J. , Alvero Ayesha B. , Glackin Carlotta A. , Mor Gil
Published: April 2023

TP53 mutation status and protein levels of p53 and Twist1 ovarian cancer cell lines. * u = unknown.
Supplemental File 1 from Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes
Authors: Ye I. Chae , Fertig Elana J. , DiGiacomo Josh W. , Considine Michael , Godet Inês , Gilkes Daniele M.
Published: April 2023

Source Code
Supplementary Figures 1-4 from Bone Microenvironment Changes in Latexin Expression Promote Chemoresistance
Authors: Zhang Mi , Osisami Mary , Dai Jinlu , Keller Jill M. , Escara-Wilke June , Mizokami Atsushi , Keller Evan T.
Published: April 2023

Supplemental Figure 1. Validation of gene for chemoresistance of prostate cancer to DTX. Supplemental Figure 2. Caliper measurements of subcutaneous tumors presented in Figure 5A. Supplemental Figure 3. Bone stromal cells decrease LXN expression and induce chemoresistance in LNCaP cells. Supplemental Figure 4. RAW cells do not reduce LXN expression or promote chemoresistance in PC-3 cells.
Supplementary Data 3B from miR-122-5p Expression and Secretion in Melanoma Cells Is Amplified by the LPAR3 SH3–Binding Domain to Regulate Wnt1
Authors: Byrnes Charnel C. , Jia Wei , Alshamrani Ali A. , Kuppa Sudeepti S. , Murph Mandi M.
Published: April 2023

Supplementary Figure 3. Microfluidics visualization of nanoparticles from LPAR3. The movies illustrate the difference between the smaller/almost indiscernible white dots, which are exosome nanoparticles, secreted by cells expressing LPAR3-wt versus the larger particles, likely multi-vesicular bodies, but not exosomes.
Table S3 from Tumor Progression Is Mediated by Thymosin-β4 through a TGFβ/MRTF Signaling Axis
Authors: Morita Tsuyoshi , Hayashi Ken'ichiro
Published: April 2023

Table S3 shows the result of Gene Ontology analysis of the down regulated genes in TÃŸ4 KO cells.
Supplementary Data 2 from miR-122-5p Expression and Secretion in Melanoma Cells Is Amplified by the LPAR3 SH3–Binding Domain to Regulate Wnt1
Authors: Byrnes Charnel C. , Jia Wei , Alshamrani Ali A. , Kuppa Sudeepti S. , Murph Mandi M.
Published: April 2023

Supplementary Figure 2. Messenger RNA expression differences between cell types. Other mRNAs were assessed to compare relative LPAR3 expression as well as CCNG1.
Supplementary Data 1 from miR-122-5p Expression and Secretion in Melanoma Cells Is Amplified by the LPAR3 SH3–Binding Domain to Regulate Wnt1
Authors: Byrnes Charnel C. , Jia Wei , Alshamrani Ali A. , Kuppa Sudeepti S. , Murph Mandi M.
Published: April 2023

Supplementary Figure 1. MiR-122-5p-5p is increased in the serum of cancer patients. The NCBI Gene Expression Omnibus DataSets (GSE106817) was downloaded and mined for the relative expression of miR-122-5p-5p among the circulation of health subjects (n=2759) versus patients with other types of solid cancer (n=1245).
Figure S3 from Tumor Progression Is Mediated by Thymosin-β4 through a TGFβ/MRTF Signaling Axis
Authors: Morita Tsuyoshi , Hayashi Ken'ichiro
Published: April 2023

Figure S3 shows expression profile of the tumor-associated genes in TÃŸ4 KO tumors.
Supplementary Table S3 from Global Increase of p16INK4a in APC-Deficient Mouse Liver Drives Clonal Growth of p16INK4a-Negative Tumors
Authors: Ueberham Elke , Glöckner Pia , Göhler Claudia , Straub Beate K. , Teupser Daniel , Schönig Kai , Braeuning Albert , Höhn Anne Kathrin , Jerchow Boris , Birchmeier Walter , Gaunitz Frank , Arendt Thomas , Sansom Owen , Gebhardt Rolf , Ueberham Uwe
Published: April 2023

List of primers used in qRT PCR.
Figure S1 from Tumor Progression Is Mediated by Thymosin-β4 through a TGFβ/MRTF Signaling Axis
Authors: Morita Tsuyoshi , Hayashi Ken'ichiro
Published: April 2023

Figure S1 shows the role of TÃŸ4 in epithelial-mesenchymal transition.
Supplemental Figure 3 from Genomic cfDNA Analysis of Aqueous Humor in Retinoblastoma Predicts Eye Salvage: The Surrogate Tumor Biopsy for Retinoblastoma
Authors: Berry Jesse L. , Xu Liya , Kooi Irsan , Murphree A. Linn , Prabakar Rishvanth K. , Reid Mark , Stachelek Kevin , Le Bao Han A. , Welter Lisa , Reiser Bibiana J. , Chévez-Barrios Patricia , Jubran Rima , Lee Thomas C. , Kim Jonathan W. , Kuhn Peter , Cobrinik David , Hicks James
Published: April 2023

Supplemental Figure 3, online only: Initial Copy Number Alteration (CNA) profile from eyes that required enucleation + indicates that in Case 11 the second AH sample (which had good alignment and demonstrates gain of 6p) is shown instead of the initial sample (see also Table 1).
Supplementary Figure S2 from Global Increase of p16INK4a in APC-Deficient Mouse Liver Drives Clonal Growth of p16INK4a-Negative Tumors
Authors: Ueberham Elke , Glöckner Pia , Göhler Claudia , Straub Beate K. , Teupser Daniel , Schönig Kai , Braeuning Albert , Höhn Anne Kathrin , Jerchow Boris , Birchmeier Walter , Gaunitz Frank , Arendt Thomas , Sansom Owen , Gebhardt Rolf , Ueberham Uwe
Published: April 2023

Pronounced proliferation in p16INK4a negative cells.
Figure S2 from Infiltrating Myeloid Cells Exert Protumorigenic Actions via Neutrophil Elastase
Authors: Lerman Irina , Garcia-Hernandez Maria de la Luz , Rangel-Moreno Javier , Chiriboga Luis , Pan Chunliu , Nastiuk Kent L. , Krolewski John J. , Sen Aritro , Hammes Stephen R.
Published: April 2023

High power image of neutrophil elastase localization in a xenograft.
Figure S1 from Infiltrating Myeloid Cells Exert Protumorigenic Actions via Neutrophil Elastase
Authors: Lerman Irina , Garcia-Hernandez Maria de la Luz , Rangel-Moreno Javier , Chiriboga Luis , Pan Chunliu , Nastiuk Kent L. , Krolewski John J. , Sen Aritro , Hammes Stephen R.
Published: April 2023

Depletion of MDSCs suppresses prostate cancer xenograft proliferation.
Figure S1 from Infiltrating Myeloid Cells Exert Protumorigenic Actions via Neutrophil Elastase
Authors: Lerman Irina , Garcia-Hernandez Maria de la Luz , Rangel-Moreno Javier , Chiriboga Luis , Pan Chunliu , Nastiuk Kent L. , Krolewski John J. , Sen Aritro , Hammes Stephen R.
Published: April 2023

High CD33 expression predicts poor outcomes in prostate cancer patients.
Supplementary Methods from Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma
Authors: Megquier Kate , Turner-Maier Jason , Swofford Ross , Kim Jong-Hyuk , Sarver Aaron L. , Wang Chao , Sakthikumar Sharadha , Johnson Jeremy , Koltookian Michele , Lewellen Mitzi , Scott Milcah C. , Schulte Ashley J. , Borst Luke , Tonomura Noriko , Alfoldi Jessica , Painter Corrie , Thomas Rachael , Karlsson Elinor K. , Breen Matthew , Modiano Jaime F. , Elvers Ingegerd , Lindblad-Toh Kerstin
Published: April 2023

Supplementary Methods
Supplemental Table 7 from Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma
Authors: Megquier Kate , Turner-Maier Jason , Swofford Ross , Kim Jong-Hyuk , Sarver Aaron L. , Wang Chao , Sakthikumar Sharadha , Johnson Jeremy , Koltookian Michele , Lewellen Mitzi , Scott Milcah C. , Schulte Ashley J. , Borst Luke , Tonomura Noriko , Alfoldi Jessica , Painter Corrie , Thomas Rachael , Karlsson Elinor K. , Breen Matthew , Modiano Jaime F. , Elvers Ingegerd , Lindblad-Toh Kerstin
Published: April 2023

Supplemental Table 7
Supplementary Figure 7 from Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism
Authors: Valli Alessandro , Morotti Matteo , Zois Christos E. , Albers Patrick K. , Soga Tomoyoshi , Feldinger Katharina , Fischer Roman , Frejno Martin , McIntyre Alan , Bridges Esther , Haider Syed , Buffa Francesca M. , Baban Dilair , Rodriguez Miguel , Yanes Oscar , Whittington Hannah J. , Lake Hannah A. , Zervou Sevasti , Lygate Craig A. , Kessler Benedikt M. , Harris Adrian L.
Published: April 2023

S7. WTN, KON, WTH, and KOH HCT116 cell proliferation after 5 days in two O2 conditions, 21% and 1% for cells knocked down for GTR3, GTR14, and HIF2α.
Supplemental Materials and Methods from Regulation of USP37 Expression by REST-Associated G9a-Dependent Histone Methylation
Authors: Dobson Tara H.W. , Hatcher Rashieda J. , Swaminathan Jyothishmathi , Das Chandra M. , Shaik Shavali , Tao Rong-Hua , Milite Ciro , Castellano Sabrina , Taylor Pete H. , Sbardella Gianluca , Gopalakrishnan Vidya
Published: April 2023

Primers for QRT-PCR Assay, Antibodies for ChIP, Primers for qChIP Assay, Antibodies for Western Blotting and Antibodies for IHC.
Supplementary Table S1 from The Aged Microenvironment Influences the Tumorigenic Potential of Malignant Prostate Epithelial Cells
Authors: Bianchi-Frias Daniella , Damodarasamy Mamatha , Hernandez Susana A. , Gil da Costa Rui M. , Vakar-Lopez Funda , Coleman Ilsa M. , Reed May J. , Nelson Peter S.
Published: April 2023

IHC Results
Supplementary Data-Expression from The Aged Microenvironment Influences the Tumorigenic Potential of Malignant Prostate Epithelial Cells
Authors: Bianchi-Frias Daniella , Damodarasamy Mamatha , Hernandez Susana A. , Gil da Costa Rui M. , Vakar-Lopez Funda , Coleman Ilsa M. , Reed May J. , Nelson Peter S.
Published: April 2023

Excel Spreadsheet of gene expression
Supplementary Figure 2 from Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism
Authors: Valli Alessandro , Morotti Matteo , Zois Christos E. , Albers Patrick K. , Soga Tomoyoshi , Feldinger Katharina , Fischer Roman , Frejno Martin , McIntyre Alan , Bridges Esther , Haider Syed , Buffa Francesca M. , Baban Dilair , Rodriguez Miguel , Yanes Oscar , Whittington Hannah J. , Lake Hannah A. , Zervou Sevasti , Lygate Craig A. , Kessler Benedikt M. , Harris Adrian L.
Published: April 2023

S2. (A) Kaplan-Meier analysis of overall survival of 440 colon adenocarcinoma patients TGCA cohort. Patient group with highest quartile showed a reduced five-year survival. (B) Heatmap illustrating the correlative gene expression profile of creatine kinase enzymes (KCRU, KCRM, KCRB) and glucose transporters (GTR1, GTR3, GTR14) compared to 47 genes representing a "hypoxia signature" based on 337 CODREAD colorectal cancer patients.
Table S1 from Epigenetic Silencing of THY1 Tracks the Acquisition of the Notch1–EGFR Signaling in a Xenograft Model of CD44+/CD24low/CD90+ Myoepithelial Cells
Authors: Montanari Micaela , Carbone Maria Rita , Coppola Luigi , Giuliano Mario , Arpino Grazia , Lauria Rossella , Nardone Agostina , Leccia Felicia , Trivedi Meghana V. , Garbi Corrado , Bianco Roberto , Avvedimento Enrico V. , De Placido Sabino , Veneziani Bianca Maria
Published: April 2023

Intrinsic subtype of breast cancer
Supplementary Figure 1 from Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma
Authors: Arend Rebecca C. , Londoño Angelina I. , Montgomery Allison M. , Smith Haller J. , Dobbin Zachary C. , Katre Ashwini A. , Martinez Alba , Yang Eddy S. , Alvarez Ronald D. , Huh Warner K. , Bevis Kerri S. , Straughn J. Michael , Estes Jacob M. , Novak Lea , Crossman David K. , Cooper Sara J. , Landen Charles N. , Leath Charles A.
Published: April 2023

R-plot PCA by cellularity.
Figure S1, A from Diffuse Intrinsic Pontine Glioma Cells Are Vulnerable to Mitotic Abnormalities Associated with BMI-1 Modulation
Authors: Senthil Kumar Shiva , Sengupta Satarupa , Zhu Xiaoting , Mishra Deepak Kumar , Phoenix Timothy , Dyer Lisa , Fuller Christine , Stevenson Charles B. , DeWire Mariko , Fouladi Maryam , Drissi Rachid
Published: April 2023

A, Representative IHC images of BMI-1 staining in DIPG patient tumors and their matched normal tissue. Images are different areas of the same section.
Mouse injection survival results from Histone H3.3K27M Represses p16 to Accelerate Gliomagenesis in a Murine Model of DIPG
Authors: Cordero Francisco J. , Huang Zhiqing , Grenier Carole , He Xingyao , Hu Guo , McLendon Roger E. , Murphy Susan K. , Hashizume Rintaro , Becher Oren J.
Published: April 2023

list of all viral infection combinations performed on mice and the median survival (days) of each model.
Supplemental Figures 1-3 from T-Cell Deletion of MyD88 Connects IL17 and IκBζ to RAS Oncogenesis
Authors: Cataisson Christophe , Salcedo Rosalba , Michalowski Aleksandra M. , Klosterman Mary , Naik Shruti , Li Luowei , Pan Michelle J. , Sweet Amalia , Chen Jin-Qiu , Kostecka Laurie G. , Karwan Megan , Smith Loretta , Dai Ren-Ming , Stewart C. Andrew , Lyakh Lyudmila , Hsieh Wang-Ting , Khan Asra , Yang Howard , Lee Maxwell , Trinchieri Giorgio , Yuspa Stuart H.
Published: April 2023

Supplemental Figures 1-3
Supplementary Table S1 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Details of Primer sequences
Supplementary Methods from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Details of Annexin V staining method
Supplementary Figure S3 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Salubrinal treatment increases annexin V positive cells
Supplementary Figure S1 from Estrogen-Induced Apoptosis in Breast Cancers Is Phenocopied by Blocking Dephosphorylation of Eukaryotic Initiation Factor 2 Alpha (eIF2α) Protein
Authors: Sengupta Surojeet , Sevigny Catherine M. , Bhattacharya Poulomi , Jordan V. Craig , Clarke Robert
Published: April 2023

Effect of estradiol on ERN1(IRE1α), XBP1 spliced:XBP1 total ratio, and ATF6 mRNA in MCF7:5C cells.
Table S1 from Targeted Next-Generation Sequencing for Detecting MLL Gene Fusions in Leukemia
Authors: Afrin Sadia , Zhang Christine R.C. , Meyer Claus , Stinson Caedyn L. , Pham Thy , Bruxner Timothy J.C. , Venn Nicola C. , Trahair Toby N. , Sutton Rosemary , Marschalek Rolf , Fink J. Lynn , Moore Andrew S.
Published: April 2023

Comparison of MLL fusions detected by cytogenetics, fluorescent in situ hybridization (FISH), Long distance Inverse polymerase chain reaction (LDI-PCR) and Anchored multiplex PCR enrichment (AMP-E).
Data File S1 from Alectinib Resistance in ALK-Rearranged Lung Cancer by Dual Salvage Signaling in a Clinically Paired Resistance Model
Authors: Tsuji Takahiro , Ozasa Hiroaki , Aoki Wataru , Aburaya Shunsuke , Funazo Tomoko , Furugaki Koh , Yoshimura Yasushi , Ajimizu Hitomi , Okutani Ryoko , Yasuda Yuto , Nomizo Takashi , Uemasu Kiyoshi , Hasegawa Koichi , Yoshida Hironori , Yagi Yoshitaka , Nagai Hiroki , Sakamori Yuichi , Ueda Mitsuyoshi , Hirai Toyohiro , Kim Young Hak
Published: April 2023

Data sets of the phosphoproteome analysis in KTOR1 and KTOR1-RE cells
Revised supplementary Table 1 from Genome-Wide Analysis Identifies MEN1 and MAX Mutations and a Neuroendocrine-Like Molecular Heterogeneity in Quadruple WT GIST
Authors: Pantaleo Maria A. , Urbini Milena , Indio Valentina , Ravegnini Gloria , Nannini Margherita , De Luca Matilde , Tarantino Giuseppe , Angelini Sabrina , Gronchi Alessandro , Vincenzi Bruno , Grignani Giovanni , Colombo Chiara , Fumagalli Elena , Gatto Lidia , Saponara Maristella , Ianni Manuela , Paterini Paola , Santini Donatella , Pirini M. Giulia , Ceccarelli Claudio , Altimari Annalisa , Gruppioni Elisa , Renne Salvatore L. , Collini Paola , Stacchiotti Silvia , Brandi Giovanni , Casali Paolo G. , Pinna Antonio D. , Astolfi Annalisa , Biasco Guido
Published: April 2023

Supplementary Table 1. Significative pathways found by functional enrichment analysis with WEB-based GEne SeT AnaLysis Toolkit.
Revised supplementary Figure 2 from Genome-Wide Analysis Identifies MEN1 and MAX Mutations and a Neuroendocrine-Like Molecular Heterogeneity in Quadruple WT GIST
Authors: Pantaleo Maria A. , Urbini Milena , Indio Valentina , Ravegnini Gloria , Nannini Margherita , De Luca Matilde , Tarantino Giuseppe , Angelini Sabrina , Gronchi Alessandro , Vincenzi Bruno , Grignani Giovanni , Colombo Chiara , Fumagalli Elena , Gatto Lidia , Saponara Maristella , Ianni Manuela , Paterini Paola , Santini Donatella , Pirini M. Giulia , Ceccarelli Claudio , Altimari Annalisa , Gruppioni Elisa , Renne Salvatore L. , Collini Paola , Stacchiotti Silvia , Brandi Giovanni , Casali Paolo G. , Pinna Antonio D. , Astolfi Annalisa , Biasco Guido
Published: April 2023

Validation of fusion genes identified in GIST127. For each fusion, a schematic representation of the chimeric gene is reported with the 5' gene exons in red and the 3' gene exons in green (full boxes: coding exons; empty boxes: non-coding exons). The chromatogram of the breakpoint and the predicted aminoacid sequence are shown below (in light red the aminoacids from the gene in 5', in light green the aminoacids from the gene in 3', and in violet the novel aminoacids deriving from the fusion event).
Revised supplementary Figure 1 from Genome-Wide Analysis Identifies MEN1 and MAX Mutations and a Neuroendocrine-Like Molecular Heterogeneity in Quadruple WT GIST
Authors: Pantaleo Maria A. , Urbini Milena , Indio Valentina , Ravegnini Gloria , Nannini Margherita , De Luca Matilde , Tarantino Giuseppe , Angelini Sabrina , Gronchi Alessandro , Vincenzi Bruno , Grignani Giovanni , Colombo Chiara , Fumagalli Elena , Gatto Lidia , Saponara Maristella , Ianni Manuela , Paterini Paola , Santini Donatella , Pirini M. Giulia , Ceccarelli Claudio , Altimari Annalisa , Gruppioni Elisa , Renne Salvatore L. , Collini Paola , Stacchiotti Silvia , Brandi Giovanni , Casali Paolo G. , Pinna Antonio D. , Astolfi Annalisa , Biasco Guido
Published: April 2023

Graphical view of copy number analysis. Copy number alterations detected on the chromosomes most frequently deleted in GIST (chr1, chr14 and chr22). For each patient a green bar indicates an heterozygously deleted region and a red bar indicates a gain of one copy.
Figure S5 from Molecular Signature and Mechanisms of Hepatitis D Virus–Associated Hepatocellular Carcinoma
Authors: Diaz Giacomo , Engle Ronald E. , Tice Ashley , Melis Marta , Montenegro Stephanie , Rodriguez-Canales Jaime , Hanson Jeffrey , Emmert-Buck Michael R. , Bock Kevin W. , Moore Ian N. , Zamboni Fausto , Govindarajan Sugantha , Kleiner David E. , Farci Patrizia
Published: April 2023

Venn diagrams of differentially expressed genes obtained from laser capture microdissected hepatocytes and whole liver tissue of patients with HDV-, HBV-and HCV-associated HCC
Legend for supplementay figures from Blockade of AP-1 Potentiates Endocrine Therapy and Overcomes Resistance
Authors: Malorni Luca , Giuliano Mario , Migliaccio Ilenia , Wang Tao , Creighton Chad J. , Lupien Mathieu , Fu Xiaoyong , Hilsenbeck Susan G. , Healy Nuala , De Angelis Carmine , Mazumdar Abhijit , Trivedi Meghana V. , Massarweh Suleiman , Gutierrez Carolina , De Placido Sabino , Jeselsohn Rinath , Brown Myles , Brown Powel H. , Osborne C. Kent , Schiff Rachel
Published: April 2023

Legend for supplementay figures
Figure S2 from Molecular Signature and Mechanisms of Hepatitis D Virus–Associated Hepatocellular Carcinoma
Authors: Diaz Giacomo , Engle Ronald E. , Tice Ashley , Melis Marta , Montenegro Stephanie , Rodriguez-Canales Jaime , Hanson Jeffrey , Emmert-Buck Michael R. , Bock Kevin W. , Moore Ian N. , Zamboni Fausto , Govindarajan Sugantha , Kleiner David E. , Farci Patrizia
Published: April 2023

Genes associated with the twenty top-scored pathways of malignant hepatocytes of HDV-HCC.
Figure S1 from Molecular Signature and Mechanisms of Hepatitis D Virus–Associated Hepatocellular Carcinoma
Authors: Diaz Giacomo , Engle Ronald E. , Tice Ashley , Melis Marta , Montenegro Stephanie , Rodriguez-Canales Jaime , Hanson Jeffrey , Emmert-Buck Michael R. , Bock Kevin W. , Moore Ian N. , Zamboni Fausto , Govindarajan Sugantha , Kleiner David E. , Farci Patrizia
Published: April 2023

Experimental design.
Figures S1-S5, Tables S1-S2, Supplemental Materials and Methods, Supplementary References from Hyperactivation of MAPK Signaling Is Deleterious to RAS/RAF-mutant Melanoma
Authors: Leung Grace P. , Feng Tianshu , Sigoillot Frederic D. , Geyer Felipe C. , Shirley Matthew D. , Ruddy David A. , Rakiec Daniel P. , Freeman Alyson K. , Engelman Jeffrey A. , Jaskelioff Mariela , Stuart Darrin D.
Published: April 2023

Figure S1. Cellular phenotypes observed in response to ERK2 overexpression in A-375 cells. Figure S2. No paracrine effect was produced by cells dying due to knockdown of the essential gene PSMA3. Figure S3. A-375 xenograft tumors with ERK2 overexpression displayed necrosis and/or fibrosis. Figure S4. Paradoxical activation triggered by low doses of BRAFi in GR-M augmented the growth suppression caused by ERK2 overexpression. Figure S5. Graphical representations of vector constructs used in this study. Table S1. MSigDB Hallmark pathways that were significantly enriched in genes upregulated after 20 h treatment with doxycycline in A-375 ERK2 cells. Table S2. Transcription factor targets (from MSigDB C3 TFT) for known ERK targets were significantly enriched in genes upregulated after 20 h treatment with doxycycline in A-375 ERK2 cells.
Supplementary Table S1 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

GEO accession numbers for publicly available data
Supplemental Figure Legends from Chromosome 20q Amplification Defines a Subtype of Microsatellite Stable, Left-Sided Colon Cancers with Wild-type RAS/RAF and Better Overall Survival
Authors: Ptashkin Ryan N. , Pagan Carlos , Yaeger Rona , Middha Sumit , Shia Jinru , O'Rourke Kevin P. , Berger Michael F. , Wang Lu , Cimera Robert , Wang Jiajing , Klimstra David S. , Saltz Leonard , Ladanyi Marc , Zehir Ahmet , Hechtman Jaclyn F.
Published: April 2023

Supplemental Figure Legends
Supplementary Figure 6 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplementary figure 6 shows EGFR RNA expression and H3K27Ac in clinical samples in addition to correlations between EGFR and transcription factor RNA expression. It also shows differences in gene expression between tumor and normal cells.
Supplementary Figure 5 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplementary figure 5 shows JQ1 treatment and BET siRNA effects on SF767 cells as well as transcription factor expression and binding to CE1 and CE2
Supplementary Figure 3 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplementary figure 3 shows the dCas9-KRAB targeting in SF767 cells
Table S3 from The Landscape of Isoform Switches in Human Cancers
Authors: Vitting-Seerup Kristoffer , Sandelin Albin
Published: April 2023

Overview of literature derived isoform switches as well as the extensions we make.
Supplementary Figure 1 from Intron 1–Mediated Regulation of EGFR Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins
Authors: Jameson Nathan M. , Ma Jianhui , Benitez Jorge , Izurieta Alejandro , Han Jee Yun , Mendez Robert , Parisian Alison , Furnari Frank
Published: April 2023

Supplemental figure 1 shows the generated ROSE super enhancers
Table S1 from The Landscape of Isoform Switches in Human Cancers
Authors: Vitting-Seerup Kristoffer , Sandelin Albin
Published: April 2023

List of analyzed isoforms along with their annotation, expression and usage.
Table S1 from Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer
Authors: Goulet Daniel R. , Foster Joseph P. , Zawistowski Jon S. , Bevill Samantha M. , Noël Mélodie P. , Olivares-Quintero José F. , Sciaky Noah , Singh Darshan , Santos Charlene , Pattenden Samantha G. , Davis Ian J. , Johnson Gary L.
Published: April 2023

WES Analysis Results
Table S1 from Digital PCR-Based T-cell Quantification–Assisted Deconvolution of the Microenvironment Reveals that Activated Macrophages Drive Tumor Inflammation in Uveal Melanoma
Authors: de Lange Mark J. , Nell Rogier J. , Lalai Rajshri N. , Versluis Mieke , Jordanova Ekaterina S. , Luyten Gre P.M. , Jager Martine J. , van der Burg Sjoerd H. , Zoutman Willem H. , van Hall Thorbald , van der Velden Pieter A.
Published: April 2023

T cell correlated genes
Figure S3 from CREBBP/EP300 Bromodomain Inhibition Affects the Proliferation of AR-Positive Breast Cancer Cell Lines
Authors: Garcia-Carpizo Veronica , Ruiz-Llorente Sergio , Sarmentero Jacinto , González-Corpas Ana , Barrero Maria J.
Published: April 2023

GSEA enrichments for genes changing expression after JQ or CBP30 treatments. (a) Top reactome pathways significantly enriched in upregulated or downregulated genes. Black boxes indicate significant enrichment with P-value<0.05. Grey indicates no enrichment. (b) Enrichment plots for the most significantly upregulated and downregulated pathways in MDA-MB-453 cells treated with CBP30 and heatmaps showing the expression of genes in the leading edge.
Figure S4 from Targeting USP22 Suppresses Tumorigenicity and Enhances Cisplatin Sensitivity Through ALDH1A3 Downregulation in Cancer-Initiating Cells from Lung Adenocarcinoma
Authors: Yun Xinwei , Zhang Keqiang , Wang Jinhui , Pangeni Rajendra P. , Yang Lu , Bonner Melissa , Wu Jun , Wang Jami , Nardi Isaac K. , Gao Ming , Raz Dan J.
Published: April 2023

Correlation between the levels of USP22 mRNA with that of ALDH1A3 mRNA in lung Adenocarcinoma tissues from TCGA portal
Supplementary Figure S1 from The mTOR Targets 4E-BP1/2 Restrain Tumor Growth and Promote Hypoxia Tolerance in PTEN-driven Prostate Cancer
Authors: Ding Mei , Van der Kwast Theodorus H. , Vellanki Ravi N. , Foltz Warren D. , McKee Trevor D. , Sonenberg Nahum , Pandolfi Pier P. , Koritzinsky Marianne , Wouters Bradly G.
Published: April 2023

Genotype analysis.
Supplementary Figure S3 from FoxO3a Mediates the Inhibitory Effects of the Antiepileptic Drug Lamotrigine on Breast Cancer Growth
Authors: Pellegrino Michele , Rizza Pietro , Nigro Alessandra , Ceraldi Rosangela , Ricci Elena , Perrotta Ida , Aquila Saveria , Lanzino Marilena , Andò Sebastiano , Morelli Catia , Sisci Diego
Published: April 2023

LTG is not toxic to BCCs.
Supplementary Figure 4 from Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression
Authors: Fedele Vita , Dai Fangping , Masilamani Anie P. , Heiland Dieter H. , Kling Eva , Gätjens-Sanchez Ana M. , Ferrarese Roberto , Platania Leonardo , Doostkam Soroush , Kim Hyunsoo , Nelander Sven , Weyerbrock Astrid , Prinz Marco , Califano Andrea , Iavarone Antonio , Bredel Markus , Carro Maria S.
Published: April 2023

Proliferation, migration and invasion assays in SNB19 cells.
Supplementary Figure Legends from KRAS Activation in Gastric Adenocarcinoma Stimulates Epithelial-to-Mesenchymal Transition to Cancer Stem–Like Cells and Promotes Metastasis
Authors: Yoon Changhwan , Till Jacob , Cho Soo-Jeong , Chang Kevin K. , Lin Jian-xian , Huang Chang-ming , Ryeom Sandra , Yoon Sam S.
Published: April 2023

Supplementary Figure Legends 1-7
Supplementary Table IV from Therapeutic Targeting of CD146/MCAM Reduces Bone Metastasis in Prostate Cancer
Authors: Zoni Eugenio , Astrologo Letizia , Ng Charlotte K.Y. , Piscuoglio Salvatore , Melsen Janine , Grosjean Joël , Klima Irena , Chen Lanpeng , Snaar-Jagalska Ewa B. , Flanagan Kenneth , van der Pluijm Gabri , Kloen Peter , Cecchini Marco G. , Kruithof-de Julio Marianna , Thalmann George N.
Published: April 2023

Enrichement analysis for Hematopoiesis.
Supplementary Table 1 from Aurora Kinase A Promotes AR Degradation via the E3 Ligase CHIP
Authors: Sarkar Sukumar , Brautigan David L. , Larner James M.
Published: April 2023

Summarized data of kinase inhibitor screenings.
supplementary fig s1 from Molecular Effects of Stromal-Selective Targeting by uPAR-Retargeted Oncolytic Virus in Breast Cancer
Authors: Jing Yuqi , Chavez Valery , Ban Yuguang , Acquavella Nicolas , El-Ashry Doraya , Pronin Alexey , Chen Xi , Merchan Jaime R.
Published: April 2023

In situ hybridization for mouse uPAR and MV-N RNA (RNAscope).
Supplementary Documents from Aurora Kinase A Promotes AR Degradation via the E3 Ligase CHIP
Authors: Sarkar Sukumar , Brautigan David L. , Larner James M.
Published: April 2023

Table S1: Summarized data of kinase inhibitor screenings. Figure S1: Aurora A phosphorylates CHIP in Vivo Figure S2: CHIP phosphorylation is independent Cdk(s).
Supplementary Tables 1 - 3 from Novel lncRNA LINC00844 Regulates Prostate Cancer Cell Migration and Invasion through AR Signaling
Authors: Lingadahalli Shreyas , Jadhao Sudhir , Sung Ying Ying , Chen Mi , Hu Lingling , Chen Xin , Cheung Edwin
Published: April 2023

S1. Differentially regulated lncRNAs FDR<0.01 S2. Differetially regulated, androgen regulated lncRNAs S3. ARBS
Supplementary Figure Legend from Loss of Fas Expression and Function Is Coupled with Colon Cancer Resistance to Immune Checkpoint Inhibitor Immunotherapy
Authors: Xiao Wei , Ibrahim Mohammed L. , Redd Priscilla S. , Klement John D. , Lu Chunwan , Yang Dafeng , Savage Natasha M. , Liu Kebin
Published: April 2023

Supplemental Figure Legends 1-5
Figure S3 from Loss of Fas Expression and Function Is Coupled with Colon Cancer Resistance to Immune Checkpoint Inhibitor Immunotherapy
Authors: Xiao Wei , Ibrahim Mohammed L. , Redd Priscilla S. , Klement John D. , Lu Chunwan , Yang Dafeng , Savage Natasha M. , Liu Kebin
Published: April 2023

FasL induces apoptosis to increase the frequency of colon cancer stem cell-like cells in MSS colon cancer cells.
Supplementary Data (Tables S1-S2 and Figures S1-S5) from Reprogramming of Isocitrate Dehydrogenases Expression and Activity by the Androgen Receptor in Prostate Cancer
Authors: Gonthier Kevin , Poluri Raghavendra Tejo Karthik , Weidmann Cindy , Tadros Maude , Audet-Walsh Étienne
Published: April 2023

Supplementary Table 1. Human qRT-PCR primers Supplementary Table 2. Human ChIP-qPCR primers Figure S1. IDH2, IDH3A, IDH3B, and IDH3G are ubiquitously expressed across the human cancer spectrum. Figure S2. Relative mRNA expression of IDH genes in LAPC4 cells following 24h of treatment with 10 nM R1881 (right panel). KLK3 expression is shown as a positive control (left panel). Figure S3. Analysis of AR recruitment to IDH2 (A), IDH3A (B), IDH3B (C), and IDH3G (D) genes following 16h treatment with 10nM R1881. Figure S4. Achilles project results for cancer cell line sensitivity to shRNA-mediated knockdown of IDH1. Figure S5. IDH1 knockdown in PC3 and DU145 AR-negative PCa cells.
Supplementary materials and methods from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary materials and methods for PCR and serum preparation.
Supplementary figures from Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-Based Subtypes
Authors: Zhang Li , MacIsaac Kenzie D. , Zhou Ting , Huang Pei-Yu , Xin Chunlin , Dobson Jason R. , Yu Kun , Chiang Derek Y. , Fan Yue , Pelletier Marc , Wang Yan , Jaeger Savina , Krishnamurthy Radhakrishnan Viveksagar , JeBailey Lellean , Skewes-Cox Peter , Zhang Jing , Fang Wenfeng , Huang Yan , Zhao Hongyun , Zhao Yuanyuan , Li En , Peng Bin , Huang Alan , Dranoff Glenn , Hammerman Peter S. , Engelman Jeffrey , Bitter Hans , Zeng Yi-Xin , Yao Yao
Published: April 2023

Supplementary Figures Figure S1: Subtype identification using random sub-sampling. Figure S2: Subtype robustness. Figure S3: Morphological evaluation of tumors. Figure S4: % Tumor content by subtype. Figure S5: Principle components analysis. Figure S6: Microenvironment signatures. Figure S7: Cytotoxic to T-cell signature ratio and IgD to IgG expression ratio by subtype. Figure S8: Correlation of EBV and tumor gene expression. Figure S9: Mutation and copy number variation for paired and unpaired cohorts. Figure S10: Identification of stromal and intratumoral TILs. Figure S11: Mutation load vs. tumor content.
Supplementary Figures S1 - S2 from Autophagic Flux Is Regulated by Interaction Between the C-terminal Domain of PATCHED1 and ATG101
Authors: Chen Xiaole , Morales-Alcala Cintli C. , Riobo-Del Galdo Natalia A.
Published: April 2023

qPCR data of LC3B and p62 expression; effect of soluble CTD on autophagy markers in HEK 293 cells.
Supplementary Tables 1-3 from Identification of TP53RK-Binding Protein (TPRKB) Dependency in TP53-Deficient Cancers
Authors: Goswami Moloy T. , VanDenBerg Kelly R. , Han Sumin , Wang Lei Lucy , Singh Bhavneet , Weiss Travis , Barlow Myles , Kamberov Steven , Wilder-Romans Kari , Rhodes Daniel R. , Feng Felix Y. , Tomlins Scott A.
Published: April 2023

Supplementary Table 1. Primers and Oligos Sequences Supplementary Table 2. shRNA and siRNA Sequences Supplementary Table 3. Antibody list
Supplementary Figure S1 from HBx-K130M/V131I Promotes Liver Cancer in Transgenic Mice via AKT/FOXO1 Signaling Pathway and Arachidonic Acid Metabolism
Authors: Chiu Amy P. , Tschida Barbara R. , Sham Tung-Ting , Lo Lilian H. , Moriarity Branden S. , Li Xiao-Xiao , Lo Regina C. , Hinton David E. , Rowlands Dewi K. , Chan Chi-On , Mok Daniel K.W. , Largaespada David A. , Warner Nadia , Keng Vincent W.
Published: April 2023

Supplementary Figure S1. In vivo and in vitro experimental approaches.
Table S2 from Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining
Authors: de Boer D. Vicky , Brink Arjen , Buijze Marijke , Stigter-van Walsum Marijke , Hunter Keith D. , Ylstra Bauke , Bloemena Elisabeth , Leemans C. René , Brakenhoff Ruud H.
Published: April 2023

Overview of our patient cohort of which we successfully brought cells in culture. From 32 patients we successfully cultured keratinocytes of 1 till 4 biopsies originating from margin tissue surrounding the tumor, directly after surgery. A previously generated culture, VU-preSCC-M3, was included in this cohort as well (van Zeeburg et al. 2013). Of note, patient #33 was included since we successfully cultured tumor cells, unfortunately the margin cultures failed.
Supplementary Figures S1-S11 from The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment
Authors: Brady Samuel W. , Ma Xiaotu , Bahrami Armita , Satas Gryte , Wu Gang , Newman Scott , Rusch Michael , Putnam Daniel K. , Mulder Heather L. , Yergeau Donald A. , Edmonson Michael N. , Easton John , Alexandrov Ludmil B. , Chen Xiang , Mardis Elaine R. , Wilson Richard K. , Downing James R. , Pappo Alberto S. , Raphael Benjamin J. , Dyer Michael A. , Zhang Jinghui
Published: April 2023

Supplementary Figures S1-S11 show sample histology, quality control data, and additional genomic analysis. S1. Histology of osteosarcoma SJOS001101. S2. Whole-genome sequencing coverage metrics. S3. Deep capture validation coverage metrics. S4. Example genes experiencing copy number alterations. S5. B-allele frequencies confirm homozygous deletions of 3q13.31 and CDKN2A. S6. Identification of cisplatin mutation signature in osteosarcoma. S7. Cisplatin does not induce kataegis. S8. Density plot analysis of SNV clusters reveals unique clones at most sites. S9. SJOS001101 pairwise osteosarcoma sample SNV comparisons reveal cross-seeding. S10. Clonal evolution of SJOS001101 as clarified by MACHINA analysis. S11. Pairwise osteosarcoma sample SNV comparisons in three additional patients.
Figure S4 from Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining
Authors: de Boer D. Vicky , Brink Arjen , Buijze Marijke , Stigter-van Walsum Marijke , Hunter Keith D. , Ylstra Bauke , Bloemena Elisabeth , Leemans C. René , Brakenhoff Ruud H.
Published: April 2023

Supplementary Figure S4: CN profiles of cultures HN539-M2 and HN433-M1. (A) HN539-M2 is one of the cultures with only CNAs and no mutations. Cells of this culture contained a focal loss at chromosome 7q, however targeted sequencing revealed no mutations in any of the genes of our cancer-panel. (B) CN profile of HN433-M1 made at passage 3, with 6 PDs. We also generated a CN profile when the cells reached 30 PDs (Figure 2B). In both profiles a similar gain at chromosome 5q, a loss of chromosome 9p and a gain at the same arm were detected.