bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figures 1-4 from The ALK Inhibitor Ceritinib Overcomes Crizotinib Resistance in Non–Small Cell Lung Cancer
Authors: Friboulet Luc , Li Nanxin , Katayama Ryohei , Lee Christian C. , Gainor Justin F. , Crystal Adam S. , Michellys Pierre-Yves , Awad Mark M. , Yanagitani Noriko , Kim Sungjoon , Pferdekamper AnneMarie C. , Li Jie , Kasibhatla Shailaja , Sun Frank , Sun Xiuying , Hua Su , McNamara Peter , Mahmood Sidra , Lockerman Elizabeth L. , Fujita Naoya , Nishio Makoto , Harris Jennifer L. , Shaw Alice T. , Engelman Jeffrey A.
Published: April 2023

PDF file 135K, Figure S1 contains data about Ceritinib specificity and potency on crizotinib na?ve EML4-ALK wild-type cells. Figure S2 contains the Cell survival curves of H3122 CR1, MGH021-4 and MGH045 cells following treatment with Crizotinib or ceritinib corresponding to Fig2A. Figure S3 contains the Cell survival curves of Ba/F3 cells following treatment with Crizotinib or ceritinib corresponding to Fig4A. Figure S4 contains tumor growth curves corresponding to the Development of crizotinib resistant H2228 xenograft tumor models used in Fig 5A-D
Supplementary Figure 1 from l-2-Hydroxyglutarate: An Epigenetic Modifier and Putative Oncometabolite in Renal Cancer
Authors: Shim Eun-Hee , Livi Carolina B. , Rakheja Dinesh , Tan Jubilee , Benson Daniel , Parekh Vishwas , Kho Eun-Young , Ghosh Arindam P. , Kirkman Richard , Velu Sadanan , Dutta Shilpa , Chenna Balachandra , Rea Shane L. , Mishur Robert J. , Li Qiuhua , Johnson-Pais Teresa L. , Guo Lining , Bae Sejong , Wei Shi , Block Karen , Sudarshan Sunil
Published: April 2023

Supplementary Figure 1. A498 cells were stable transduced with the indicated construct. Protein lysates were harvested and immunoblotted for the indicated proteins.
Supplementary Methods, Figure Legends from Brain Tumor Cells in Circulation Are Enriched for Mesenchymal Gene Expression
Authors: Sullivan James P. , Nahed Brian V. , Madden Marissa W. , Oliveira Samantha M. , Springer Simeon , Bhere Deepak , Chi Andrew S. , Wakimoto Hiroaki , Rothenberg S. Michael , Sequist Lecia V. , Kapur Ravi , Shah Khalid , Iafrate A. John , Curry William T. , Loeffler Jay S. , Batchelor Tracy T. , Louis David N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: April 2023

Methods and Supplementary Figure Legends
Supplementary Table S1.4 from Metabolic and Functional Genomic Studies Identify Deoxythymidylate Kinase as a Target in LKB1-Mutant Lung Cancer
Authors: Liu Yan , Marks Kevin , Cowley Glenn S. , Carretero Julian , Liu Qingsong , Nieland Thomas J.F. , Xu Chunxiao , Cohoon Travis J. , Gao Peng , Zhang Yong , Chen Zhao , Altabef Abigail B. , Tchaicha Jeremy H. , Wang Xiaoxu , Choe Sung , Driggers Edward M. , Zhang Jianming , Bailey Sean T. , Sharpless Norman E. , Hayes D. Neil , Patel Nirali M. , Janne Pasi A. , Bardeesy Nabeel , Engelman Jeffrey A. , Manning Brendan D. , Shaw Reuben J. , Asara John M. , Scully Ralph , Kimmelman Alec , Byers Lauren A. , Gibbons Don L. , Wistuba Ignacio I. , Heymach John V. , Kwiatkowski David J. , Kim William Y. , Kung Andrew L. , Gray Nathanael S. , Root David E. , Cantley Lewis C. , Wong Kwok-Kin
Published: April 2023

70 genes selected for validation.
Supplementary Table S5 from Infection Exposure Is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility
Authors: Martín-Lorenzo Alberto , Hauer Julia , Vicente-Dueñas Carolina , Auer Franziska , González-Herrero Inés , García-Ramírez Idoia , Ginzel Sebastian , Thiele Ralf , Constantinescu Stefan N. , Bartenhagen Christoph , Dugas Martin , Gombert Michael , Schäfer Daniel , Blanco Oscar , Mayado Andrea , Orfao Alberto , Alonso-López Diego , Rivas Javier De Las , Cobaleda César , García-Cenador Maria Begoña , García-Criado Francisco Javier , Sánchez-García Isidro , Borkhardt Arndt
Published: April 2023

SNVs detected by whole exam sequencing in the three index Pax5+/- pB-ALL.
Supplementary Table S1 from Infection Exposure Is a Causal Factor in B-cell Precursor Acute Lymphoblastic Leukemia as a Result of Pax5-Inherited Susceptibility
Authors: Martín-Lorenzo Alberto , Hauer Julia , Vicente-Dueñas Carolina , Auer Franziska , González-Herrero Inés , García-Ramírez Idoia , Ginzel Sebastian , Thiele Ralf , Constantinescu Stefan N. , Bartenhagen Christoph , Dugas Martin , Gombert Michael , Schäfer Daniel , Blanco Oscar , Mayado Andrea , Orfao Alberto , Alonso-López Diego , Rivas Javier De Las , Cobaleda César , García-Cenador Maria Begoña , García-Criado Francisco Javier , Sánchez-García Isidro , Borkhardt Arndt
Published: April 2023

Health monitoring report of PAx5+/- held in the SPF and conventional animal facility.
Supplementary Tables 1 - 3 from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Table 1. Clinical characteristics of AML patients tested in this study. Supplementary Table 2. Antibodies used in this study. Supplementary Table 3. Comparison of clinical (fluorescent) flow cytometry (on left), to mass cytometry analsyis (on right).
Supplementary Table 5 from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Table 5. Number of cell events collected for each sample.
Supplementary Table 4 from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Table 4. The raw median ion counts (per cell) for each marker (table heading) in each manually gated immunophenotypic population (columns) of each patient sample (rows) are shown.
Supplementary Methods from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Methods
Supplementary Figures 1 - 8 from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Figure 1. SPADE plots of normal bone marrow sample no. 6. Supplementary Figure 2. The frequency of cells in the indicated (manually-gated) populations. Supplementary Figure 3. Multi-dimensional binning analysis of the CD34+CD38 low subset confirmed that distinct karyotype and genotype-specific immunophenotypic patterns are observed in high-dimensional space. Supplementary Figure 4. AML subtypes are characterized by distinct phosphoprotein signaling patterns. Supplementary Figure 5. viSNE analysis of CD34+CD38 low subset demonstrates signaling aberrancy is most pronounced in cells outside the viSNE space occupied by normal cells. Supplementary Figure 6. Median basal intracellular signaling of CD34+CD38low cells from AML samples of each subtype. Supplementary Figure 7. HU treatment does not increase the fraction of apoptotic cells measured by cPARP levels. Supplementary Figure 8. Histone 3 lysine 9 acetylation decreases with immunophenotypic differentiation in both normal and AML patient samples.
Supplementary Figures S1 - S5 from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Authors: Aguirre Andrew J. , Meyers Robin M. , Weir Barbara A. , Vazquez Francisca , Zhang Cheng-Zhong , Ben-David Uri , Cook April , Ha Gavin , Harrington William F. , Doshi Mihir B. , Kost-Alimova Maria , Gill Stanley , Xu Han , Ali Levi D. , Jiang Guozhi , Pantel Sasha , Lee Yenarae , Goodale Amy , Cherniack Andrew D. , Oh Coyin , Kryukov Gregory , Cowley Glenn S. , Garraway Levi A. , Stegmaier Kimberly , Roberts Charles W. , Golub Todd R. , Meyerson Matthew , Root David E. , Tsherniak Aviad , Hahn William C.
Published: April 2023

Supplementary Figure S1. Genome-scale CRISPR-Cas9 screening identifies a strong correlation between copy number and sensitivity to CRISPR-Cas9 genome editing. Supplementary Figure S2. Global summary of the relationship of CRISPR-Cas9 guide scores to genomic copy number for all 33 cell lines screened. Supplementary Figure S3. Amplified genes represent the strongest perceived dependencies in pooled CRISPR-Cas9 screening data. Figure S4. Evaluation of the influence of copy number on CRISPR-Cas9 dependency scores in published data from Hart et al. (25). Figure S5. Representative examples of structural variations leading to copy number amplification underlying the gene-independent anti-proliferative response to CRISPRCas9 targeting of loci within these regions.
Supplementary Figure Legends from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Authors: Aguirre Andrew J. , Meyers Robin M. , Weir Barbara A. , Vazquez Francisca , Zhang Cheng-Zhong , Ben-David Uri , Cook April , Ha Gavin , Harrington William F. , Doshi Mihir B. , Kost-Alimova Maria , Gill Stanley , Xu Han , Ali Levi D. , Jiang Guozhi , Pantel Sasha , Lee Yenarae , Goodale Amy , Cherniack Andrew D. , Oh Coyin , Kryukov Gregory , Cowley Glenn S. , Garraway Levi A. , Stegmaier Kimberly , Roberts Charles W. , Golub Todd R. , Meyerson Matthew , Root David E. , Tsherniak Aviad , Hahn William C.
Published: April 2023

Supplementary Figure Legends
Supplementary Figure 9 from Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy
Authors: Behbehani Gregory K. , Samusik Nikolay , Bjornson Zach B. , Fantl Wendy J. , Medeiros Bruno C. , Nolan Garry P.
Published: April 2023

Supplementary Figure 9. Gating strategy is shown for each population.
Supplementary Figure Legends from Tumor Cell–Independent Estrogen Signaling Drives Disease Progression through Mobilization of Myeloid-Derived Suppressor Cells
Authors: Svoronos Nikolaos , Perales-Puchalt Alfredo , Allegrezza Michael J. , Rutkowski Melanie R. , Payne Kyle K. , Tesone Amelia J. , Nguyen Jenny M. , Curiel Tyler J. , Cadungog Mark G. , Singhal Sunil , Eruslanov Evgeniy B. , Zhang Paul , Tchou Julia , Zhang Rugang , Conejo-Garcia Jose R.
Published: April 2023

Supplementary Figure Legends
Supplementary Table 1 from Mechanism, Consequences, and Therapeutic Targeting of Abnormal IL15 Signaling in Cutaneous T-cell Lymphoma
Authors: Mishra Anjali , La Perle Krista , Kwiatkowski Sonya , Sullivan Laura A. , Sams Gregory H. , Johns Jessica , Curphey Douglas P. , Wen Jing , McConnell Kathleen , Qi Jun , Wong Henry , Russo Giandomenico , Zhang Jianying , Marcucci Guido , Bradner James E. , Porcu Pierluigi , Caligiuri Michael A.
Published: April 2023

Supplementary Table 1A (ST1A). Clinical features of CTCL (MF and SS) patients used in Figure 1B and Figure 4E (denoted with *). Stage 1B and IIB are MF samples and Stage III/IV are SS samples. Supplementary Table 1B (ST1B). Clinical features of SS patients whose CD4+ T cells were used in Figure 1C. Supplementary Table 1C (ST1C). Clinical features of SS patients whose CD4+ T cells were used in Figure 5B and Supplementary Figure 1D-F (denoted with #). Supplementary Table 1D (ST1D). Clinical features of SS patients whose CD4+ T cells were used in Figure 4D and 5A.
Supplementary Figures 1 - 3, Table 1 from Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia
Authors: Trinquand Amélie , dos Santos Nuno R. , Tran Quang Christine , Rocchetti Francesca , Zaniboni Benedetta , Belhocine Mohamed , Da Costa de Jesus Cindy , Lhermitte Ludovic , Tesio Melania , Dussiot Michael , Cosset François-Loïc , Verhoeyen Els , Pflumio Françoise , Ifrah Norbert , Dombret Hervé , Spicuglia Salvatore , Chatenoud Lucienne , Gross David-Alexandre , Hermine Olivier , Macintyre Elizabeth , Ghysdael Jacques , Asnafi Vahid
Published: April 2023

Supplementary Figure 1. Anti-CD3 stimulation of primary human T-ALLs. Supplementary Figure 2. TCR stimulation by in vivo administration of agonistic monoclonal antibody in a preventive setting inhibits human TCR+ T-ALL development. Supplementary Figure 3. TCR signaling is essential to the anti-leukemic effect of OKT3. Supplementary Table 1. Immunophenotypic and oncogenic characteristics of T-ALL samples.
Supplementary Figure Legends, Figures 1 - 5 from TGFβ1-Mediated SMAD3 Enhances PD-1 Expression on Antigen-Specific T Cells in Cancer
Authors: Park Benjamin V. , Freeman Zachary T. , Ghasemzadeh Ali , Chattergoon Michael A. , Rutebemberwa Alleluiah , Steigner Jordana , Winter Matthew E. , Huynh Thanh V. , Sebald Suzanne M. , Lee Se-Jin , Pan Fan , Pardoll Drew M. , Cox Andrea L.
Published: April 2023

Supplementary Figure 1. The effect of various cytokines on PD-1 expression is shown as fold changes in MFI relative to the αCD3/αCD28 condition with no cytokines in both CD4+ (black bars) 4 and CD8+ (white bars) T cells. Supplementary Figure 2. qPCR analysis of Smad2 and Smad3 mRNA levels in Jurkat T cells. Supplementary Figure 3. Foxp3 expression in CD4+ PD-1+ T cells infiltrating the tumor 56 microenvironment in WT, Smad2 cKO and Smad3 cKO mice. Supplementary Figure 4. Representative histograms of CFSE (left), PD-1(middle) and LAG3 (right) 66 expression on WT (thin grey histogram) and Smad3 (thin black histogram) cKO OT-I cells originating 67 from the draining lymph nodes (DLN) (top) and non-draining lymph nodes (NDLN) (bottom). Supplementary Figure 5. (a) WT and DNTGFβRII Tg+ mice were injected with 105 B16 melanoma 74 cells in foot-pads, and tumor volume (mm3) is shown as mean +/- SEM on different days.
Supplementary Tables 1-6 from Safety and Antitumor Activity of the Multitargeted Pan-TRK, ROS1, and ALK Inhibitor Entrectinib: Combined Results from Two Phase I Trials (ALKA-372-001 and STARTRK-1)
Authors: Drilon Alexander , Siena Salvatore , Ou Sai-Hong Ignatius , Patel Manish , Ahn Myung Ju , Lee Jeeyun , Bauer Todd M. , Farago Anna F. , Wheler Jennifer J. , Liu Stephen V. , Doebele Robert , Giannetta Laura , Cerea Giulio , Marrapese Giovanna , Schirru Michele , Amatu Alessio , Bencardino Katia , Palmeri Laura , Sartore-Bianchi Andrea , Vanzulli Angelo , Cresta Sara , Damian Silvia , Duca Matteo , Ardini Elena , Li Gang , Christiansen Jason , Kowalski Karey , Johnson Ann D. , Patel Rupal , Luo David , Chow-Maneval Edna , Hornby Zachary , Multani Pratik S. , Shaw Alice T. , De Braud Filippo G.
Published: April 2023

DOC- 25K, Supplementary Tables 1-6
Supplementary Figures 1 - 2 from Safety and Antitumor Activity of the Multitargeted Pan-TRK, ROS1, and ALK Inhibitor Entrectinib: Combined Results from Two Phase I Trials (ALKA-372-001 and STARTRK-1)
Authors: Drilon Alexander , Siena Salvatore , Ou Sai-Hong Ignatius , Patel Manish , Ahn Myung Ju , Lee Jeeyun , Bauer Todd M. , Farago Anna F. , Wheler Jennifer J. , Liu Stephen V. , Doebele Robert , Giannetta Laura , Cerea Giulio , Marrapese Giovanna , Schirru Michele , Amatu Alessio , Bencardino Katia , Palmeri Laura , Sartore-Bianchi Andrea , Vanzulli Angelo , Cresta Sara , Damian Silvia , Duca Matteo , Ardini Elena , Li Gang , Christiansen Jason , Kowalski Karey , Johnson Ann D. , Patel Rupal , Luo David , Chow-Maneval Edna , Hornby Zachary , Multani Pratik S. , Shaw Alice T. , De Braud Filippo G.
Published: April 2023

Supplementary Figure 1. "Phase 2-Eligible" Population. Supplementary Figure 2. ALKA-372-001 and STARTRK-1 Dosing Regimens.
Supplementary Video S1 from Real-Time Imaging Reveals Local, Transient Vascular Permeability, and Tumor Cell Intravasation Stimulated by TIE2hi Macrophage–Derived VEGFA
Authors: Harney Allison S. , Arwert Esther N. , Entenberg David , Wang Yarong , Guo Peng , Qian Bin-Zhi , Oktay Maja H. , Pollard Jeffrey W. , Jones Joan G. , Condeelis John S.
Published: April 2023

Supplementary Video S1. Tumor cell intravasation occurs at TMEM along with local, transient blood vessel permeability. Time-lapse microscopy of 155 kDa dextran-TMR extravasation (red in left panel, white right panel) and site of tumor cell intravasation (green cells) at TMEM. Macrophages in cyan. Time is indicated in minutes:seconds.
Supplementary Methods, Figure Legends from Real-Time Imaging Reveals Local, Transient Vascular Permeability, and Tumor Cell Intravasation Stimulated by TIE2hi Macrophage–Derived VEGFA
Authors: Harney Allison S. , Arwert Esther N. , Entenberg David , Wang Yarong , Guo Peng , Qian Bin-Zhi , Oktay Maja H. , Pollard Jeffrey W. , Jones Joan G. , Condeelis John S.
Published: April 2023

Supplementary Methods, Figure Legends
Supplementary Tables S1 - S6 from Obesity-Induced Inflammation and Desmoplasia Promote Pancreatic Cancer Progression and Resistance to Chemotherapy
Authors: Incio Joao , Liu Hao , Suboj Priya , Chin Shan M. , Chen Ivy X. , Pinter Matthias , Ng Mei R. , Nia Hadi T. , Grahovac Jelena , Kao Shannon , Babykutty Suboj , Huang Yuhui , Jung Keehoon , Rahbari Nuh N. , Han Xiaoxing , Chauhan Vikash P. , Martin John D. , Kahn Julia , Huang Peigen , Desphande Vikram , Michaelson James , Michelakos Theodoros P. , Ferrone Cristina R. , Soares Raquel , Boucher Yves , Fukumura Dai , Jain Rakesh K.
Published: April 2023

Supplementary Tables S1 - S6. Supplementary Table S1. CT values for demosplasia-related genes in PAN02 tumors. Data obtained from PCR array. Supplementary Table S2. CT values for demosplasia-related genes in AK4.4 tumors. Data obtained from PCR array. Supplementary Table S3. Univariate analysis of prognostic factors for resected pancreatic cancer patients with body mass index (BMI) {less than or equal to}25. Supplementary Table S4. Multivariate analysis of prognostic factors for resected pancreatic cancer patients with body mass index (BMI) {less than or equal to}25. Supplementary Table S5. Univariate analysis of prognostic factors for resected pancreatic cancer patients with body mass index (BMI) >25. Supplementary Table S6. Multivariate analysis of prognostic factors for resected pancreatic cancer patients with body mass index (BMI) >25.
Supplementary Methods from Obesity-Induced Inflammation and Desmoplasia Promote Pancreatic Cancer Progression and Resistance to Chemotherapy
Authors: Incio Joao , Liu Hao , Suboj Priya , Chin Shan M. , Chen Ivy X. , Pinter Matthias , Ng Mei R. , Nia Hadi T. , Grahovac Jelena , Kao Shannon , Babykutty Suboj , Huang Yuhui , Jung Keehoon , Rahbari Nuh N. , Han Xiaoxing , Chauhan Vikash P. , Martin John D. , Kahn Julia , Huang Peigen , Desphande Vikram , Michaelson James , Michelakos Theodoros P. , Ferrone Cristina R. , Soares Raquel , Boucher Yves , Fukumura Dai , Jain Rakesh K.
Published: April 2023

Supplementary Methods
Supplementary Table S5 from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Table S5: Structural insight into the impact of cancer-associated APC/C mutations.
Supplementary Table S4 from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Table S4: APC/C mutation frequencies in TCGA.
Supplementary Table 6 from Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma
Authors: Cottini Francesca , Hideshima Teru , Suzuki Rikio , Tai Yu-Tzu , Bianchini Giampaolo , Richardson Paul G. , Anderson Kenneth C. , Tonon Giovanni
Published: April 2023

Supplementary Table 6. Pathways implicated in ROS and NOS metabolism collected from MSigDB.
Supplementary Table S2 from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Table S2: Gene ontology enrichment analysis from whole-genome RNAi screen identifies APC/C subunits.
Supplementary Table 5 from Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma
Authors: Cottini Francesca , Hideshima Teru , Suzuki Rikio , Tai Yu-Tzu , Bianchini Giampaolo , Richardson Paul G. , Anderson Kenneth C. , Tonon Giovanni
Published: April 2023

Supplementary Table 5. Multivariate analysis of survival groups.
Supplementary Table S1 from APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability
Authors: Sansregret Laurent , Patterson James O. , Dewhurst Sally , López-García Carlos , Koch André , McGranahan Nicholas , Chao William Chong Hang , Barry David J. , Rowan Andrew , Instrell Rachael , Horswell Stuart , Way Michael , Howell Michael , Singleton Martin R. , Medema René H. , Nurse Paul , Petronczki Mark , Swanton Charles
Published: April 2023

Supplementary Table S1: Chromosome segregation error rates per chromosome used to determine average missegregation rates in our studies.
Supplementary Figures S1 - S16 from Synthetic Lethal Approaches Exploiting DNA Damage in Aggressive Myeloma
Authors: Cottini Francesca , Hideshima Teru , Suzuki Rikio , Tai Yu-Tzu , Bianchini Giampaolo , Richardson Paul G. , Anderson Kenneth C. , Tonon Giovanni
Published: April 2023

Supplementary Figure S1. 53BP1 and RPA32 staining in MM cells. Supplementary Figure S2. Replicative stress markers in MM cells. Supplementary Figure S3. Replicative stress markers in peripheral blood mononuclear cells (PBMCs). Supplementary Figure S4. Phospho-histone H3 and phospho-H2A.X staining in MM cells. Supplementary Figure S5. 53BP1 and RPA32 in primary MM cells. Supplementary Figure S6. ATR in MM patient and cell lines. Supplementary Figure S7. Gene expression levels of probe sets related to oxidative stress in MM patients. Supplementary Figure S8. Oxidative stress markers in MM cells upon MYC modulation and N-Acetyl Cysteine, VE-821, or Ku55933 treatment. Supplementary Figure S9. Piperlongumine effects on MM cells. Supplementary Figure S10. Effects of arsenic trioxide treatment of MM cells. Supplementary Figure S11. Piperlongumine and glutathione in MM cells. Supplementary Figure S12. Piperlongumine on peripheral blood mononuclear cells (PBMCs). Supplementary Figure S13. Cytotoxicity effects of piperlongumine in combination with VE-821. Supplementary Figure S14. Cytotoxicity effects of arsenic trioxide in combination with VE-821. Supplementary Figure S15. Cytotoxicity effects of piperlongumine in combination with proteasome inhibitors. Supplementary Figure S16. Cytotoxicity effects of VE-821 in combination with proteasome inhibitors.
Supplementary Table 1 from Blastic Plasmacytoid Dendritic Cell Neoplasm Is Dependent on BCL2 and Sensitive to Venetoclax
Authors: Montero Joan , Stephansky Jason , Cai Tianyu , Griffin Gabriel K. , Cabal-Hierro Lucia , Togami Katsuhiro , Hogdal Leah J. , Galinsky Ilene , Morgan Elizabeth A. , Aster Jon C. , Davids Matthew S. , LeBoeuf Nicole R. , Stone Richard M. , Konopleva Marina , Pemmaraju Naveen , Letai Anthony , Lane Andrew A.
Published: April 2023

Genetic analysis of the primary BPDCNs and AMLs, and PDXs.
Supplementary Video S1 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression
Authors: Oudin Madeleine J. , Jonas Oliver , Kosciuk Tatsiana , Broye Liliane C. , Guido Bruna C. , Wyckoff Jeff , Riquelme Daisy , Lamar John M. , Asokan Sreeja B. , Whittaker Charlie , Ma Duanduan , Langer Robert , Cima Michael J. , Wisinski Kari B. , Hynes Richard O. , Lauffenburger Douglas A. , Keely Patricia J. , Bear James E. , Gertler Frank B.
Published: April 2023

Supplementary Video S1. MenaINV drives haptotaxis in vivo.
Supplementary Figure S6 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression
Authors: Oudin Madeleine J. , Jonas Oliver , Kosciuk Tatsiana , Broye Liliane C. , Guido Bruna C. , Wyckoff Jeff , Riquelme Daisy , Lamar John M. , Asokan Sreeja B. , Whittaker Charlie , Ma Duanduan , Langer Robert , Cima Michael J. , Wisinski Kari B. , Hynes Richard O. , Lauffenburger Douglas A. , Keely Patricia J. , Bear James E. , Gertler Frank B.
Published: April 2023

Supplementary Figure S6. MenaINV-driven ECM reorganization in vitro and in vivo.
Supplementary Figure 2 from Blastic Plasmacytoid Dendritic Cell Neoplasm Is Dependent on BCL2 and Sensitive to Venetoclax
Authors: Montero Joan , Stephansky Jason , Cai Tianyu , Griffin Gabriel K. , Cabal-Hierro Lucia , Togami Katsuhiro , Hogdal Leah J. , Galinsky Ilene , Morgan Elizabeth A. , Aster Jon C. , Davids Matthew S. , LeBoeuf Nicole R. , Stone Richard M. , Konopleva Marina , Pemmaraju Naveen , Letai Anthony , Lane Andrew A.
Published: April 2023

Venetoclax induces dose-dependent apoptotic cell death in BPDCN and AML cell lines. (A) Representative Annexin V-FITC vs propidium iodide (PI) flow cytometry staining to measure apoptosis induction in CAL1 cells after 24 hours of exposure to vehicle, or 10 nM or 100 nM venetoclax are shown. (B) Quantitation of cell death by Annexin V and PI flow cytometry after 24 hours of exposure to the indicated concentrations of venetoclax. Graphs represent mean +/- SEM of 3 independent experiments, *P<0.05 by t-test compared to vehicle.
Supplementary Figure 1 from Blastic Plasmacytoid Dendritic Cell Neoplasm Is Dependent on BCL2 and Sensitive to Venetoclax
Authors: Montero Joan , Stephansky Jason , Cai Tianyu , Griffin Gabriel K. , Cabal-Hierro Lucia , Togami Katsuhiro , Hogdal Leah J. , Galinsky Ilene , Morgan Elizabeth A. , Aster Jon C. , Davids Matthew S. , LeBoeuf Nicole R. , Stone Richard M. , Konopleva Marina , Pemmaraju Naveen , Letai Anthony , Lane Andrew A.
Published: April 2023

BPDCN expresses BCL-2 protein. Photomicrographs of H&E stains and BCL-2, CD123, and TCL-1 immunohistochemistry for BPDCN and AML biopsies from bone marrow and skin are shown. Each of the biopsies (each row) is from a different patient. The BPDCN from Figure 1A is re-presented here for comparison to other BPDCNs and AMLs.
Supplementary Figure S3 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression
Authors: Oudin Madeleine J. , Jonas Oliver , Kosciuk Tatsiana , Broye Liliane C. , Guido Bruna C. , Wyckoff Jeff , Riquelme Daisy , Lamar John M. , Asokan Sreeja B. , Whittaker Charlie , Ma Duanduan , Langer Robert , Cima Michael J. , Wisinski Kari B. , Hynes Richard O. , Lauffenburger Douglas A. , Keely Patricia J. , Bear James E. , Gertler Frank B.
Published: April 2023

Supplementary Figure S3. TCGA analysis supplementary analysis and characterization of MenaINV-specific monoclonal antibody.
Supplementary Figure S2 from Tumor Cell–Driven Extracellular Matrix Remodeling Drives Haptotaxis during Metastatic Progression
Authors: Oudin Madeleine J. , Jonas Oliver , Kosciuk Tatsiana , Broye Liliane C. , Guido Bruna C. , Wyckoff Jeff , Riquelme Daisy , Lamar John M. , Asokan Sreeja B. , Whittaker Charlie , Ma Duanduan , Langer Robert , Cima Michael J. , Wisinski Kari B. , Hynes Richard O. , Lauffenburger Douglas A. , Keely Patricia J. , Bear James E. , Gertler Frank B.
Published: April 2023

Supplementary Figure S2. MenaINV drives haptotaxis at high FN concentrations.
Supplementary Figure Legends, Figures S1 - S6 from Isocitrate Dehydrogenase Mutations Confer Dasatinib Hypersensitivity and SRC Dependence in Intrahepatic Cholangiocarcinoma
Authors: Saha Supriya K. , Gordan John D. , Kleinstiver Benjamin P. , Vu Phuong , Najem Mortada S. , Yeo Jia-Chi , Shi Lei , Kato Yasutaka , Levin Rebecca S. , Webber James T. , Damon Leah J. , Egan Regina K. , Greninger Patricia , McDermott Ultan , Garnett Mathew J. , Jenkins Roger L. , Rieger-Christ Kimberly M. , Sullivan Travis B. , Hezel Aram F. , Liss Andrew S. , Mizukami Yusuke , Goyal Lipika , Ferrone Cristina R. , Zhu Andrew X. , Joung J. Keith , Shokat Kevan M. , Benes Cyril H. , Bardeesy Nabeel
Published: April 2023

Supplementary Figure S1. IDHm ICC are insensitive to IDH inhibition. Supplementary Figure S2. Similarity matrix for drug response of BTC cell lines. Supplementary Figure S3. Hypersensitivity of ICC cells harboring endogenous IDH mutations to dasatinib. Supplementary Figure S4. Torin 1 inhibits growth of ICC cell lines. Supplementary Figure S5. Critical role for SRC in IDHm ICC cells. Supplementary Figure S6. Ectopic expression of mutant IDH has only a modest effect on dasatinib sensitivity.
Supplementary Table S5 from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

CDXs list.
Supplementary Table S5 from CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M.
Published: April 2023

A list of CREBBP mutations in cohort 3.
Supplementary Table S2 from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

10 gene Miseq primers.
Supplementary Methods from Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma
Authors: Girotti Maria Romina , Gremel Gabriela , Lee Rebecca , Galvani Elena , Rothwell Dominic , Viros Amaya , Mandal Amit Kumar , Lim Kok Haw Jonathan , Saturno Grazia , Furney Simon J. , Baenke Franziska , Pedersen Malin , Rogan Jane , Swan Jacqueline , Smith Matthew , Fusi Alberto , Oudit Deemesh , Dhomen Nathalie , Brady Ged , Lorigan Paul , Dive Caroline , Marais Richard
Published: April 2023

Supplementary Methods
Supplementary Table S1 from CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas
Authors: Jiang Yanwen , Ortega-Molina Ana , Geng Huimin , Ying Hsia-Yuan , Hatzi Katerina , Parsa Sara , McNally Dylan , Wang Ling , Doane Ashley S. , Agirre Xabier , Teater Matt , Meydan Cem , Li Zhuoning , Poloway David , Wang Shenqiu , Ennishi Daisuke , Scott David W. , Stengel Kristy R. , Kranz Janice E. , Holson Edward , Sharma Sneh , Young James W. , Chu Chi-Shuen , Roeder Robert G. , Shaknovich Rita , Hiebert Scott W. , Gascoyne Randy D. , Tam Wayne , Elemento Olivier , Wendel Hans-Guido , Melnick Ari M.
Published: April 2023

All pathways used in pathway enrichment analysis.
Supplementary Figure 7 from GM-CSF Mediates Mesenchymal–Epithelial Cross-talk in Pancreatic Cancer
Authors: Waghray Meghna , Yalamanchili Malica , Dziubinski Michele , Zeinali Mina , Erkkinen Marguerite , Yang Huibin , Schradle Kara A. , Urs Sumithra , Pasca Di Magliano Marina , Welling Theodore H. , Palmbos Phillip L. , Abel Ethan V. , Sahai Vaibhav , Nagrath Sunitha , Wang Lidong , Simeone Diane M.
Published: April 2023

Supplementary Figure 7. A. Sections from orthotopic pancreatic tumors from control shRNA- MSC vs GM-CSF-shRNA-MSC were analyzed for expression of F4/80, and Arg1 by immunohistochemical and immunofluorescence staining. B. Quantitation of F4/80 positively labeled cells was performed by light microscopy at an optical magnification of 400Ã-, (n=5 animals per group *p<0.05 vs. tumor).
Supplementary Methods, Figures 1 - 11 from Chromosomal Instability Affects the Tumorigenicity of Glioblastoma Tumor-Initiating Cells
Authors: Godek Kristina M. , Venere Monica , Wu Quilian , Mills Kevin D. , Hickey William F. , Rich Jeremy N. , Compton Duane A.
Published: April 2023

Supplementary Figure 1 shows Nestin expression. Supplementary Figure 2 shows Sox2 expression. Supplementary Figure 3 shows differentiation of GNS cells. Supplementary Figure 4 shows checkpoint assay and FISH data. Supplementary Figure 5 shows karyotypes of GliNS2 cells. Supplementary Figure 6 shows p53 and p21 response. Supplementary Figure 7 shows FISH and karyotypes of PDX lines.Supplementary Figure 8 shows Sox2 and Nestin expression in stable GFP expressing lines. Supplementary Figure 9 shows limiting dilution assay in vitro. Supplementary Figure 10 shows FACS profiles for growth assay. Supplementary Figure 11 shows astrocyte differentiation of GFP expressing lines.
Supplementary Figure 5 from GM-CSF Mediates Mesenchymal–Epithelial Cross-talk in Pancreatic Cancer
Authors: Waghray Meghna , Yalamanchili Malica , Dziubinski Michele , Zeinali Mina , Erkkinen Marguerite , Yang Huibin , Schradle Kara A. , Urs Sumithra , Pasca Di Magliano Marina , Welling Theodore H. , Palmbos Phillip L. , Abel Ethan V. , Sahai Vaibhav , Nagrath Sunitha , Wang Lidong , Simeone Diane M.
Published: April 2023

Supplementary Figure 5. Representative Western blot demonstrating the expression of GM-CSF receptors CSF2RÎ± and CSF2RÎ² in primary human pancreatic cancer cells.
Supplementary Video S3 from BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance
Authors: Tasdemir Nilgun , Banito Ana , Roe Jae-Seok , Alonso-Curbelo Direna , Camiolo Matthew , Tschaharganeh Darjus F. , Huang Chun-Hao , Aksoy Ozlem , Bolden Jessica E. , Chen Chi-Chao , Fennell Myles , Thapar Vishal , Chicas Agustin , Vakoc Christopher R. , Lowe Scott W.
Published: April 2023

Co-culture of NK cells and S/shRen IMR90 cells.
Supplementary Figure S3 from Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation
Authors: Elf Shannon , Abdelfattah Nouran S. , Chen Edwin , Perales-Patón Javier , Rosen Emily A. , Ko Amy , Peisker Fabian , Florescu Natalie , Giannini Silvia , Wolach Ofir , Morgan Elizabeth A. , Tothova Zuzana , Losman Julie-Aurore , Schneider Rebekka K. , Al-Shahrour Fatima , Mullally Ann
Published: April 2023

Supplementary Figure S3. (A) Pre-ranked GSEA in CALRMUT versus CALRWT expressing Ba/F3-MPL cells 24 hours post-IL-3 withdrawal. Stat5 (left) and Stat3 (right) target genes (Baker et al, 2007) are both enriched in CALRMUT compared to CALRWT-expressing Ba/F3-MPL cells (B) Immunoblotting demonstrates differential phosphorylation of STAT5 in CALRMUT-expressing UT-7-MPL cells. (C) Immunoblotting demonstrates differential phosphorylation of Stat5 and Stat3 in Calr-targeted Ba/F3-MPL-Cas9 cells.
Supplementary Tables S1 - S14 from Molecular Mechanisms of Resistance to First- and Second-Generation ALK Inhibitors in ALK-Rearranged Lung Cancer
Authors: Gainor Justin F. , Dardaei Leila , Yoda Satoshi , Friboulet Luc , Leshchiner Ignaty , Katayama Ryohei , Dagogo-Jack Ibiayi , Gadgeel Shirish , Schultz Katherine , Singh Manrose , Chin Emily , Parks Melissa , Lee Dana , DiCecca Richard H. , Lockerman Elizabeth , Huynh Tiffany , Logan Jennifer , Ritterhouse Lauren L. , Le Long P. , Muniappan Ashok , Digumarthy Subba , Channick Colleen , Keyes Colleen , Getz Gad , Dias-Santagata Dora , Heist Rebecca S. , Lennerz Jochen , Sequist Lecia V. , Benes Cyril H. , Iafrate A. John , Mino-Kenudson Mari , Engelman Jeffrey A. , Shaw Alice T.
Published: April 2023

Supplementary Table S1. ALK inhibitors in clinical development. Supplementary Table S2. Summary of clinical characteristics of ALK-positive patients undergoing biopsies at the time of ALK inhibitor resistance. Supplementary Table S3. Paired, post-crizotinib and post second-generation ALK inhibitor biopsies. Supplementary Table S4. Treatment course of ALK-positive patients undergoing post-ceritinib biopsies. Supplementary Table S5. Treatment course of ALK-positive patients undergoing post-alectinib biopsies. Supplementary Table S6. Treatment course of ALK-positive patients undergoing post-brigatinib biopsies. Supplementary Table S7. Resistant biopsies with {greater than or equal to}2 resistance mutations. Supplementary Table S8. Mutations in ceritinib-resistant biopsies. Supplementary Table S9. Mutations in alectinib-resistant biopsies. Supplementary Table S10. Mutations in brigatinib-resistant biopsies. Supplementary Table S11. Single-nucleotide variants identified in patient-derived cell lines. Supplementary Table S12. EMT in ceritinib-resistant biopsies. Supplementary Table S13. Cells seeded for survival assays. Supplementary Table S14. Cells seeded for growth assays.
Supplementary Table 3 from A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma
Authors: Mirabello Lisa , Koster Roelof , Moriarity Branden S. , Spector Logan G. , Meltzer Paul S. , Gary Joy , Machiela Mitchell J. , Pankratz Nathan , Panagiotou Orestis A. , Largaespada David , Wang Zhaoming , Gastier-Foster Julie M. , Gorlick Richard , Khanna Chand , de Toledo Silvia Regina Caminada , Petrilli Antonio S. , Patiño-Garcia Ana , Sierrasesúmaga Luis , Lecanda Fernando , Andrulis Irene L. , Wunder Jay S. , Gokgoz Nalan , Serra Massimo , Hattinger Claudia , Picci Piero , Scotlandi Katia , Flanagan Adrienne M. , Tirabosco Roberto , Amary Maria Fernanda , Halai Dina , Ballinger Mandy L. , Thomas David M. , Davis Sean , Barkauskas Donald A. , Marina Neyssa , Helman Lee , Otto George M. , Becklin Kelsie L. , Wolf Natalie K. , Weg Madison T. , Tucker Margaret , Wacholder Sholom , Fraumeni Joseph F. , Caporaso Neil E. , Boland Joseph F. , Hicks Belynda D. , Vogt Aurelie , Burdett Laurie , Yeager Meredith , Hoover Robert N. , Chanock Stephen J. , Savage Sharon A.
Published: April 2023

Top 30 loci associated with metastasis at diagnosis in the discovery set of 541 European osteosarcoma cases.
Supplementary Table 1 from A Genome-Wide Scan Identifies Variants in NFIB Associated with Metastasis in Patients with Osteosarcoma
Authors: Mirabello Lisa , Koster Roelof , Moriarity Branden S. , Spector Logan G. , Meltzer Paul S. , Gary Joy , Machiela Mitchell J. , Pankratz Nathan , Panagiotou Orestis A. , Largaespada David , Wang Zhaoming , Gastier-Foster Julie M. , Gorlick Richard , Khanna Chand , de Toledo Silvia Regina Caminada , Petrilli Antonio S. , Patiño-Garcia Ana , Sierrasesúmaga Luis , Lecanda Fernando , Andrulis Irene L. , Wunder Jay S. , Gokgoz Nalan , Serra Massimo , Hattinger Claudia , Picci Piero , Scotlandi Katia , Flanagan Adrienne M. , Tirabosco Roberto , Amary Maria Fernanda , Halai Dina , Ballinger Mandy L. , Thomas David M. , Davis Sean , Barkauskas Donald A. , Marina Neyssa , Helman Lee , Otto George M. , Becklin Kelsie L. , Wolf Natalie K. , Weg Madison T. , Tucker Margaret , Wacholder Sholom , Fraumeni Joseph F. , Caporaso Neil E. , Boland Joseph F. , Hicks Belynda D. , Vogt Aurelie , Burdett Laurie , Yeager Meredith , Hoover Robert N. , Chanock Stephen J. , Savage Sharon A.
Published: April 2023

Description of participating case studies.
Supplementary Tables S1 - S18 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer
Authors: Anagnostou Valsamo , Smith Kellie N. , Forde Patrick M. , Niknafs Noushin , Bhattacharya Rohit , White James , Zhang Theresa , Adleff Vilmos , Phallen Jillian , Wali Neha , Hruban Carolyn , Guthrie Violeta B. , Rodgers Kristen , Naidoo Jarushka , Kang Hyunseok , Sharfman William , Georgiades Christos , Verde Franco , Illei Peter , Li Qing Kay , Gabrielson Edward , Brock Malcolm V. , Zahnow Cynthia A. , Baylin Stephen B. , Scharpf Robert B. , Brahmer Julie R. , Karchin Rachel , Pardoll Drew M. , Velculescu Victor E.
Published: April 2023

Supplementary Table S1. Summary of Patient and Sample Characteristics. Supplementary Table S2. Summary of Next-Generation Sequencing Analyses. Supplementary Table S3. Somatic Sequence Alterations*. Supplementary Table S4. Somatic Copy Number Alterations. Supplementary Table S5. Neoantigen Predictions. Supplementary Table S6. Characteristics of a Subset of Eliminated Candidate Neoantigens in the NSCLC patients*. Supplementary Table S7. Summary of Functionally Validated Eliminated, Gained, and Retained cMANAs. Supplementary Table S8. Eliminated MANA-specific T Cell Clonotypes in CGLU116, CGLU127 and CGLU161. Supplementary Table S9. Retained and Gained MANA-specific T Cell Clonotypes in CGLU116. Supplementary Table S10. Allelic Imbalance Analysis and Cellularity Estimates for CGLU116. Supplementary Table S11. Allelic Imbalance Analysis and Cellularity Estimates for CGLU117. Supplementary Table S12. Allelic Imbalance Analysis and Cellularity Estimates for CGLU127. Supplementary Table S13. Allelic Imbalance Analysis and Cellularity Estimates for CGLU161. Supplementary Table S14. Summary of Eliminated Neoantigens in NSCLC Cases. Supplementary Table S15. TCR-beta Sequencing Analysis. Supplementary Table S16. PD-L1 and CD8 Immunohistochemistry. Supplementary Table S17. Regions of Allelic Imbalance. Supplementary Table S18. Tumor Purity and Ploidy Estimates.
Supplementary Table 1 from Response to MET Inhibitors in Patients with Stage IV Lung Adenocarcinomas Harboring MET Mutations Causing Exon 14 Skipping
Authors: Paik Paul K. , Drilon Alexander , Fan Pang-Dian , Yu Helena , Rekhtman Natasha , Ginsberg Michelle S. , Borsu Laetitia , Schultz Nikolaus , Berger Michael F. , Rudin Charles M. , Ladanyi Marc
Published: April 2023

nanoString probe sequences for MET exons 3, 4, 14, 20, and 21.
Supplementary Figure 2 from Response to MET Inhibitors in Patients with Stage IV Lung Adenocarcinomas Harboring MET Mutations Causing Exon 14 Skipping
Authors: Paik Paul K. , Drilon Alexander , Fan Pang-Dian , Yu Helena , Rekhtman Natasha , Ginsberg Michelle S. , Borsu Laetitia , Schultz Nikolaus , Berger Michael F. , Rudin Charles M. , Ladanyi Marc
Published: April 2023

Plot of MET exon 14 vs. exon 3-4 mRNA expression for 1) the 5 patients with MET exon 14 splice site mutations (red); and 2) 24 clinical cases that were MET wild-type (black). The H596 cell line was also tested as a positive control. The average expression of MET exon 14 was significantly lower in the patients with MET exon 14 splice site mutations than in the control patient samples (one-sided Wilcoxon test).
Supplementary Methods, Tables S1 - S2, S4, Figures S1 - S11 from Tracking the Genomic Evolution of Esophageal Adenocarcinoma through Neoadjuvant Chemotherapy
Authors: Murugaesu Nirupa , Wilson Gareth A. , Birkbak Nicolai J. , Watkins Thomas B.K. , McGranahan Nicholas , Kumar Sacheen , Abbassi-Ghadi Nima , Salm Max , Mitter Richard , Horswell Stuart , Rowan Andrew , Phillimore Benjamin , Biggs Jennifer , Begum Sharmin , Matthews Nik , Hochhauser Daniel , Hanna George B. , Swanton Charles
Published: April 2023

Supplementary Materials and Methods Supplementary Table S1 - Sequencing coverage for tumor regions and germline samples Supplementary Table S2 - Clinical characteristics of patients with EAC Supplementary Table S4 - Annotation of chromosomal segments that overlap with TCGA ESCA recurrent amplifications and tumor regions in our EAC cohort Supplementary Figure S1 - Mutations identified using M-seq compared with a single biopsy Supplementary Figure S2 - Relationship of intratumor heterogeneity and response to NAC treatment Supplementary Figure S3 - Tumor Phylograms Supplementary Figure S4 - Copy number events lead to mutational heterogeneity Supplementary Figure S5 - Heatmap of the all driver mutations identified across all tumor regions Supplementary Figure S6 - Driver mutations identified using M-seq compared with a single biopsy Supplementary Figure S7 - Copy number states across the genome for each tumor region Supplementary Figure S8 - Chromosome view of chromosome 19, tumor sample EAC017, region R1, demonstrating chromothripsis Supplementary Figure S9 - wGII scores for the TCGA ESCA cohort and M-seq EAC cohort Supplementary Figure S10 - The trinucleotide context for temporally dissected combined EAC cohort Supplementary Figure S11 - Assessing copy number heterogeneity using a minimum consecutive segment method
Supplementary Table 1 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Table 1. List of cell lines used in this study.
Table S2 from A Transposon Screen Identifies Loss of Primary Cilia as a Mechanism of Resistance to SMO Inhibitors
Authors: Zhao Xuesong , Pak Ekaterina , Ornell Kimberly J. , Pazyra-Murphy Maria F. , MacKenzie Ethan L. , Chadwick Emily J. , Ponomaryov Tatyana , Kelleher Joseph F. , Segal Rosalind A.
Published: April 2023

Supplementary Table S2, related to Figure 6. Mutations in ciliary genes were identified from whole-exome sequencing data of untreated and resistant BCC samples previously published (1). Ciliary genes were determined using the SYSCILIA gold standard list of 303 genes for known ciliary components (2). Provided as a separate Excel file.
Supplemental information from A Transposon Screen Identifies Loss of Primary Cilia as a Mechanism of Resistance to SMO Inhibitors
Authors: Zhao Xuesong , Pak Ekaterina , Ornell Kimberly J. , Pazyra-Murphy Maria F. , MacKenzie Ethan L. , Chadwick Emily J. , Ponomaryov Tatyana , Kelleher Joseph F. , Segal Rosalind A.
Published: April 2023

Supplementary Figures, tables, methods and references
Data S2 from MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia
Authors: Brown Fiona C. , Still Eric , Koche Richard P. , Yim Christina Y. , Takao Sumiko , Cifani Paolo , Reed Casie , Gunasekera Shehana , Ficarro Scott B. , Romanienko Peter , Mark Willie , McCarthy Craig , de Stanchina Elisa , Gonen Mithat , Seshan Venkatraman , Bhola Patrick , O'Donnell Conor , Spitzer Barbara , Stutzke Crystal , Lavallée Vincent-Philippe , Hébert Josée , Krivtsov Andrei V. , Melnick Ari , Paietta Elisabeth M. , Tallman Martin S. , Letai Anthony , Sauvageau Guy , Pouliot Gayle , Levine Ross , Marto Jarrod A , Armstrong Scott A. , Kentsis Alex
Published: April 2023

Processed data for S222A+ and S222A- cells by RNA and ATAC sequencing