bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Methods, Figure Legends, Table Legends, Figures S1 - S4, Tables S1 - S5 from Acquired Resistance to the TRK Inhibitor Entrectinib in Colorectal Cancer
Authors: Russo Mariangela , Misale Sandra , Wei Ge , Siravegna Giulia , Crisafulli Giovanni , Lazzari Luca , Corti Giorgio , Rospo Giuseppe , Novara Luca , Mussolin Benedetta , Bartolini Alice , Cam Nicholas , Patel Roopal , Yan Shunqi , Shoemaker Robert , Wild Robert , Di Nicolantonio Federica , Bianchi Andrea Sartore , Li Gang , Siena Salvatore , Bardelli Alberto
Published: April 2023

Supplementary Figure S1. LMNA-NTRK1 genetic rearrangement detected in patient's plasma and xeno. Supplementary Figure S2. Acquisition of mutations in the TRKA kinase domain drives secondary resistance to entrectinib in Ba/F3 TRKA WT cells. Supplementary Figure S3. NTRK1 mutations confer resistance to TRKA inhibition. Supplementary Figure S4. Homology alignment of NTRK1 p.G595 and p.G667 variants. Supplementary Table S1. NGS analysis of NTRK1 gene in patient's plasma and xeno. Supplementary Table S2. NGS analysis of patient's derived samples. Supplementary Table S3. Summary of serial ctDNA analyses. Supplementary Table S4. The p.G595R and p.G667C mutations confer resistance to multiple TRK inhibitors. Supplementary Table S5. NTRK1 p. G595R, p.G667C and LMNA-NTRK1 fusion probes for ddPCR.
Supplementary Table S3 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 S3: 30 TCGA studies used in this paper.
Supplementary Table 4 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 4. Patient survival data and classification, based on (1), and the K1/K2 clustering.
Supplementary Table 1 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 1. The 5 most enriched pathways in MM cell lines with increased DNA damage (high expression levels in cell lines with increased DNA damage).
Supplementary Figure 4 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

Pathological analysis of human BPDCN growing as a patient-derived xenograft (PDX) in mice. Splenic tissue is shown stained with H&E (at 40x and 100x magnification), and human BCL-2, CD45, CD4, CD56, and CD123 (all at 40x) from animals bearing a representative BPDCN PDX.
Supplementary Table S2 from Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma
Authors: Brayer Kathryn J. , Frerich Candace A. , Kang Huining , Ness Scott A.
Published: April 2023

Chimeric RNA-seq reads.
Supplementary Table S1 from Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor–Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma
Authors: Brayer Kathryn J. , Frerich Candace A. , Kang Huining , Ness Scott A.
Published: April 2023

Tumor sample information.
Supplementary Table S6 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 primer sequences used in Figure 5.
Supplementary Table S2 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 the enriched pathways in various analyses.
Supplementary Figure 6 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 6. Pancreatic CA-MSCs promote tumor sphere formation. GFP-labeled tumor cells were grown in growth media, in combination with CM from CA-MSCs and CM from CAFs or co-cultured with CA-MSCs or CAFs (red). Enhanced size of tumor spheres when tumor cells were grown with CA-MSCs in sphere forming media (*p <0.05 vs growth medium).
Supplementary Figure 3 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 3. Pancreatic CA-MSCs promote tumor growth. A. BXPC-3 (wild type KRAS) pancreatic cancer cells (5 x 104) transduced with a luciferase-expressing lentivirus were orthotopically injected alone or with same number of CAF or CA-MSC into the pancreatic tail of NOD/SCID mice (n=4 per group). Representative bioluminescent images of animals in each group are shown at 4 weeks after injection depicting tumor growth. B. Bioluminescent-based tumor growth (measured by signal intensity p/s/cm2) of luciferase tumors alone or in combination with CAFs or CA-MSCs (MSCs). Pooled results of the average tumor size {plus minus} SEM from each group. *p<0.05 vs. tumor alone group.
Supplementary Figure 1 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 1. A. FACS analysis of freshly digested pancreatic tumor tissue from two different PDA patients (left) and outgrown CAFs from matching patients cultured using the outgrowth method for 2 weeks (right), demonstrating the percentage of CA-MSCs expressing CD44+ CD73+ CD90+ CD49Î±+ markers. B. ELISA data quantifying amount of GM-CSF secreted by freshly isolated CA-MSCs and cultured CA-MSCs. C. Sorted single CA-MSCs demonstrate multipotent differentiation capacity in differential culture conditions. Specific cell stains used were Alizarin Red for bone, Oil Red O for adipose and Alcian Blue for cartilage.
Supplementary Table S2 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 Table S2. sgRNA sequences and Primer sequences used for CRISPR/Cas9 genome editing.
Supplementary Table S1 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

Lists of senescence-activated and senescence-inactivated TEs and SEs.
Supplementary Figure S4 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 S4. (A) Comparison between human and mouse wild-type (WT) calreticulin Cterminal tail. Blues indicates non-conserved regions between human and mouse. The wild-type proteins are highly conserved between the two species and contain many negatively-charged glutamic acid (E) amino acids. (B) Comparison between human and mouse amino acid sequences corresponding to the mutant C-terminal part of the human and mouse mutant with red shading indicating non-conserved regions. Despite the large number of mismatches, both mutant C-terminal tails are rich in positively charged amino acids (arginine (R) and lysine (K)).
Supplementary Figures S1 - S6 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

Supplementary Figure S1. Senescence-activated SASP enhancers are marked by H3K4Me1 in proliferating IMR90 cells. Supplementary Figure S2. Reproducibility analyses of biological replicates for H3K27Ac and BRD4 ChIP-Seq. Supplementary Figure S3. Enhancer remodeling during oncogene-induced senescence parallels gene expression changes. Supplementary Figure S4. Genetic and pharmacologic inhibition of BRD4 impairs SASP gene expression during oncogene-induced senescence (OIS). Supplementary Figure S5. BRD4 couples enhancer remodeling to SASP gene expression during etoposide-induced senescence. Supplementary Figure S6. Systemic and cell-autonomous suppression of Brd4 impairs the immune surveillance of senescent hepatocytes.
Supplementary Figure S1 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 S1. (A) Relative frequency of GFP positive cells in peripheral blood over time in BMT mice receiving empty vector, CALRWT or CALRMUT-expressing c-Kit+ BM cells. (B) Histopathologic H&E sections of BM from representative EV, CALRWT or CALRMUT recipient mice demonstrates megakaryocytic hyperplasia in CALRMUT recipient animals (100X magnification) (C) A N-terminal anti-CALR antibody demonstrated strong, diffuse cytoplasmic reactivity in megakaryocytes in representative normal and CALR-mutant patient bone marrow biopsies. In addition, cytoplasmic reactivity was noted in smaller mononuclear cells, which were morphologically most suggestive of early myeloid forms. Strong reactivity was not observed in mature erythrocytes or in mature granulocytes. (D) Flow cytometric analysis of Linâˆ’Sca-1+c-Kit+ (LSK) and Linâˆ’Sca-1âˆ’c-Kit+ (LK) cell numbers in the bone marrow of BMT mice receiving empty vector, CALRWT or CALRMUTexpressing BM cells 16 weeks post bone marrow transplantation demonstrates a significant increase in LSK cells in CALRMUT recipients. All p values were determined by unpaired two-tailed Student's t test. (*0.01 < p < 0.05; (**0.001 < p < 0.01; ns, not significant).
Supplementary Figures S1 - S9 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 Figure S1. ALK G1202R versus ALK G1202del. Supplementary Figure S2. ALK G1202del in ALK-rearranged lung cancer. Supplementary Figure S3. Swimmer's plot - alectinib. Supplementary Figure S4. Evaluation of MGH075-2E in drug screen. Supplementary Figure S5. MGH067-1 harbors an ALK rearrangement. Supplementary Figure S6. MGH021-5A. Supplementary Figure S7. MGH051-2C and MGH084-1D. Supplementary Figure S8. MGH049-1A and MGH075-2E. Supplementary Figure S9. MGH034-2A.
Supplementary Table 6 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

SNPs in the NFIB locus associated with metastasis at diagnosis with P{less than or equal to}1x10-5 in the discovery stage, and functionally annotated with information from the ENCODE and 1000 Genomes Project data.
Supplementary Figure S3. Tools used for targeting of Il6 and Stat3. from MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
Authors: Nowak Dawid G. , Cho Hyejin , Herzka Tali , Watrud Kaitlin , DeMarco Daniel V. , Wang Victoria M.Y. , Senturk Serif , Fellmann Christof , Ding David , Beinortas Tumas , Kleinman David , Chen Muhan , Sordella Raffaella , Wilkinson John E. , Castillo-Martin Mireia , Cordon-Cardo Carlos , Robinson Brian D. , Trotman Lloyd C.
Published: April 2023

Supplementary Figure S3. Tools used for targeting of Il6 and Stat3. (A) Il6 neutralizing antibody specifically decreases the proliferation of Pten/ Trp53 deficient primary MEFs. ANOVA, Dunnett's post-hoc test, **p<0.01, *p<0.05 vs wt, error bars are SD, n=4. (B) Il6-neutralizing antibody decreases phosphorylation of Stat3 compared to control IgG. Inhibition of Stat3 phosphorylation leads to inhibition of the Stat3 transcriptional target, Myc. (C) Western analysis of Stat3 activation in Pten/ Trp53 deficient primary MEFs shows partial response to the pan PI 3-kinase inhibitors Ly294002 but not to rapamycin. (D) Guava flow cytometry system analysis of genetic interference with Stat3 signaling by mutant Stat3 plasmid expression.
Supplementary Table S3 from CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions
Authors: Munoz Diana M. , Cassiani Pamela J. , Li Li , Billy Eric , Korn Joshua M. , Jones Michael D. , Golji Javad , Ruddy David A. , Yu Kristine , McAllister Gregory , DeWeck Antoine , Abramowski Dorothee , Wan Jessica , Shirley Matthew D. , Neshat Sarah Y. , Rakiec Daniel , de Beaumont Rosalie , Weber Odile , Kauffmann Audrey , McDonald E. Robert , Keen Nicholas , Hofmann Francesco , Sellers William R. , Schmelzle Tobias , Stegmeier Frank , Schlabach Michael R.
Published: April 2023

Annotations for the sgRNA/shRNA libraries containing average Zscore and copy number information.
Supplementary Table S2 from CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions
Authors: Munoz Diana M. , Cassiani Pamela J. , Li Li , Billy Eric , Korn Joshua M. , Jones Michael D. , Golji Javad , Ruddy David A. , Yu Kristine , McAllister Gregory , DeWeck Antoine , Abramowski Dorothee , Wan Jessica , Shirley Matthew D. , Neshat Sarah Y. , Rakiec Daniel , de Beaumont Rosalie , Weber Odile , Kauffmann Audrey , McDonald E. Robert , Keen Nicholas , Hofmann Francesco , Sellers William R. , Schmelzle Tobias , Stegmeier Frank , Schlabach Michael R.
Published: April 2023

Annotations for the sgRNA libraries containing sequences, target gene information, Zscore and RNAseq data for each cell line screened.
Supplementary Tables S1 - S6 from Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney
Authors: Mehra Rohit , Vats Pankaj , Cieslik Marcin , Cao Xuhong , Su Fengyun , Shukla Sudhanshu , Udager Aaron M. , Wang Rui , Pan Jincheng , Kasaian Katayoon , Lonigro Robert , Siddiqui Javed , Premkumar Kumpati , Palapattu Ganesh , Weizer Alon , Hafez Khaled S. , Wolf J. Stuart , Sangoi Ankur R. , Trpkov Kiril , Osunkoya Adeboye O. , Zhou Ming , Giannico Giovanna , McKenney Jesse K. , Dhanasekaran Saravana M. , Chinnaiyan Arul M.
Published: April 2023

Supplementary Tables S1 - S6. Supplementary Table S1. Patient clinical characteristics and summary of the observed molecular aberrations in the MTSCC cases studied. Supplementary Table S2. Sequencing quality metrics. Supplementary Table S3. Detailed list of somatic mutation calls in MTSCC cohort. Supplementary Table S4. Twenty three genes commonly regulated by PTPN14 siRNAs in the 3 cell lines identified by analysis of RNAseq data. (Supplementary Fig S4E). Supplementary Table S5. Geneset Enrichment analysis dataset details. Supplementary Table S6. Summary of immunohistochemistry staining results.
Supplementary Figure Legends, Table Legends from Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney
Authors: Mehra Rohit , Vats Pankaj , Cieslik Marcin , Cao Xuhong , Su Fengyun , Shukla Sudhanshu , Udager Aaron M. , Wang Rui , Pan Jincheng , Kasaian Katayoon , Lonigro Robert , Siddiqui Javed , Premkumar Kumpati , Palapattu Ganesh , Weizer Alon , Hafez Khaled S. , Wolf J. Stuart , Sangoi Ankur R. , Trpkov Kiril , Osunkoya Adeboye O. , Zhou Ming , Giannico Giovanna , McKenney Jesse K. , Dhanasekaran Saravana M. , Chinnaiyan Arul M.
Published: April 2023

Supplementary Figure Legends, Table Legends
Supplementary Figures S1 - S7 from Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer
Authors: Carter Hannah , Marty Rachel , Hofree Matan , Gross Andrew M. , Jensen James , Fisch Kathleen M. , Wu Xingyu , DeBoever Christopher , Van Nostrand Eric L. , Song Yan , Wheeler Emily , Kreisberg Jason F. , Lippman Scott M. , Yeo Gene W. , Gutkind J. Silvio , Ideker Trey
Published: April 2023

Supplementary Figure S1. Description of the TCGA data. Supplementary Figure S2. Flow chart describing data preprocessing, association testing and validation testing stages of the study. Supplementary Figure S3. QQ-plots and genomic inflation (G.I.) estimates for germlines associations with tumor site of origin. Supplementary Figure S4. Odds ratios for published cancer-associated markers from the NHGRI GWAS Catalog were compared to odds ratios for the same markers when testing for associations with tumor site of origin. Supplementary Figure S5. Power analysis and comparison of effect sizes between discovery and validation phases. Supplementary Figure S6. QQ-plots for germline associations with somatic status of cancer genes with validated associations. Supplementary Figure S7. Western blots.
Supplementary Figure S2 from Acquired METD1228V Mutation and Resistance to MET Inhibition in Lung Cancer
Authors: Bahcall Magda , Sim Taebo , Paweletz Cloud P. , Patel Jyoti D. , Alden Ryan S. , Kuang Yanan , Sacher Adrian G. , Kim Nam Doo , Lydon Christine A. , Awad Mark M. , Jaklitsch Michael T. , Sholl Lynette M. , Jänne Pasi A. , Oxnard Geoffrey R.
Published: April 2023

Supplementary Figure S2 shows expression of D1228V mutation in PC9 cells as confirmed by RT-PCR and cDNA sequencing.
Supplementary Table S7 from CD38-Mediated Immunosuppression as a Mechanism of Tumor Cell Escape from PD-1/PD-L1 Blockade
Authors: Chen Limo , Diao Lixia , Yang Yongbin , Yi Xiaohui , Rodriguez B. Leticia , Li Yanli , Villalobos Pamela A. , Cascone Tina , Liu Xi , Tan Lin , Lorenzi Philip L. , Huang Anfei , Zhao Qiang , Peng Di , Fradette Jared J. , Peng David H. , Ungewiss Christin , Roybal Jonathon , Tong Pan , Oba Junna , Skoulidis Ferdinandos , Peng Weiyi , Carter Brett W. , Gay Carl M. , Fan Youhong , Class Caleb A. , Zhu Jingfen , Rodriguez-Canales Jaime , Kawakami Masanori , Byers Lauren Averett , Woodman Scott E. , Papadimitrakopoulou Vassiliki A. , Dmitrovsky Ethan , Wang Jing , Ullrich Stephen E. , Wistuba Ignacio I. , Heymach John V. , Qin F. Xiao-Feng , Gibbons Don L.
Published: April 2023

Patient sample information as well as CD38 and PD-L1 IHC score in lung cancer tissue microarray bank TMA3.
Data S4 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 MRT199665 and DMSO treated OCI-AML2 cells by RNA sequencing
Data S3 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

Table of results for recombinant protein kinase screen for pS222 MEF2C
Supplementary figures with descriptions from Transcriptomic Profiling of the Tumor Microenvironment Reveals Distinct Subgroups of Clear Cell Renal Cell Cancer: Data from a Randomized Phase III Trial
Authors: Hakimi A. Ari , Voss Martin H. , Kuo Fengshen , Sanchez Alejandro , Liu Ming , Nixon Briana G. , Vuong Lynda , Ostrovnaya Irina , Chen Ying-Bei , Reuter Victor , Riaz Nadeem , Cheng Yuan , Patel Parul , Marker Mahtab , Reising Albert , Li Ming O. , Chan Timothy A. , Motzer Robert J.
Published: April 2023

Supplementary figures with descriptions
Figure S3 from Endothelial Activation and Blood–Brain Barrier Disruption in Neurotoxicity after Adoptive Immunotherapy with CD19 CAR-T Cells
Authors: Gust Juliane , Hay Kevin A. , Hanafi Laïla-Aïcha , Li Daniel , Myerson David , Gonzalez-Cuyar Luis F. , Yeung Cecilia , Liles W. Conrad , Wurfel Mark , Lopez Jose A. , Chen Junmei , Chung Dominic , Harju-Baker Susanna , Özpolat Tahsin , Fink Kathleen R. , Riddell Stanley R. , Maloney David G. , Turtle Cameron J.
Published: April 2023

Supplementary Figure 3. Early peak of serum IL-6 is associated with a higher risk of life-threatening neurotoxicity
Supplementary Table S6 from An LKB1–SIK Axis Suppresses Lung Tumor Growth and Controls Differentiation
Authors: Murray Christopher W. , Brady Jennifer J. , Tsai Min K. , Li Chuan , Winters Ian P. , Tang Rui , Andrejka Laura , Ma Rosanna K. , Kunder Christian A. , Chu Pauline , Winslow Monte M.
Published: April 2023

Expression levels of immunomodulatory genes in KT;H11LSL-Cas9 sgSik relative to KT tumors.
Supplementary Table S5 from An LKB1–SIK Axis Suppresses Lung Tumor Growth and Controls Differentiation
Authors: Murray Christopher W. , Brady Jennifer J. , Tsai Min K. , Li Chuan , Winters Ian P. , Tang Rui , Andrejka Laura , Ma Rosanna K. , Kunder Christian A. , Chu Pauline , Winslow Monte M.
Published: April 2023

Summary of GSEA analysis on Sik-targeted tumors using gene sets from previous publications centered on transcriptional profiling of the Lkb1-deficient state.
Supplementary Table S2 from An LKB1–SIK Axis Suppresses Lung Tumor Growth and Controls Differentiation
Authors: Murray Christopher W. , Brady Jennifer J. , Tsai Min K. , Li Chuan , Winters Ian P. , Tang Rui , Andrejka Laura , Ma Rosanna K. , Kunder Christian A. , Chu Pauline , Winslow Monte M.
Published: April 2023

Summary of published human lung adenocarcinoma datasets for which genotype and histological subtype annotations are available.
Supplementary Figure Legends from The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression
Authors: Pushalkar Smruti , Hundeyin Mautin , Daley Donnele , Zambirinis Constantinos P. , Kurz Emma , Mishra Ankita , Mohan Navyatha , Aykut Berk , Usyk Mykhaylo , Torres Luisana E. , Werba Gregor , Zhang Kevin , Guo Yuqi , Li Qianhao , Akkad Neha , Lall Sarah , Wadowski Benjamin , Gutierrez Johana , Kochen Rossi Juan Andres , Herzog Jeremy W. , Diskin Brian , Torres-Hernandez Alejandro , Leinwand Josh , Wang Wei , Taunk Pardeep S. , Savadkar Shivraj , Janal Malvin , Saxena Anjana , Li Xin , Cohen Deirdre , Sartor R. Balfour , Saxena Deepak , Miller George
Published: April 2023

Figure Legends for Figures S1-S8.
Tables from Age-Related Changes in HAPLN1 Increase Lymphatic Permeability and Affect Routes of Melanoma Metastasis
Authors: Ecker Brett L. , Kaur Amanpreet , Douglass Stephen M. , Webster Marie R. , Almeida Filipe V. , Marino Gloria E. , Sinnamon Andrew J. , Neuwirth Madalyn G. , Alicea Gretchen M. , Ndoye Abibatou , Fane Mitchell , Xu Xiaowei , Sim Myung Shin , Deutsch Gary B. , Faries Mark B. , Karakousis Giorgos C. , Weeraratna Ashani T.
Published: April 2023

TABLES S1 and S2
Supplementary Figure Legends from Age-Related Changes in HAPLN1 Increase Lymphatic Permeability and Affect Routes of Melanoma Metastasis
Authors: Ecker Brett L. , Kaur Amanpreet , Douglass Stephen M. , Webster Marie R. , Almeida Filipe V. , Marino Gloria E. , Sinnamon Andrew J. , Neuwirth Madalyn G. , Alicea Gretchen M. , Ndoye Abibatou , Fane Mitchell , Xu Xiaowei , Sim Myung Shin , Deutsch Gary B. , Faries Mark B. , Karakousis Giorgos C. , Weeraratna Ashani T.
Published: April 2023

Supplementary Figure Legends
Figure S5 from Age-Related Changes in HAPLN1 Increase Lymphatic Permeability and Affect Routes of Melanoma Metastasis
Authors: Ecker Brett L. , Kaur Amanpreet , Douglass Stephen M. , Webster Marie R. , Almeida Filipe V. , Marino Gloria E. , Sinnamon Andrew J. , Neuwirth Madalyn G. , Alicea Gretchen M. , Ndoye Abibatou , Fane Mitchell , Xu Xiaowei , Sim Myung Shin , Deutsch Gary B. , Faries Mark B. , Karakousis Giorgos C. , Weeraratna Ashani T.
Published: April 2023

Supplementary Figure 5
Figure S1 from Age-Related Changes in HAPLN1 Increase Lymphatic Permeability and Affect Routes of Melanoma Metastasis
Authors: Ecker Brett L. , Kaur Amanpreet , Douglass Stephen M. , Webster Marie R. , Almeida Filipe V. , Marino Gloria E. , Sinnamon Andrew J. , Neuwirth Madalyn G. , Alicea Gretchen M. , Ndoye Abibatou , Fane Mitchell , Xu Xiaowei , Sim Myung Shin , Deutsch Gary B. , Faries Mark B. , Karakousis Giorgos C. , Weeraratna Ashani T.
Published: April 2023

Figure S1
Figure S1, Figure S2, Figure S3, Figure S4 from Clinical and Biological Correlates of Neurotoxicity Associated with CAR T-cell Therapy in Patients with B-cell Acute Lymphoblastic Leukemia
Authors: Santomasso Bianca D. , Park Jae H. , Salloum Darin , Riviere Isabelle , Flynn Jessica , Mead Elena , Halton Elizabeth , Wang Xiuyan , Senechal Brigitte , Purdon Terence , Cross Justin R. , Liu Hui , Vachha Behroze , Chen Xi , DeAngelis Lisa M. , Li Daniel , Bernal Yvette , Gonen Mithat , Wendel Hans-Guido , Sadelain Michel , Brentjens Renier J.
Published: April 2023

Figure S1: Detailed time course of neurotoxicity for each patient; Figure S2: Serum cytokines in relation to tocilizumab and corticosteroid administration; Figure S3: Hematopoietic toxicity and coagulopathy in severe neurotoxicity; Figure S4: Angiopoietin 1 and 2 alterations in severe neurotoxicity
Supplementary Tables S2-S10 from Tissue-Specific Oncogenic Activity of KRASA146T
Authors: Poulin Emily J. , Bera Asim K. , Lu Jia , Lin Yi-Jang , Strasser Samantha Dale , Paulo Joao A. , Huang Tannie Q. , Morales Carolina , Yan Wei , Cook Joshua , Nowak Jonathan A. , Brubaker Douglas K. , Joughin Brian A. , Johnson Christian W. , DeStefanis Rebecca A. , Ghazi Phaedra C. , Gondi Sudershan , Wales Thomas E. , Iacob Roxana E. , Bogdanova Lana , Gierut Jessica J. , Li Yina , Engen John R. , Perez-Mancera Pedro A. , Braun Benjamin S. , Gygi Steven P. , Lauffenburger Douglas A. , Westover Kenneth D. , Haigis Kevin M.
Published: April 2023

Proteomics data from mouse tissues.
Supplementary Tables S14-S17 from Tissue-Specific Oncogenic Activity of KRASA146T
Authors: Poulin Emily J. , Bera Asim K. , Lu Jia , Lin Yi-Jang , Strasser Samantha Dale , Paulo Joao A. , Huang Tannie Q. , Morales Carolina , Yan Wei , Cook Joshua , Nowak Jonathan A. , Brubaker Douglas K. , Joughin Brian A. , Johnson Christian W. , DeStefanis Rebecca A. , Ghazi Phaedra C. , Gondi Sudershan , Wales Thomas E. , Iacob Roxana E. , Bogdanova Lana , Gierut Jessica J. , Li Yina , Engen John R. , Perez-Mancera Pedro A. , Braun Benjamin S. , Gygi Steven P. , Lauffenburger Douglas A. , Westover Kenneth D. , Haigis Kevin M.
Published: April 2023

Proteomics data from human cell lines.
Supplementary Methods, References and Legends from Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation
Authors: Song Chunying , Piva Marco , Sun Lu , Hong Aayoung , Moriceau Gatien , Kong Xiangju , Zhang Hong , Lomeli Shirley , Qian Jin , Yu Clarissa C. , Damoiseaux Robert , Kelley Mark C. , Dahlman Kimberley B. , Scumpia Philip O. , Sosman Jeffrey A. , Johnson Douglas B. , Ribas Antoni , Hugo Willy , Lo Roger S.
Published: April 2023

Supplementary Methods, References and Legends
Figure S7 from Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation
Authors: Song Chunying , Piva Marco , Sun Lu , Hong Aayoung , Moriceau Gatien , Kong Xiangju , Zhang Hong , Lomeli Shirley , Qian Jin , Yu Clarissa C. , Damoiseaux Robert , Kelley Mark C. , Dahlman Kimberley B. , Scumpia Philip O. , Sosman Jeffrey A. , Johnson Douglas B. , Ribas Antoni , Hugo Willy , Lo Roger S.
Published: April 2023

Figure S7
Suppl Videos S1-S8 from Homophilic CD44 Interactions Mediate Tumor Cell Aggregation and Polyclonal Metastasis in Patient-Derived Breast Cancer Models
Authors: Liu Xia , Taftaf Rokana , Kawaguchi Madoka , Chang Ya-Fang , Chen Wenjing , Entenberg David , Zhang Youbin , Gerratana Lorenzo , Huang Simo , Patel Dhwani B. , Tsui Elizabeth , Adorno-Cruz Valery , Chirieleison Steven M. , Cao Yue , Harney Allison S. , Patel Shivani , Patsialou Antonia , Shen Yang , Avril Stefanie , Gilmore Hannah L. , Lathia Justin D. , Abbott Derek W. , Cristofanilli Massimo , Condeelis John S. , Liu Huiping
Published: April 2023

Supplementary videos (autoplay) in ppt
Table S1 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

Crystallographic data collection and refinement statistics.
Supplementary Table S8-9 from Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition
Authors: Ennishi Daisuke , Takata Katsuyoshi , Béguelin Wendy , Duns Gerben , Mottok Anja , Farinha Pedro , Bashashati Ali , Saberi Saeed , Boyle Merrill , Meissner Barbara , Ben-Neriah Susana , Woolcock Bruce W. , Telenius Adèle , Lai Daniel , Teater Matt , Kridel Robert , Savage Kerry J. , Sehn Laurie H. , Morin Ryan D. , Marra Marco A. , Shah Sohrab P. , Connors Joseph M. , Gascoyne Randy D. , Scott David W. , Melnick Ari M. , Steidl Christian
Published: April 2023

Prognostic values of MHC expression
Figure S3 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

The relative allelic fraction of T790M does not change the potency of JBJ-04-125-02 in H3255 cells but the presence of EGF blunts the efficacy of JBJ-04-125-02 in Ba/F3 and H1975 cells.
Figure S2 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

JBJ-04-125-02 as a single agent does not result in any toxicity issues associated with weight loss.
Figure S1 from Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor
Authors: To Ciric , Jang Jaebong , Chen Ting , Park Eunyoung , Mushajiang Mierzhati , De Clercq Dries J.H. , Xu Man , Wang Stephen , Cameron Michael D. , Heppner David E. , Shin Bo Hee , Gero Thomas W. , Yang Annan , Dahlberg Suzanne E. , Wong Kwok-Kin , Eck Michael J. , Gray Nathanael S. , Jänne Pasi A.
Published: April 2023

JBJ-04-125-02 is more potent than EAI045 and JBJ-02-112-05 in the presence of cetuximab and is effective in inhibiting EGFR-dependent proliferation and phosphorylation in L858R/ C797S Ba/F3 cells.
Supplementary Table 1, Figures 1-6 from nab-Paclitaxel Potentiates Gemcitabine Activity by Reducing Cytidine Deaminase Levels in a Mouse Model of Pancreatic Cancer
Authors: Frese Kristopher K. , Neesse Albrecht , Cook Natalie , Bapiro Tashinga E. , Lolkema Martijn P. , Jodrell Duncan I. , Tuveson David A.
Published: April 2023

PDF file - 392K
Supplementary Methods, Figure Legends 1-6, Table 1 from nab-Paclitaxel Potentiates Gemcitabine Activity by Reducing Cytidine Deaminase Levels in a Mouse Model of Pancreatic Cancer
Authors: Frese Kristopher K. , Neesse Albrecht , Cook Natalie , Bapiro Tashinga E. , Lolkema Martijn P. , Jodrell Duncan I. , Tuveson David A.
Published: April 2023

PDF file - 122K
Supplementary Figures from In Vivo E2F Reporting Reveals Efficacious Schedules of MEK1/2–CDK4/6 Targeting and mTOR–S6 Resistance Mechanisms
Authors: Teh Jessica L.F. , Cheng Phil F. , Purwin Timothy J. , Nikbakht Neda , Patel Prem , Chervoneva Inna , Ertel Adam , Fortina Paolo M. , Kleiber Ines , HooKim Kim , Davies Michael A. , Kwong Lawrence N. , Levesque Mitch P. , Dummer Reinhard , Aplin Andrew E.
Published: April 2023

Supplementary Figures
Supplementary Data from Immunotherapy Resistance by Inflammation-Induced Dedifferentiation
Authors: Mehta Arnav , Kim Yeon Joo , Robert Lidia , Tsoi Jennifer , Comin-Anduix Begoña , Berent-Maoz Beata , Cochran Alistair J. , Economou James S. , Tumeh Paul C. , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

The supplementary data contains supplemental methods, figures, tables and the clinical trial protocol in which patients from this study were enrolled.
Figure S7 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S7
Figure S3 from ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells
Authors: Jimenez-Pascual Ana , Hale James S. , Kordowski Anja , Pugh Jamie , Silver Daniel J. , Bayik Defne , Roversi Gustavo , Alban Tyler J. , Rao Shilpa , Chen Rui , McIntyre Thomas M. , Colombo Giorgio , Taraboletti Giulia , Holmberg Karl O. , Forsberg-Nilsson Karin , Lathia Justin D. , Siebzehnrubl Florian A.
Published: April 2023

Supplementary Figure S3
Supplementary Table 3 from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors
Authors: Wang Tao , Lu Rong , Kapur Payal , Jaiswal Bijay S. , Hannan Raquibul , Zhang Ze , Pedrosa Ivan , Luke Jason J. , Zhang He , Goldstein Leonard D. , Yousuf Qurratulain , Gu Yi-Feng , McKenzie Tiffani , Joyce Allison , Kim Min S. , Wang Xinlei , Luo Danni , Onabolu Oreoluwa , Stevens Christina , Xie Zhiqun , Chen Mingyi , Filatenkov Alexander , Torrealba Jose , Luo Xin , Guo Wenbin , He Jingxuan , Stawiski Eric , Modrusan Zora , Durinck Steffen , Seshagiri Somasekar , Brugarolas James
Published: April 2023

Gene ontology analysis shows enriched GO terms of the 904 eTME genes (20x cutoff) (first sheet), the 778 and the 610 eTME genes (20x cutoff) that are not captured by the Immunome alone and Immunome+ESTIMATE+Winslow gene signatures (second and third sheets).
Supplementary Table 2 from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors
Authors: Wang Tao , Lu Rong , Kapur Payal , Jaiswal Bijay S. , Hannan Raquibul , Zhang Ze , Pedrosa Ivan , Luke Jason J. , Zhang He , Goldstein Leonard D. , Yousuf Qurratulain , Gu Yi-Feng , McKenzie Tiffani , Joyce Allison , Kim Min S. , Wang Xinlei , Luo Danni , Onabolu Oreoluwa , Stevens Christina , Xie Zhiqun , Chen Mingyi , Filatenkov Alexander , Torrealba Jose , Luo Xin , Guo Wenbin , He Jingxuan , Stawiski Eric , Modrusan Zora , Durinck Steffen , Seshagiri Somasekar , Brugarolas James
Published: April 2023

Annotation of eTME genes. eTME genes (3x) are shown in the table. The "eTME (20x)" column shows eTME genes that satisfy the 20x cutoff. The other columns show the interpretation of the eTME genes using BLUEPRINT data, the Winslow signatures, Immunome signatures, and the ESTIMATE signature (immune and stromal signatures combined).
Supplementary File from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors
Authors: Wang Tao , Lu Rong , Kapur Payal , Jaiswal Bijay S. , Hannan Raquibul , Zhang Ze , Pedrosa Ivan , Luke Jason J. , Zhang He , Goldstein Leonard D. , Yousuf Qurratulain , Gu Yi-Feng , McKenzie Tiffani , Joyce Allison , Kim Min S. , Wang Xinlei , Luo Danni , Onabolu Oreoluwa , Stevens Christina , Xie Zhiqun , Chen Mingyi , Filatenkov Alexander , Torrealba Jose , Luo Xin , Guo Wenbin , He Jingxuan , Stawiski Eric , Modrusan Zora , Durinck Steffen , Seshagiri Somasekar , Brugarolas James
Published: April 2023

The full technical details of DisHet
Supplementary Data from Immune Checkpoint Blockade Enhances Shared Neoantigen-Induced T-cell Immunity Directed against Mutated Calreticulin in Myeloproliferative Neoplasms
Authors: Cimen Bozkus Cansu , Roudko Vladimir , Finnigan John P. , Mascarenhas John , Hoffman Ronald , Iancu-Rubin Camelia , Bhardwaj Nina
Published: April 2023

This file contains supplementary methods, reference, tables (3), figures (10) and the corresponding legends for tables and figures.
Figure S1-S5 from Allele-Specific Mechanisms of Activation of MEK1 Mutants Determine Their Properties
Authors: Gao Yijun , Chang Matthew T. , McKay Daniel , Na Na , Zhou Bing , Yaeger Rona , Torres Neilawattie M. , Muniz Keven , Drosten Matthias , Barbacid Mariano , Caponigro Giordano , Stuart Darrin , Moebitz Henrik , Solit David B. , Abdel-Wahab Omar , Taylor Barry S. , Yao Zhan , Rosen Neal
Published: April 2023

Supplemental Data
Table S3 from Galectin-3, a Druggable Vulnerability for KRAS-Addicted Cancers
Authors: Seguin Laetitia , Camargo Maria F. , Wettersten Hiromi I. , Kato Shumei , Desgrosellier Jay S. , von Schalscha Tami , Elliott Kathryn C. , Cosset Erika , Lesperance Jacqueline , Weis Sara M. , Cheresh David A.
Published: April 2023

shRNA constructs
Supplementary Table from Response to ERBB3-Directed Targeted Therapy in NRG1-Rearranged Cancers
Authors: Drilon Alexander , Somwar Romel , Mangatt Biju P. , Edgren Henrik , Desmeules Patrice , Ruusulehto Anja , Smith Roger S. , Delasos Lukas , Vojnic Morana , Plodkowski Andrew J. , Sabari Joshua , Ng Kenneth , Montecalvo Joseph , Chang Jason , Tai Huichun , Lockwood William W. , Martinez Victor , Riely Gregory J. , Rudin Charles M. , Kris Mark G. , Arcila Maria E. , Matheny Christopher , Benayed Ryma , Rekhtman Natasha , Ladanyi Marc , Ganji Gopinath
Published: April 2023

Table S1
Table S1 from Galectin-3, a Druggable Vulnerability for KRAS-Addicted Cancers
Authors: Seguin Laetitia , Camargo Maria F. , Wettersten Hiromi I. , Kato Shumei , Desgrosellier Jay S. , von Schalscha Tami , Elliott Kathryn C. , Cosset Erika , Lesperance Jacqueline , Weis Sara M. , Cheresh David A.
Published: April 2023

Characteristics of cell lines
Table S3 from Deletion 6q Drives T-cell Leukemia Progression by Ribosome Modulation
Authors: Gachet Stéphanie , El-Chaar Tiama , Avran David , Genesca Eulalia , Catez Frédéric , Quentin Samuel , Delord Marc , Thérizols Gabriel , Briot Delphine , Meunier Godelieve , Hernandez Lucie , Pla Marika , Smits Willem K. , Buijs-Gladdines Jessica G. , Van Loocke Wouter , Menschaert Gerben , André-Schmutz Isabelle , Taghon Tom , Van Vlierberghe Pieter , Meijerink Jules P. , Baruchel André , Dombret Hervé , Clappier Emmanuelle , Diaz Jean-Jacques , Gazin Claude , de Thé Hugues , Sigaux François , Soulier Jean
Published: April 2023

Differentially Expressed Proteins Deleted versus non-deleted clones
Supplementary Figure Legends from Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer
Authors: Janjigian Yelena Y. , Sanchez-Vega Francisco , Jonsson Philip , Chatila Walid K. , Hechtman Jaclyn F. , Ku Geoffrey Y. , Riches Jamie C. , Tuvy Yaelle , Kundra Ritika , Bouvier Nancy , Vakiani Efsevia , Gao Jianjiong , Heins Zachary J. , Gross Benjamin E. , Kelsen David P. , Zhang Liying , Strong Vivian E. , Schattner Mark , Gerdes Hans , Coit Daniel G. , Bains Manjit , Stadler Zsofia K. , Rusch Valerie W. , Jones David R. , Molena Daniela , Shia Jinru , Robson Mark E. , Capanu Marinela , Middha Sumit , Zehir Ahmet , Hyman David M. , Scaltriti Maurizio , Ladanyi Marc , Rosen Neal , Ilson David H. , Berger Michael F. , Tang Laura , Taylor Barry S. , Solit David B. , Schultz Nikolaus
Published: April 2023

Text legends for Supplementary Figures S1-S4.
Supplementary Figures from Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition
Authors: Harding James J. , Lowery Maeve A. , Shih Alan H. , Schvartzman Juan M. , Hou Shengqi , Famulare Christopher , Patel Minal , Roshal Mikhail , Do Richard K. , Zehir Ahmet , You Daoqi , Selcuklu S. Duygu , Viale Agnes , Tallman Martin S. , Hyman David M. , Reznik Ed , Finley Lydia W.S. , Papaemmanuil Elli , Tosolini Alessandra , Frattini Mark G. , MacBeth Kyle J. , Liu Guowen , Fan Bin , Choe Sung , Wu Bin , Janjigian Yelena Y. , Mellinghoff Ingo K. , Diaz Luis A. , Levine Ross L. , Abou-Alfa Ghassan K. , Stein Eytan M. , Intlekofer Andrew M.
Published: April 2023

Figures S1 through S4
Supplementary Data from Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition
Authors: Harding James J. , Lowery Maeve A. , Shih Alan H. , Schvartzman Juan M. , Hou Shengqi , Famulare Christopher , Patel Minal , Roshal Mikhail , Do Richard K. , Zehir Ahmet , You Daoqi , Selcuklu S. Duygu , Viale Agnes , Tallman Martin S. , Hyman David M. , Reznik Ed , Finley Lydia W.S. , Papaemmanuil Elli , Tosolini Alessandra , Frattini Mark G. , MacBeth Kyle J. , Liu Guowen , Fan Bin , Choe Sung , Wu Bin , Janjigian Yelena Y. , Mellinghoff Ingo K. , Diaz Luis A. , Levine Ross L. , Abou-Alfa Ghassan K. , Stein Eytan M. , Intlekofer Andrew M.
Published: April 2023

Next-generation sequencing and droplet digital PCR
Supplementary Table 1 from Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor
Authors: Zhang Xiaoyang , Choi Peter S. , Francis Joshua M. , Gao Galen F. , Campbell Joshua D. , Ramachandran Aruna , Mitsuishi Yoichiro , Ha Gavin , Shih Juliann , Vazquez Francisca , Tsherniak Aviad , Taylor Alison M. , Zhou Jin , Wu Zhong , Berger Ashton C. , Giannakis Marios , Hahn William C. , Cherniack Andrew D. , Meyerson Matthew
Published: April 2023

Table S1: KLF5 E419Q-gained super-enhancers and the nearest genes
Supplementary Figures and Table from A Novel MCL1 Inhibitor Combined with Venetoclax Rescues Venetoclax-Resistant Acute Myelogenous Leukemia
Authors: Ramsey Haley E. , Fischer Melissa A. , Lee Taekyu , Gorska Agnieszka E. , Arrate Maria Pia , Fuller Londa , Boyd Kelli L. , Strickland Stephen A. , Sensintaffar John , Hogdal Leah J. , Ayers Gregory D. , Olejniczak Edward T. , Fesik Stephen W. , Savona Michael R.
Published: April 2023

Supplementary figures and table