bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S1 from Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma
Authors: Lamy Philippe , Nordentoft Iver , Birkenkamp-Demtröder Karin , Thomsen Mathilde Borg Houlberg , Villesen Palle , Vang Søren , Hedegaard Jakob , Borre Michael , Jensen Jørgen Bjerggaard , Høyer Søren , Pedersen Jakob Skou , Ørntoft Torben F. , Dyrskjøt Lars
Published: April 2023

Clinical and histopathological information together with information on exome and RNA sequencing.
Supplementary Figures S1-S19 from Paired Exome Analysis Reveals Clonal Evolution and Potential Therapeutic Targets in Urothelial Carcinoma
Authors: Lamy Philippe , Nordentoft Iver , Birkenkamp-Demtröder Karin , Thomsen Mathilde Borg Houlberg , Villesen Palle , Vang Søren , Hedegaard Jakob , Borre Michael , Jensen Jørgen Bjerggaard , Høyer Søren , Pedersen Jakob Skou , Ørntoft Torben F. , Dyrskjøt Lars
Published: April 2023

Frequently mutated genes (S1); Analysis of differences and changes in mutations types (S2); Mutational signatures based on trinucleotide contexts (S3); Contributions and comparison of most prevalent mutational signatures across Samples (S4); Comparisons of contributions of most prevalent mutational signatures from initial tumor to most recent tumor in NPD and PD patients (S5); Comparison of mutation rate and APOBEC score (S6); APOBEC enzymes expression (S7); Comparison of deleterious mutations in different sub-groups (S8); Disease evolution inferred by phylogenetic tree analysis for patients with two tumors analyzed (S9); Mutational heat maps for patients with three or more tumor samples analyzed (S10); Clonality status of all Cat 1 Tier 0-1 mutations found in NPD patients (S11); Clonality status of all Cat 1 Tier 0-1 mutations found in PD patients (S12); List of genes with their clonality status in all samples from NPD patients (S13); List of genes with their clonality status in all samples from PD patients (S14); Correlation between allele frequencies estimated from exome-seq versus amplicon-seq (S15); Subclonal populations inferred by PyClone in patients with two samples analyzed (S16); Subclonal populations inferred by PyClone in patients with three samples analyzed (S17); Subclonal populations inferred by PyClone in the patient with five samples analyzed (S18); APOBEC enzymes expression in tumor samples from patients with three or more metachronous tumor samples (S19).
Supplementary Figures S1-S2 and Supplementary Tables S1-S2 from Merkel Cell Polyomavirus Small T Antigen Initiates Merkel Cell Carcinoma-like Tumor Development in Mice
Authors: Verhaegen Monique E. , Mangelberger Doris , Harms Paul W. , Eberl Markus , Wilbert Dawn M. , Meireles Julia , Bichakjian Christopher K. , Saunders Thomas L. , Wong Sunny Y. , Dlugosz Andrzej A.
Published: April 2023

Supplementary Figure S1. Transgenic constructs and validation of transgene expression in vivo. Supplementary Figure S2. Paranuclear dot-like expression of K8 and K5 in mouse MCC-like tumors. Supplementary Table S1. Correlation between transgene expression level, based on immunostaining, and phenotype severity. Supplementary Table S2.Primary antibodies and dilutions.
Supplementary Materials and Methods from TWIST1-WDR5-Hottip Regulates Hoxa9 Chromatin to Facilitate Prostate Cancer Metastasis
Authors: Malek Reem , Gajula Rajendra P. , Williams Russell D. , Nghiem Belinda , Simons Brian W. , Nugent Katriana , Wang Hailun , Taparra Kekoa , Lemtiri-Chlieh Ghali , Yoon Arum R. , True Lawrence , An Steven S. , DeWeese Theodore L. , Ross Ashley E. , Schaeffer Edward M. , Pienta Kenneth J. , Hurley Paula J. , Morrissey Colm , Tran Phuoc T.
Published: April 2023

This document contains experimental details for microarray data acquisition and analysis, immunohistochemistry, immunofluorescence, western blotting, migration assay, invasion assay, anoikis assay, soft agar colony formation assay, RNA-immunoprecipitation, protein co-immunoprecipitation, Chromatin immunoprecipitation (ChIP), ChIP-Re-ChIP.
Table S2 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

A panel of 24 small molecule inhibitors known to target epigenetic regulators obtained from The Structure Genomics Consortium
Table S1 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

Probe and primer sequences for 3C
Figure S6 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

Combination of JQ1 and cisplatin treatment in vivo.
Supplementary Table S4 from PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells
Authors: Kaur Amanpreet , Denisova Oxana V. , Qiao Xi , Jumppanen Mikael , Peuhu Emilia , Ahmed Shafiq U. , Raheem Olayinka , Haapasalo Hannu , Eriksson John , Chalmers Anthony J. , Laakkonen Pirjo , Westermarck Jukka
Published: April 2023

List of PME-1 regulated PP2A B-subunits and their known interactor proteins.
Supplementary Table S3 from PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells
Authors: Kaur Amanpreet , Denisova Oxana V. , Qiao Xi , Jumppanen Mikael , Peuhu Emilia , Ahmed Shafiq U. , Raheem Olayinka , Haapasalo Hannu , Eriksson John , Chalmers Anthony J. , Laakkonen Pirjo , Westermarck Jukka
Published: April 2023

Structure-activity relationship (SAR) analysis of STS derivatives to identify active synthetic lethality in PME-1 depleted cells.
Figure S4 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

BRD4 directly targets stem-related genes in ovarian cancer cells, and their expression is suppressed by the BET inhibitor JQ1.
Figure S2 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

JQ1 synergizes with cisplatin and downregulates ALDH1A1.
Figure S1 from BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer
Authors: Yokoyama Yuhki , Zhu Hengrui , Lee Jeong Heon , Kossenkov Andrew V. , Wu Sherry Y. , Wickramasinghe Jayamanna M. , Yin Xiangfan , Palozola Katherine C. , Gardini Alessandro , Showe Louise C. , Zaret Kenneth S. , Liu Qin , Speicher David , Conejo-Garcia Jose R. , Bradner James E. , Zhang Zhiguo , Sood Anil K. , Ordog Tamas , Bitler Benjamin G. , Zhang Rugang
Published: April 2023

BET inhibition reduces ALDH activity and decreases ALDH1A1 expression in ovarian cancer cells.
Supplementary Figure legends from PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells
Authors: Kaur Amanpreet , Denisova Oxana V. , Qiao Xi , Jumppanen Mikael , Peuhu Emilia , Ahmed Shafiq U. , Raheem Olayinka , Haapasalo Hannu , Eriksson John , Chalmers Anthony J. , Laakkonen Pirjo , Westermarck Jukka
Published: April 2023

Supplementary Figure legends
Supplementary figures from Combination Therapy Targeting BCL6 and Phospho-STAT3 Defeats Intratumor Heterogeneity in a Subset of Non–Small Cell Lung Cancers
Authors: Deb Dhruba , Rajaram Satwik , Larsen Jill E. , Dospoy Patrick D. , Marullo Rossella , Li Long Shan , Avila Kimberley , Xue Fengtian , Cerchietti Leandro , Minna John D. , Altschuler Steven J. , Wu Lani F.
Published: April 2023

This file shows all the supplementary figures as follows: Supplementary Figure 1: Clonal variability introduced by the TP53, KRAS, and MYC manipulations Supplementary Figure 2: Quantitation of signaling alterations for beta-CATENIN, P65, FOXO1 and p-ERK1/2 Supplementary Figure 3: Comparison between parental HBEC and HBECPKM cells for their sensitivity to the MEK inhibitor AZD6244 Supplementary Figure 4: Similar distributions of SMAD2/3 signaling with total or phospho antibodies Supplementary Figure 5: Alterations of p-STAT3 signaling in high EGF growth condition Supplementary Figure 6: Identification of lower EGF concentration (<5000 pg/mL) in which both parental HBEC and HBECPKM grow healthy colonies Supplementary Figure 7: Stattic treatment reduces the level of p-STAT3 Supplementary Figure 8: SMAD2/3 signaling alteration is not simply due to change in cell size from parental HBEC to HBECPKM Supplementary Figure 9: siRNA mediated knockdown of BCL6 Supplementary Table 1: signaling readouts of interest for immunofluorescence assay Supplementary Table 2: Primary antibodies for immunoblot Supplementary Table 3: Treatment schedule for H1993 cell line derived subcutaneous xenografts
Supplementary Methods from ATM Deficiency Is Associated with Sensitivity to PARP1- and ATR Inhibitors in Lung Adenocarcinoma
Authors: Schmitt Anna , Knittel Gero , Welcker Daniela , Yang Tsun-Po , George Julie , Nowak Michael , Leeser Uschi , Büttner Reinhard , Perner Sven , Peifer Martin , Reinhardt Hans Christian
Published: April 2023

This file contains a list of additional methods used in this study, e.g. in situ hybridisation, PCR, immunoblotting, apoptotic assay, population doubling, and statistical analysis.
Supplementary Figures from ATM Deficiency Is Associated with Sensitivity to PARP1- and ATR Inhibitors in Lung Adenocarcinoma
Authors: Schmitt Anna , Knittel Gero , Welcker Daniela , Yang Tsun-Po , George Julie , Nowak Michael , Leeser Uschi , Büttner Reinhard , Perner Sven , Peifer Martin , Reinhardt Hans Christian
Published: April 2023

In this file we show additional data which support the main findings in our manuscript, e.g. an overview of all immunofluorescent and histological images, population doubling of the cell lines used, additional in vivo data on etoposide and cisplatin treatment and in vivo data of the p53-proficiet setting.
Supplemental Figures 1-12 from A PET Imaging Strategy to Visualize Activated T Cells in Acute Graft-versus-Host Disease Elicited by Allogenic Hematopoietic Cell Transplant
Authors: Ronald John A. , Kim Byung-Su , Gowrishankar Gayatri , Namavari Mohammad , Alam Israt S. , D'Souza Aloma , Nishikii Hidekazu , Chuang Hui-Yen , Ilovich Ohad , Lin Chih-Feng , Reeves Robert , Shuhendler Adam , Hoehne Aileen , Chan Carmel T. , Baker Jeanette , Yaghoubi Shahriar S. , VanBrocklin Henry F. , Hawkins Randall , Franc Benjamin L. , Jivan Salma , Slater James B. , Verdin Emily F. , Gao Kenneth T. , Benjamin Jonathan , Negrin Robert , Gambhir Sanjiv Sam
Published: April 2023

Supplementary Figure 1 shows [18F]F-AraG Structure and Schematic of AraG Uptake into T Cells Supplementary Figure 2 shows [18F]F-AraG and [3H]F-AraC Uptake and Retention Across Various Immune Cell Lines Supplementary Figure 3 shows AraG Competitive Inhibition of [18F]F-AraG Uptake Across Various Immune Cell Lines Supplementary Figure 4 shows Comparison of [18F]F-AraG and [3H]F-AraC Uptake and Retention Across Various Solid Tumor Cell Lines Supplementary Figure 5 shows Western Blot Analysis of dCK Expression in Wild-type and Mutant CCRF-CEM cells Supplementary Figure 6 shows dGK overexpression in CHO-K1 cells leads to increased [18F]F-AraG uptake and retention Supplementary Figure 7 shows [3H]F-AraC Accumulates in Cells via dCK Activity Supplementary Figure 8 shows Uptake of [18F]F-AraG in Activated Versus Resting Murine T Cells Supplementary Figure 9 shows Isolation and Activation of Primary Human T Cells Supplementary Figure 10 shows Uptake and Retention of [3H]AraG and [3H]F-AraC in Resting and Activated Human Primary T Cells Supplementary Figure 11 shows Evaluation of GFP+ Donor T cells in Spleens and Cervical Lymph Nodes (CLNs) at Day 3 and Day 10 of Acute GVHD Supplementary Figure 12 shows Evaluation of Proliferation of Donor T Cells in Cervical Lymph Nodes
Supplementary Figures S1-S10 from Assessing Immune-Related Adverse Events of Efficacious Combination Immunotherapies in Preclinical Models of Cancer
Authors: Liu Jing , Blake Stephen J. , Harjunpää Heidi , Fairfax Kirsten A. , Yong Michelle C.R. , Allen Stacey , Kohrt Holbrook E. , Takeda Kazuyoshi , Smyth Mark J. , Teng Michele W.L.
Published: April 2023

Kinetics of Treg depletion in tumor-bearing Foxp3-DTR mice (S1); Development of blepharitis in tumor-bearing Foxp3-DTR mice after multiple DT treatment (S2); Prolonged Treg depletion induces severe irAEs in MC38 tumor-bearing mice (S3); Transient Treg depletion or multiple anti-CTLA-4 and anti-PD-1 treatment induce similar biochemical autoimmunity in tumor-bearing mice (S4); Transient Treg depletion of tumor-bearing mice increases the expression of PD-1, TIM-3 and CD137 on T cells from spleen but not tumor (S5); Transient Treg depletion in combination with anti-PD-1, anti-TIM-3 or anti-CD137 can all suppress established 4T1.2 or MC38 tumor growth (S6); Transient Treg depletion in combination with anti-PD-1, anti-TIM-3 or anti-CD137 differentially suppressed established CT26L5 tumor growth (S7); Transient Treg depletion in combination with anti-CD137 in tumor-bearing Foxp3-DTR mice induces severe irAEs (S8); Transient Treg depletion in combination with anti-CD137 increases the proportion of CD8+ T cells in multiple organs of tumor-bearing mice (S9); Transient Treg depletion in combination with anti-CD137 increases inflammatory cytokines in sera of tumor bearing mice (S10).
Supplementary file: Legends of supplementary material from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

This file contains the legends of supplementary figures and tables.
Supplementary Table S2: Table shows the correlation score (r) between allele frequency and gene expression from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

Table shows the correlation score (r) between allele frequency and gene expression in OUH and TCGA cohort
Supplementary Figure S5. Frequency plot of the CNAs of periampullary adenocarcinomas based on site of origin. from The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma
Authors: Sandhu Vandana , Wedge David C. , Bowitz Lothe Inger Marie , Labori Knut Jørgen , Dentro Stefan C. , Buanes Trond , Skrede Martina L. , Dalsgaard Astrid M. , Munthe Else , Myklebost Ola , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Ikdahl Tone , Van Loo Peter , Nord Silje , Kure Elin H.
Published: April 2023

The x-axis represents the genomic position and is divided into 22 facets for 22 chromosomes. The y-axis represents the frequency of chromosomal gain and losses for five subtypes based on site of origin. The number of samples in each subtypes are PDAC: 28, bile duct: 4, ampulla P: 6, ampulla I: 7, duodenum: 9.
Supplementary Materials and Methods from Activation of Wnt/β-Catenin in Ewing Sarcoma Cells Antagonizes EWS/ETS Function and Promotes Phenotypic Transition to More Metastatic Cell States
Authors: Pedersen Elisabeth A. , Menon Rajasree , Bailey Kelly M. , Thomas Dafydd G. , Van Noord Raelene A. , Tran Jenny , Wang Hongwei , Qu Ping Ping , Hoering Antje , Fearon Eric R. , Chugh Rashmi , Lawlor Elizabeth R.
Published: April 2023

Detailed methods and reagents lists for lentiviral transduction, AQUA, in situ hybridization and microscopy.
Supplemental Table S2. Primers from Activation of Wnt/β-Catenin in Ewing Sarcoma Cells Antagonizes EWS/ETS Function and Promotes Phenotypic Transition to More Metastatic Cell States
Authors: Pedersen Elisabeth A. , Menon Rajasree , Bailey Kelly M. , Thomas Dafydd G. , Van Noord Raelene A. , Tran Jenny , Wang Hongwei , Qu Ping Ping , Hoering Antje , Fearon Eric R. , Chugh Rashmi , Lawlor Elizabeth R.
Published: April 2023

Supplemental table S2. qRT-PCR primer sequences.
Supplementary tables S1-S7 from Cellular Prion Protein PrPC and Ecto-5′-Nucleotidase Are Markers of the Cellular Stress Response to Aneuploidy
Authors: Domingues Patrícia H. , Nanduri Lalitha S.Y. , Seget Katarzyna , Venkateswaran Sharavan V. , Agorku David , Viganó Cristina , von Schubert Conrad , Nigg Erich A. , Swanton Charles , Sotillo Rocío , Bosio Andreas , Storchová Zuzana , Hardt Olaf
Published: April 2023

Supplementary Tables S1-S3. Detailed description of antibodies used for the cell surface screenings performed with the initial 300 antibody high-throughput screening panel (S1), the 49-marker validation screening panel (S2), and the 36-marker mouse tumor screening panel (S3). Supplementary Table S4. Mean fluorescence intensity and percentage of positive cells for each surface marker staining across the cell lines initially analyzed with the MACS® Marker Screening panel. Supplementary Table S5. Mean fluorescence intensity and percentage of positive cells for the 49 surface markers selected for validation across all the cell lines, grouped according to the karyotype and normalized with the corresponding parental cells. Supplementary Tables S6. Aneuploid-to-diploid ratios obtained from previously published proteome data (7) for the proteins analyzed in this study. Supplementary Table S7. Immunophenotypic characterization of mouse models of aneuploidy (breast tumors, n=7) with a 29-marker screening panel, as well as normal mammary gland (control; n=2).
Supplementary figure 9 from The WASF3–NCKAP1–CYFIP1 Complex Is Essential for Breast Cancer Metastasis
Authors: Teng Yong , Qin Haiyan , Bahassan Abdulaziz , Bendzunas N. George , Kennedy Eileen J. , Cowell John K.
Published: April 2023

Effects of WANT3 on prostate and colon cancer cells
Supplementary Figure S5 from Cellular Prion Protein PrPC and Ecto-5′-Nucleotidase Are Markers of the Cellular Stress Response to Aneuploidy
Authors: Domingues Patrícia H. , Nanduri Lalitha S.Y. , Seget Katarzyna , Venkateswaran Sharavan V. , Agorku David , Viganó Cristina , von Schubert Conrad , Nigg Erich A. , Swanton Charles , Sotillo Rocío , Bosio Andreas , Storchová Zuzana , Hardt Olaf
Published: April 2023

Effect of oxidative stress on CD73, CD230, CD47, CD49b, CD55 and CD95 expression in parental and aneuploid cell lines. Ratios of H2O2-treated cells (100µM 48h) and control cells are shown for the mean fluorescence intensity values (black bars) and percentage of positive cells (grey bars).
Supplementary figure 8 from The WASF3–NCKAP1–CYFIP1 Complex Is Essential for Breast Cancer Metastasis
Authors: Teng Yong , Qin Haiyan , Bahassan Abdulaziz , Bendzunas N. George , Kennedy Eileen J. , Cowell John K.
Published: April 2023

western blot showing dose response of WANT3 suppression of WASF3 protein levels
Supplementary Figure S4 from Cellular Prion Protein PrPC and Ecto-5′-Nucleotidase Are Markers of the Cellular Stress Response to Aneuploidy
Authors: Domingues Patrícia H. , Nanduri Lalitha S.Y. , Seget Katarzyna , Venkateswaran Sharavan V. , Agorku David , Viganó Cristina , von Schubert Conrad , Nigg Erich A. , Swanton Charles , Sotillo Rocío , Bosio Andreas , Storchová Zuzana , Hardt Olaf
Published: April 2023

Effect of ER stress on CD73, CD230, CD47, CD49b, CD55 and CD95 expression in parental and aneuploid cell lines. Ratios of cells treated with multiple ER stress inducers - glucose-deprivation (black bars), brefeldin A (BFA; red bars) 1ug/mL, thapsigargin (Thaps; blue bars) 0.25ug/ml or tunicamycin (TuniM; green bars) 2.5ug/mL for 48h - and control cells are shown for the mean fluorescence intensity values (top graph) and percentage of positive cells (bottom graph).
Supplementary Figure S3 from Cellular Prion Protein PrPC and Ecto-5′-Nucleotidase Are Markers of the Cellular Stress Response to Aneuploidy
Authors: Domingues Patrícia H. , Nanduri Lalitha S.Y. , Seget Katarzyna , Venkateswaran Sharavan V. , Agorku David , Viganó Cristina , von Schubert Conrad , Nigg Erich A. , Swanton Charles , Sotillo Rocío , Bosio Andreas , Storchová Zuzana , Hardt Olaf
Published: April 2023

Knockdown efficiency of the candidates by siRNA and its effect on cell proliferation and cell death. (A) Expression intensities of CD73, CD230, CD47, CD49b, CD55 and CD95 after knockdown using siRNAs (red lines), as well as both not transfected (black line) and non-targeting siRNA (grey line) controls, in HCT116 parental and HPT1 post-tetraploid cells, analyzed at the cell surface level by flow cytometry. (B) Effect of CD73, CD230, CD47 and CD49b siRNA knockdown on cell death, analyzed by % of AnnexinV+ cells. Representative AnnexinV-A vs DAPI-A dot plots are shown for both HCT116 parental and HPT1 post-tetraploid cells. (C) Effect on cell proliferation evaluated by % of cells which incorporated EdU after siRNA knockdown in comparison to not transfected and non-targeting siRNA controls; bar graphs represent the mean �U+ cells (and standard deviations) for three replicates on both HCT116 parental (black bars) and HPT1 (grey bars) cells (no statistically significant differences).
Supplementary Figure S2 from Cellular Prion Protein PrPC and Ecto-5′-Nucleotidase Are Markers of the Cellular Stress Response to Aneuploidy
Authors: Domingues Patrícia H. , Nanduri Lalitha S.Y. , Seget Katarzyna , Venkateswaran Sharavan V. , Agorku David , Viganó Cristina , von Schubert Conrad , Nigg Erich A. , Swanton Charles , Sotillo Rocío , Bosio Andreas , Storchová Zuzana , Hardt Olaf
Published: April 2023

Hierarchical clustering of cell surface markers in HCT116 and RPE1 trisomic cell lines. The expression of 49 cell surface markers (each column represents a single protein) in tri- and tetrasomic clones derived from HCT116 (A) and RPE1 (B) parental cell lines - each row represents a different clone, namely HCT116 3/3 (trisomy 3 clones 11 and 13), 5/3 (trisomy 5), 8/3 (trisomy 8 clones 3, 5 and 7), 13/3 (trisomy 13 clones 2 and 3), 18/3 (trisomy 18 clones 1 and 2), 21/3 (trisomy 21 clones 1 and 3), 5/3 3/3 (trisomy 5 and 3), 5/4 (tetrasomy 5) and RPE1 3/3 (trisomy 3 clone 1 and 2), 5/3 (trisomy 5 clone 3 and 7), 12/3 (trisomy 12), 5/3 12/3 (trisomy 5 and 12), 21/3 (trisomy 21) - are shown in a matrix format. The values were normalized to the corresponding parental cell line and are represented by a color scale where red and green colors indicate values of increased- and decreased-expression, respectively.
Supplementary figure 5 from The WASF3–NCKAP1–CYFIP1 Complex Is Essential for Breast Cancer Metastasis
Authors: Teng Yong , Qin Haiyan , Bahassan Abdulaziz , Bendzunas N. George , Kennedy Eileen J. , Cowell John K.
Published: April 2023

western blot showing destabilization of WASF3 complex following knockdown of member proteins
Supplementary figure 3 from The WASF3–NCKAP1–CYFIP1 Complex Is Essential for Breast Cancer Metastasis
Authors: Teng Yong , Qin Haiyan , Bahassan Abdulaziz , Bendzunas N. George , Kennedy Eileen J. , Cowell John K.
Published: April 2023

proliferation rate in NCKAP1 knockdown cells
Supplementary Methods from Ubiquitous Release of Exosomal Tumor Suppressor miR-6126 from Ovarian Cancer Cells
Authors: Kanlikilicer Pinar , Rashed Mohammed H. , Bayraktar Recep , Mitra Rahul , Ivan Cristina , Aslan Burcu , Zhang Xinna , Filant Justyna , Silva Andreia M. , Rodriguez-Aguayo Cristian , Bayraktar Emine , Pichler Martin , Ozpolat Bulent , Calin George A. , Sood Anil K. , Lopez-Berestein Gabriel
Published: April 2023

Supplementary Methods includes experimental details on western blotting, invasion, wound healing, tube formation, EdU cell proliferation assays, quantitativce RT-PCR, luciferase reporter assay, gene expression analysis and Ingenuity Pathway Analysis.
Legends from BTK Modulates p53 Activity to Enhance Apoptotic and Senescent Responses
Authors: Althubiti Mohammad , Rada Miran , Samuel Jesvin , Escorsa Josep M. , Najeeb Hishyar , Lee Koon-Guan , Lam Kong-Peng , Jones George D.D. , Barlev Nickolai A. , Macip Salvador
Published: April 2023

Legends for supplementary figures
Figure S5 from Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand
Published: April 2023

Analysis of MGLL and AT1R levels
Figure S4 from Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand
Published: April 2023

Quantification of Western and IHC images
Figure S2 from BTK Modulates p53 Activity to Enhance Apoptotic and Senescent Responses
Authors: Althubiti Mohammad , Rada Miran , Samuel Jesvin , Escorsa Josep M. , Najeeb Hishyar , Lee Koon-Guan , Lam Kong-Peng , Jones George D.D. , Barlev Nickolai A. , Macip Salvador
Published: April 2023

Supplementary Figure 2. p53 phosphorylation.
Table S1. Antibody Array Key from CCL2 Produced by the Glioma Microenvironment Is Essential for the Recruitment of Regulatory T Cells and Myeloid-Derived Suppressor Cells
Authors: Chang Alan L. , Miska Jason , Wainwright Derek A. , Dey Mahua , Rivetta Claudia V. , Yu Dou , Kanojia Deepak , Pituch Katarzyna C. , Qiao Jian , Pytel Peter , Han Yu , Wu Meijing , Zhang Lingjiao , Horbinski Craig M. , Ahmed Atique U. , Lesniak Maciej S.
Published: April 2023

Antibody Array Key (RayBiotech Cat# AAM-CYT-6, related to Figure 3.
Figure S1 from Oncogenic Role of SND1 in Development and Progression of Hepatocellular Carcinoma
Authors: Jariwala Nidhi , Rajasekaran Devaraja , Mendoza Rachel G. , Shen Xue-Ning , Siddiq Ayesha , Akiel Maaged A. , Robertson Chadia L. , Subler Mark A. , Windle Jolene J. , Fisher Paul B. , Sanyal Arun J. , Sarkar Devanand
Published: April 2023

Generation and characterization of Alb/SND1 mouse
Supplemental Methods from SIRT2 Deacetylates and Inhibits the Peroxidase Activity of Peroxiredoxin-1 to Sensitize Breast Cancer Cells to Oxidant Stress-Inducing Agents
Authors: Fiskus Warren , Coothankandaswamy Veena , Chen Jianguang , Ma Hongwei , Ha Kyungsoo , Saenz Dyana T. , Krieger Stephanie S. , Mill Christopher P. , Sun Baohua , Huang Peng , Mumm Jeffrey S. , Melnick Ari M. , Bhalla Kapil N.
Published: April 2023

Expanded, detailed methods and detailed reagent descriptions
Supplemental Figure Legends from SIRT2 Deacetylates and Inhibits the Peroxidase Activity of Peroxiredoxin-1 to Sensitize Breast Cancer Cells to Oxidant Stress-Inducing Agents
Authors: Fiskus Warren , Coothankandaswamy Veena , Chen Jianguang , Ma Hongwei , Ha Kyungsoo , Saenz Dyana T. , Krieger Stephanie S. , Mill Christopher P. , Sun Baohua , Huang Peng , Mumm Jeffrey S. , Melnick Ari M. , Bhalla Kapil N.
Published: April 2023

Figure legends for Supplemental Data
Figure S3. Gating strategy for T cell and myeloid flow cytometric analysis of brain tumor leukocytes. from CCL2 Produced by the Glioma Microenvironment Is Essential for the Recruitment of Regulatory T Cells and Myeloid-Derived Suppressor Cells
Authors: Chang Alan L. , Miska Jason , Wainwright Derek A. , Dey Mahua , Rivetta Claudia V. , Yu Dou , Kanojia Deepak , Pituch Katarzyna C. , Qiao Jian , Pytel Peter , Han Yu , Wu Meijing , Zhang Lingjiao , Horbinski Craig M. , Ahmed Atique U. , Lesniak Maciej S.
Published: April 2023

(A) CCR4 and CCR2 expression on CD4+Foxp3- conventional CD4 T cells, CD4+Foxp3+ Tregs, and CD8+ T cells across various tissues at 1 week post-GL261 implantation. (B) Gating strategy for quantification of myeloid cells in brains of PBS-injected or GL261-implanted mice at 1-week post-intracranial implantation. Data are representative of at least 4 independent experiments.
Supplementary Table S9 from JARID1B Enables Transit between Distinct States of the Stem-like Cell Population in Oral Cancers
Authors: Facompre Nicole D. , Harmeyer Kayla M. , Sole Xavier , Kabraji Sheheryar , Belden Zachary , Sahu Varun , Whelan Kelly , Tanaka Koji , Weinstein Gregory S. , Montone Kathleen T. , Roesch Alexander , Gimotty Phyllis A. , Herlyn Meenhard , Rustgi Anil K. , Nakagawa Hiroshi , Ramaswamy Sridhar , Basu Devraj
Published: April 2023

Top (most significant) 200 up-regulated gene sets enriched in JARID1Bhigh LNT14 cells vs. bulk population.
Supplementary Table S7 from JARID1B Enables Transit between Distinct States of the Stem-like Cell Population in Oral Cancers
Authors: Facompre Nicole D. , Harmeyer Kayla M. , Sole Xavier , Kabraji Sheheryar , Belden Zachary , Sahu Varun , Whelan Kelly , Tanaka Koji , Weinstein Gregory S. , Montone Kathleen T. , Roesch Alexander , Gimotty Phyllis A. , Herlyn Meenhard , Rustgi Anil K. , Nakagawa Hiroshi , Ramaswamy Sridhar , Basu Devraj
Published: April 2023

Differentially expressed genes in JARID1Bhigh vs. G0-like LNT14 cells.
Figure S3 from The Damaging Effect of Passenger Mutations on Cancer Progression
Authors: McFarland Christopher D. , Yaglom Julia A. , Wojtkowiak Jonathan W. , Scott Jacob G. , Morse David L. , Sherman Michael Y. , Mirny Leonid A.
Published: April 2023

Figure S3 - Regularization constraint for LASSO linear model of cell fitness in experimental cell lines and human breast cancers.
Figure S1 from The Damaging Effect of Passenger Mutations on Cancer Progression
Authors: McFarland Christopher D. , Yaglom Julia A. , Wojtkowiak Jonathan W. , Scott Jacob G. , Morse David L. , Sherman Michael Y. , Mirny Leonid A.
Published: April 2023

Figure S1- Overview of Genotyping Approach and data
Supplementary tables S1, S2, S3, and S4 from Identification of Novel Breast Cancer Risk Loci
Authors: Chan Claire Hian Tzer , Munusamy Prabhakaran , Loke Sau Yeen , Koh Geok Ling , Wong Edward Sern Yuen , Law Hai Yang , Yoon Chui Sheun , Tan Min-Han , Yap Yoon Sim , Ang Peter , Lee Ann Siew Gek
Published: April 2023

Supplementary data contains list of genes and SNP details
Supplementary Figure 7 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 7 shows Epithelial and Mesenchymal cells in mixed tumors before and after immunotherapy
Supplementary Figure 6 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 6 shows the ability of mesenchymal cells to protect epithelial cells from immune attack.
Supplementary Figure 5 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 5 shows activation of an EMT leads to an immunosuppressive phenotype.
Supplementary Figure 4 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 4 shows differential expression of molecules associated with immune-evasion and immune-suppression by epithelial and mesenchymal cells
Figure S1 from Oncolytic Adenovirus and Tumor-Targeting Immune Modulatory Therapy Improve Autologous Cancer Vaccination
Authors: Jiang Hong , Rivera-Molina Yisel , Gomez-Manzano Candelaria , Clise-Dwyer Karen , Bover Laura , Vence Luis M. , Yuan Ying , Lang Frederick F. , Toniatti Carlo , Hossain Mohammad B. , Fueyo Juan
Published: April 2023

Expression of mOX40L by Delta-24-RGDOX
Supplementary Figure 3 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 3 shows immunosuppressive cells in tumors arising from Snail+ cells relative to epithelial Slug+ cells
Supplementary Figure 1 from Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas
Authors: Dongre Anushka , Rashidian Mohammad , Reinhardt Ferenc , Bagnato Aaron , Keckesova Zuzana , Ploegh Hidde L. , Weinberg Robert A.
Published: April 2023

Supplementary Figure 1 shows enrichment of immunosuppressive cells in tumors arising from mesenchymal cell lines
Supplementary Tables S1-S2 from Adaptation to TKI Treatment Reactivates ERK Signaling in Tyrosine Kinase–Driven Leukemias and Other Malignancies
Authors: Bruner J. Kyle , Ma Hayley S. , Li Li , Qin Alice Can Ran , Rudek Michelle A. , Jones Richard J. , Levis Mark J. , Pratz Keith W. , Pratilas Christine A. , Small Donald
Published: April 2023

Table S1: AML Patient Characteristics Table S2: Plasma sample characteristics
Supplemental Figures from Arl13b Promotes Gastric Tumorigenesis by Regulating Smo Trafficking and Activation of the Hedgehog Signaling Pathway
Authors: Shao Jia , Xu Linlin , Chen Limin , Lu Quqin , Xie Xinsheng , Shi Wei , Xiong Huanting , Shi Chao , Huang Xuan , Mei Jinhong , Rao Hai , Lu Hua , Lu Nonghua , Luo Shiwen
Published: April 2023

IMPDH inhibitor MPA reduces the interaction of Arl13b and Smo. Arl13b regulates activity of Smo. Arl13b regulates Hh signaling activity. Knockdown of Arl13b inhibits the proliferation, migration and invasion of gastric cancer cells. Overexpression of Arl13b promotes the proliferation, migration and invasion of gastric cancer cells. Knockdown of Arl13b inhibits the growth of SGC7901 cells in vivo. Anti-Smo and Anti-Arl13b antibodies effectively and specifically recognize the indicated proteins. Arl13b expression at RNA level is elevated in gastric cancer tissues.
Supplementary Figures from MCPIP1 Downregulation in Clear Cell Renal Cell Carcinoma Promotes Vascularization and Metastatic Progression
Authors: Marona Paulina , Górka Judyta , Mazurek Zofia , Wilk Waclaw , Rys Janusz , Majka Marcin , Jura Jolanta , Miekus Katarzyna
Published: April 2023

Supplementary Figure S1. Downregulation level of MCPIP1 using siRNA or shRNA. Supplementary Figure S2. Effect of MCPIP1 downregulation level on tutor growth. Supplementary Figure S3. MCPIP1 upregulation in Caki-1 and Caki-2 cell lines and tutor growth. Supplementary Figure S4. Impact of MCPIP1 level in ccRCC cells on protein level and phosphorylation of VE-cadherin. Supplementary Figure S5. MCPIP1 overexpression effect on SDF-1/CXCR4 axis in ccRCC cell lines. Supplementary Figure S6. MCPIP1 downregulation induces EMT in ccRCC.
Supplementary Table 1 from PHGDH as a Key Enzyme for Serine Biosynthesis in HIF2α-Targeting Therapy for Renal Cell Carcinoma
Authors: Yoshino Hirofumi , Nohata Nijiro , Miyamoto Kazutaka , Yonemori Masaya , Sakaguchi Takashi , Sugita Satoshi , Itesako Toshihiko , Kofuji Satoshi , Nakagawa Masayuki , Dahiya Rajvir , Enokida Hideki
Published: April 2023

Summary of Hazard Ratios in ccRCC
Source code for splice variant algorithm from A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers
Authors: Guo Theresa , Sakai Akihiro , Afsari Bahman , Considine Michael , Danilova Ludmila , Favorov Alexander V. , Yegnasubramanian Srinivasan , Kelley Dylan Z. , Flam Emily , Ha Patrick K. , Khan Zubair , Wheelan Sarah J. , Gutkind J. Silvio , Fertig Elana J. , Gaykalova Daria A. , Califano Joseph
Published: April 2023

R code for splice variant analysis and outlier statistics for identification of significant splice variants
Figure S4 from PHGDH as a Key Enzyme for Serine Biosynthesis in HIF2α-Targeting Therapy for Renal Cell Carcinoma
Authors: Yoshino Hirofumi , Nohata Nijiro , Miyamoto Kazutaka , Yonemori Masaya , Sakaguchi Takashi , Sugita Satoshi , Itesako Toshihiko , Kofuji Satoshi , Nakagawa Masayuki , Dahiya Rajvir , Enokida Hideki
Published: April 2023

PHGDH
Cell line authentication SCC61 from A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers
Authors: Guo Theresa , Sakai Akihiro , Afsari Bahman , Considine Michael , Danilova Ludmila , Favorov Alexander V. , Yegnasubramanian Srinivasan , Kelley Dylan Z. , Flam Emily , Ha Patrick K. , Khan Zubair , Wheelan Sarah J. , Gutkind J. Silvio , Fertig Elana J. , Gaykalova Daria A. , Califano Joseph
Published: April 2023

Cell line authentication for SCC 61
Figure S3 from Chromatin-Associated Protein SIN3B Prevents Prostate Cancer Progression by Inducing Senescence
Authors: Bainor Anthony J. , Deng Fang-Ming , Wang Yu , Lee Peng , Cantor David J. , Logan Susan K. , David Gregory
Published: April 2023

SIN3B protects against loss-of-PTEN-induced proliferation. KI67 staining using the dorsolateral lobe of prostates taken from 6- and 12-month-old mice.
Figure S2 from Chromatin-Associated Protein SIN3B Prevents Prostate Cancer Progression by Inducing Senescence
Authors: Bainor Anthony J. , Deng Fang-Ming , Wang Yu , Lee Peng , Cantor David J. , Logan Susan K. , David Gregory
Published: April 2023

Images of 12-month-old prostates from each genotype before removal from the mouse. Sin3bpc-/- Ptenpc-/- tumors originate from the prostate epithelium as evidenced by their positive staining for both AR and CK18.
Supplementary Figures from EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
Authors: Etemadmoghadam Dariush , Azar Walid J. , Lei Ying , Moujaber Tania , Garsed Dale W. , Kennedy Catherine J. , Fereday Sian , Mitchell Chris , Chiew Yoke-Eng , Hendley Joy , Sharma Raghwa , Harnett Paul R. , Li Jason , Christie Elizabeth L. , Patch Ann-Marie , George Joshy , Au-Yeung George , Mir Arnau Gisela , Holloway Timothy P. , Semple Timothy , Pearson John V. , Waddell Nicola , Grimmond Sean M. , Köbel Martin , Rizos Helen , Lomakin Ivan B. , Bowtell David D.L. , deFazio Anna
Published: April 2023

Supplementary Figure S1. Representative hematoxylin and eosin stained sections from sequenced LGSC; Supplementary Figure S2. Age distribution analysis of patients from the Australian Ovarian Cancer Study. Includes patients with advanced stage, serous epithelial ovarian cancer (n = 684); Supplementary Figure S3. RAS pathway mutations in LGSC; Supplementary Figure S4. Verification of EIF1AX mutations; Supplementary Figure S5. Characterization of the AOCS2 cell line; Supplementary Figure S6. Functional effect of EIF1AX mutations and gene suppression in a LGSC cell line; Supplementary Figure S7. (a) EIF1AX and NRAS function in the mTOR and RAS/ERK signaling pathways to regulate protein translation, cell proliferation and cell survival
Figure S2 from ATM Deficiency Generating Genomic Instability Sensitizes Pancreatic Ductal Adenocarcinoma Cells to Therapy-Induced DNA Damage
Authors: Perkhofer Lukas , Schmitt Anna , Romero Carrasco Maria Carolina , Ihle Michaela , Hampp Stephanie , Ruess Dietrich Alexander , Hessmann Elisabeth , Russell Ronan , Lechel André , Azoitei Ninel , Lin Qiong , Liebau Stefan , Hohwieler Meike , Bohnenberger Hanibal , Lesina Marina , Algül Hana , Gieldon Laura , Schröck Evelin , Gaedcke Jochen , Wagner Martin , Wiesmüller Lisa , Sipos Bence , Seufferlein Thomas , Reinhardt Hans Christian , Frappart Pierre-Olivier , Kleger Alexander
Published: April 2023

Tumour growth upon Olaparib and Gemcitabine Treatment in Allografts model
Supplementary Figure legend from ETV1-Positive Cells Give Rise to BRAFV600E-Mutant Gastrointestinal Stromal Tumors
Authors: Ran Leili , Murphy Devan , Sher Jessica , Cao Zhen , Wang Shangqian , Walczak Edward , Guan Youxin , Xie Yuanyuan , Shukla Shipra , Zhan Yu , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

Supplementary Figure legend
Figure S4 from ETV1-Positive Cells Give Rise to BRAFV600E-Mutant Gastrointestinal Stromal Tumors
Authors: Ran Leili , Murphy Devan , Sher Jessica , Cao Zhen , Wang Shangqian , Walczak Edward , Guan Youxin , Xie Yuanyuan , Shukla Shipra , Zhan Yu , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

Combination of homozygous BrafV600E activation and Trp53 loss induced dramatic ICC hyperplasia in stomach, cecum and large intestine, but not in small intestine.
Table S4 from Oncogenic RAS Regulates Long Noncoding RNA Orilnc1 in Human Cancer
Authors: Zhang Dongmei , Zhang Gao , Hu Xiaowen , Wu Lawrence , Feng Yi , He Sidan , Zhang Youyou , Hu Zhongyi , Yang Lu , Tian Tian , Xu Weiting , Wei Zhi , Lu Yiling , Flaherty Keith T. , Zhong Xiaomin , Mills Gordon B. , Gimotty Phyllis A. , Xu Xiaowei , Herlyn Meenhard , Zhang Lin
Published: April 2023

Table S4. The protein expression that was analyzed by a RPPA assay
Figure S2 from ETV1-Positive Cells Give Rise to BRAFV600E-Mutant Gastrointestinal Stromal Tumors
Authors: Ran Leili , Murphy Devan , Sher Jessica , Cao Zhen , Wang Shangqian , Walczak Edward , Guan Youxin , Xie Yuanyuan , Shukla Shipra , Zhan Yu , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

BrafV600E activation induced hyperplasias in stomach and cecum, but not in small intestine.
Supplemental Figure 5 from Enhanced Therapeutic Efficacy and Memory of Tumor-Specific CD8 T Cells by Ex Vivo PI3K-δ Inhibition
Authors: Abu Eid Rasha , Ahmad Shamim , Lin Yuan , Webb Mason , Berrong Zuzana , Shrimali Rajeev , Kumai Takumi , Ananth Sudha , Rodriguez Paulo C. , Celis Esteban , Janik John , Mkrtichyan Mikayel , Khleif Samir N.
Published: April 2023

PI3K-delta controls the differentiation of CD8 T-cells through the downstream Akt1 and Akt2
Supplemental Fig. 3 from Enhanced Therapeutic Efficacy and Memory of Tumor-Specific CD8 T Cells by Ex Vivo PI3K-δ Inhibition
Authors: Abu Eid Rasha , Ahmad Shamim , Lin Yuan , Webb Mason , Berrong Zuzana , Shrimali Rajeev , Kumai Takumi , Ananth Sudha , Rodriguez Paulo C. , Celis Esteban , Janik John , Mkrtichyan Mikayel , Khleif Samir N.
Published: April 2023

PI3K-delta KD in murine cells and PI3K-delta inhibition in human cell
Supplementary Methods from Modeling Cytostatic and Cytotoxic Responses to New Treatment Regimens for Ovarian Cancer
Authors: Falcetta Francesca , Bizzaro Francesca , D'Agostini Elisa , Bani Maria Rosa , Giavazzi Raffaella , Ubezio Paolo
Published: April 2023

A. Cell-cycle based model of proliferation - untreated conditions. B. Modeling proliferation during/after treatment. C. Optimization and software. - References
Supplementary Methods, Supplementary Figures 1 through 6, and Supplementary Table 1 from CIB2 Negatively Regulates Oncogenic Signaling in Ovarian Cancer via Sphingosine Kinase 1
Authors: Zhu Wenying , Jarman Kate E. , Lokman Noor A. , Neubauer Heidi A. , Davies Lorena T. , Gliddon Briony L. , Taing Houng , Moretti Paul A.B. , Oehler Martin K. , Pitman Melissa R. , Pitson Stuart M.
Published: April 2023

Supplementary Methods. Supplementary Figure S1. Validation of the physiological interaction between CIB2 and SK1 using proximity ligation assays with different antibody combinations. Supplementary Figure S2. N-myristoylation of CIB2 does not affect its interaction with SK1. Supplementary Figure S3. Over-expression of CIB2 sensitises cells to TNFα-induced caspase 3/7 activation. Supplementary Figure S4. Stratification of CIB2 gene expression in ovarian cancer tissues. Supplementary Figure S5. Gene expression of SK1 in ovarian tissues. Supplementary Figure S6. CIB2 inhibits neoplastic growth and cell migration of OV90 ovarian cancer cells. Supplementary Table S1. Clinical characteristics of the ovarian cancer patient cohort from which ovirian cancer cells were derived.
Figure S2 from Modeling Cytostatic and Cytotoxic Responses to New Treatment Regimens for Ovarian Cancer
Authors: Falcetta Francesca , Bizzaro Francesca , D'Agostini Elisa , Bani Maria Rosa , Giavazzi Raffaella , Ubezio Paolo
Published: April 2023

Simulations of three PTX administrations with different intervals
Supplemetary data from STING Activation Reverses Lymphoma-Mediated Resistance to Antibody Immunotherapy
Authors: Dahal Lekh N. , Dou Lang , Hussain Khiyam , Liu Rena , Earley Alexander , Cox Kerry L. , Murinello Salome , Tracy Ian , Forconi Francesco , Steele Andrew J. , Duriez Patrick J. , Gomez-Nicola Diego , Teeling Jessica L. , Glennie Martin J. , Cragg Mark S. , Beers Stephen A.
Published: April 2023

This file contains supplementary data showing phenotypic/cytokine/chemokine changes in immune cell population following stimulation/tumour inoculation. The data also demonstrate that monocyte and neutrophil are not required for mAb mediated deletion of target cell in adoptive transfer model.
Supp Figure 5 from HIF-2α Promotes Dissemination of Plasma Cells in Multiple Myeloma by Regulating CXCL12/CXCR4 and CCR1
Authors: Vandyke Kate , Zeissig Mara N. , Hewett Duncan R. , Martin Sally K. , Mrozik Krzysztof M. , Cheong Chee Man , Diamond Peter , To L. Bik , Gronthos Stan , Peet Daniel J. , Croucher Peter I. , Zannettino Andrew C.W.
Published: April 2023

Supp. Figure 5. Cell surface expression of CXCR4 and CCR1 in newly diagnosed MM patients
Supp Figure 4 from HIF-2α Promotes Dissemination of Plasma Cells in Multiple Myeloma by Regulating CXCL12/CXCR4 and CCR1
Authors: Vandyke Kate , Zeissig Mara N. , Hewett Duncan R. , Martin Sally K. , Mrozik Krzysztof M. , Cheong Chee Man , Diamond Peter , To L. Bik , Gronthos Stan , Peet Daniel J. , Croucher Peter I. , Zannettino Andrew C.W.
Published: April 2023

Supp. Figure 4. CXCL12 does not inhibit response to CCL3 in human MM cell lines
Supplementary Figure 4 from Distinct Roles of HES1 in Normal Stem Cells and Tumor Stem-like Cells of the Intestine
Authors: Goto Norihiro , Ueo Taro , Fukuda Akihisa , Kawada Kenji , Sakai Yoshiharu , Miyoshi Hiroyuki , Taketo Makoto Mark , Chiba Tsutomu , Seno Hiroshi
Published: April 2023

LacZ staining in Lgr5CreERT2/+; Hes1+/+; ApcMin/+; Rosa26LacZ/+ control mice and qRT-PCR of Hes1-deleted Lgr5+ NSCs.
Supp Figure 3 from HIF-2α Promotes Dissemination of Plasma Cells in Multiple Myeloma by Regulating CXCL12/CXCR4 and CCR1
Authors: Vandyke Kate , Zeissig Mara N. , Hewett Duncan R. , Martin Sally K. , Mrozik Krzysztof M. , Cheong Chee Man , Diamond Peter , To L. Bik , Gronthos Stan , Peet Daniel J. , Croucher Peter I. , Zannettino Andrew C.W.
Published: April 2023

Supp. Figure 3. CCR1 expression is upregulated by hypoxia in human MM cell lines