The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Autor: Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E. Rood, Orr Ashenberg, Ethan Cerami, Robert J. Coffey, Emek Demir, Li Ding, Edward D. Esplin, James M. Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W. Gray, Justin Guinney, Sean E. Hanlon, Shannon K. Hughes, E. Shelley Hwang, Christine A. Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E. Johnson, Ken S. Lau, Tracy Lively, Sarah A. Mazzilli, Dana Pe’er, Sandro Santagata, Alex K. Shalek, Denis Schapiro, Michael P. Snyder, Peter K. Sorger, Avrum E. Spira, Sudhir Srivastava, Kai Tan, Robert B. West, Elizabeth H. Williams, Denise Aberle, Samuel I. Achilefu, Foluso O. Ademuyiwa, Andrew C. Adey, Rebecca L. Aft, Rachana Agarwal, Ruben A. Aguilar, Fatemeh Alikarami, Viola Allaj, Christopher Amos, Robert A. Anders, Michael R. Angelo, Kristen Anton, Jon C. Aster, Ozgun Babur, Amir Bahmani, Akshay Balsubramani, David Barrett, Jennifer Beane, Diane E. Bender, Kathrin Bernt, Lynne Berry, Courtney B. Betts, Julie Bletz, Katie Blise, Adrienne Boire, Genevieve Boland, Alexander Borowsky, Kristopher Bosse, Matthew Bott, Ed Boyden, James Brooks, Raphael Bueno, Erik A. Burlingame, Qiuyin Cai, Joshua Campbell, Wagma Caravan, Hassan Chaib, Joseph M. Chan, Young Hwan Chang, Deyali Chatterjee, Ojasvi Chaudhary, Alyce A. Chen, Bob Chen, Changya Chen, Chia-hui Chen, Feng Chen, Yu-An Chen, Milan G. Chheda, Koei Chin, Roxanne Chiu, Shih-Kai Chu, Rodrigo Chuaqui, Jaeyoung Chun, Luis Cisneros, Graham A. Colditz, Kristina Cole, Natalie Collins, Kevin Contrepois, Lisa M. Coussens, Allison L. Creason, Daniel Crichton, Christina Curtis, Tanja Davidsen, Sherri R. Davies, Ino de Bruijn, Laura Dellostritto, Angelo De Marzo, David G. DeNardo, Dinh Diep, Sharon Diskin, Xengie Doan, Julia Drewes, Stephen Dubinett, Michael Dyer, Jacklynn Egger, Jennifer Eng, Barbara Engelhardt, Graham Erwin, Laura Esserman, Alex Felmeister, Heidi S. Feiler, Ryan C. Fields, Stephen Fisher, Keith Flaherty, Jennifer Flournoy, Angelo Fortunato, Allison Frangieh, Jennifer L. Frye, Robert S. Fulton, Danielle Galipeau, Siting Gan, Jianjiong Gao, Long Gao, Peng Gao, Vianne R. Gao, Tim Geiger, Ajit George, Gad Getz, Marios Giannakis, David L. Gibbs, William E. Gillanders, Simon P. Goedegebuure, Alanna Gould, Kate Gowers, William Greenleaf, Jeremy Gresham, Jennifer L. Guerriero, Tuhin K. Guha, Alexander R. Guimaraes, David Gutman, Nir Hacohen, Sean Hanlon, Casey R. Hansen, Olivier Harismendy, Kathleen A. Harris, Aaron Hata, Akimasa Hayashi, Cody Heiser, Karla Helvie, John M. Herndon, Gilliam Hirst, Frank Hodi, Travis Hollmann, Aaron Horning, James J. Hsieh, Shannon Hughes, Won Jae Huh, Stephen Hunger, Shelley E. Hwang, Heba Ijaz, Benjamin Izar, Connor A. Jacobson, Samuel Janes, Reyka G. Jayasinghe, Lihua Jiang, Brett E. Johnson, Bruce Johnson, Tao Ju, Humam Kadara, Klaus Kaestner, Jacob Kagan, Lukas Kalinke, Robert Keith, Aziz Khan, Warren Kibbe, Albert H. Kim, Erika Kim, Junhyong Kim, Annette Kolodzie, Mateusz Kopytra, Eran Kotler, Robert Krueger, Kostyantyn Krysan, Anshul Kundaje, Uri Ladabaum, Blue B. Lake, Huy Lam, Rozelle Laquindanum, Ashley M. Laughney, Hayan Lee, Marc Lenburg, Carina Leonard, Ignaty Leshchiner, Rochelle Levy, Jerry Li, Christine G. Lian, Kian-Huat Lim, Jia-Ren Lin, Yiyun Lin, Qi Liu, Ruiyang Liu, William J.R. Longabaugh, Teri Longacre, Cynthia X. Ma, Mary Catherine Macedonia, Tyler Madison, Christopher A. Maher, Anirban Maitra, Netta Makinen, Danika Makowski, Carlo Maley, Zoltan Maliga, Diego Mallo, John Maris, Nick Markham, Jeffrey Marks, Daniel Martinez, Robert J. Mashl, Ignas Masilionais, Jennifer Mason, Joan Massagué, Pierre Massion, Marissa Mattar, Richard Mazurchuk, Linas Mazutis, Eliot T. McKinley, Joshua F. McMichael, Daniel Merrick, Matthew Meyerson, Julia R. Miessner, Gordon B. Mills, Meredith Mills, Suman B. Mondal, Motomi Mori, Yuriko Mori, Elizabeth Moses, Yael Mosse, Jeremy L. Muhlich, George F. Murphy, Nicholas E. Navin, Michel Nederlof, Reid Ness, Stephanie Nevins, Milen Nikolov, Ajit Johnson Nirmal, Garry Nolan, Edward Novikov, Brendan O’Connell, Michael Offin, Stephen T. Oh, Anastasiya Olson, Alex Ooms, Miguel Ossandon, Kouros Owzar, Swapnil Parmar, Tasleema Patel, Gary J. Patti, Itsik Pe'er, Tao Peng, Daniel Persson, Marvin Petty, Hanspeter Pfister, Kornelia Polyak, Kamyar Pourfarhangi, Sidharth V. Puram, Qi Qiu, Álvaro Quintanal-Villalonga, Arjun Raj, Marisol Ramirez-Solano, Rumana Rashid, Ashley N. Reeb, Mary Reid, Adam Resnick, Sheila M. Reynolds, Jessica L. Riesterer, Scott Rodig, Joseph T. Roland, Sonia Rosenfield, Asaf Rotem, Sudipta Roy, Charles M. Rudin, Marc D. Ryser, Maria Santi-Vicini, Kazuhito Sato, Deborah Schrag, Nikolaus Schultz, Cynthia L. Sears, Rosalie C. Sears, Subrata Sen, Triparna Sen, Alex Shalek, Jeff Sheng, Quanhu Sheng, Kooresh I. Shoghi, Martha J. Shrubsole, Yu Shyr, Alexander B. Sibley, Kiara Siex, Alan J. Simmons, Dinah S. Singer, Shamilene Sivagnanam, Michal Slyper, Artem Sokolov, Sheng-Kwei Song, Austin Southard-Smith, Avrum Spira, Janet Stein, Phillip Storm, Elizabeth Stover, Siri H. Strand, Timothy Su, Damir Sudar, Ryan Sullivan, Lea Surrey, Mario Suvà, Nadezhda V. Terekhanova, Luke Ternes, Lisa Thammavong, Guillaume Thibault, George V. Thomas, Vésteinn Thorsson, Ellen Todres, Linh Tran, Madison Tyler, Yasin Uzun, Anil Vachani, Eliezer Van Allen, Simon Vandekar, Deborah J. Veis, Sébastien Vigneau, Arastoo Vossough, Angela Waanders, Nikhil Wagle, Liang-Bo Wang, Michael C. Wendl, Robert West, Chi-yun Wu, Hao Wu, Hung-Yi Wu, Matthew A. Wyczalkowski, Yubin Xie, Xiaolu Yang, Clarence Yapp, Wenbao Yu, Yinyin Yuan, Dadong Zhang, Kun Zhang, Mianlei Zhang, Nancy Zhang, Yantian Zhang, Yanyan Zhao, Daniel Cui Zhou, Zilu Zhou, Houxiang Zhu, Qin Zhu, Xiangzhu Zhu, Yuankun Zhu, Xiaowei Zhuang

Publikováno v: Cell

Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d2ea82738e14282269df985158663c08
https://doi.org/10.1016/j.cell.2020.03.053

Simultaneous Detection of RNAs and Proteins with Subcellular Resolution

Autor: Sunjong, Kwon, Koei, Chin, Michel, Nederlof

Publikováno v: Methods in molecular biology (Clifton, N.J.). 2161

We describe the detailed methods of "immunoFISH" to analyze the expression level and the spatial localization of RNA transcripts and proteins on cultured cells and formal-fixed, paraffin-embedded (FFPE) tissue sections. On cultured cells, we detect s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::eaa6bbdd86f6d7a68bfbf3725f31bff8
https://pubmed.ncbi.nlm.nih.gov/32681506

Simultaneous Detection of RNAs and Proteins with Subcellular Resolution

Autor: Koei Chin, Sunjong Kwon, Michel Nederlof

Publikováno v: Methods in Molecular Biology ISBN: 9781071606797

We describe the detailed methods of "immunoFISH" to analyze the expression level and the spatial localization of RNA transcripts and proteins on cultured cells and formal-fixed, paraffin-embedded (FFPE) tissue sections. On cultured cells, we detect s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::62c13cdba0edb7d04c0aad0a3d3f626a
https://doi.org/10.1007/978-1-0716-0680-3_6

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

Autor: Nicholas A. Clark, Marc R. Birtwistle, Jennifer E. Van Eyk, Moshe C. Silverstein, Caitlin E. Mills, Mario Niepel, Marcin Pilarczyk, Alexander Lachmann, Elizabeth H. Williams, Simon Koplev, Nathanael S. Gray, Uzma Hussain, Albert Lee, Ajay Pillai, Edward He, Mark A. Dane, Evren U. Azeloglu, Dusica Vidovic, Jeannette Osterloh, Maria G. Banuelos, Maxim V. Kuleshov, Rick J. Koch, Stephan C. Schürer, Karen Sachs, Damir Sudar, Divya Ramamoorthy, Dhruv Sareen, Shana White, Heidi S. Feiler, Siva Sivaganesan, Kathleen M. Jagodnik, Clive N. Svendsen, Mohammad Fallahi-Sichani, Miriam Adam, Jaroslaw Meller, Todd R. Golub, Ravi Iyengar, Jennifer Stocksdale, Amar Koleti, David Wrobel, Sherry L. Jenkins, Jacob D. Jaffe, Alexandra B Keenan, Renan Escalante-Chong, Daniel J. Cooper, Loren Ornelas, Joe W. Gray, Alexander LeNail, Ritchie Ho, Alyssa Coye, Avi Ma'ayan, Steve Finkbiener, Lixia Zhang, Andrea Matlock, Eric A. Sobie, Vidya Venkatraman, Anders B. Dohlman, Jeffrey D. Rothstein, Michele Forlin, Jonathan Z. Li, Rebecca Smith, Naim Al Mahi, Kaylyn Devlin, Caty Chung, Marc Hafner, Malvina Papanastasiou, Wen Niu, Michal Kouril, Ryan G. Lim, Yan Ren, Julia A. Kaye, Malcolm Casale, Jie Wu, Mario Medvedovic, Jeremy L. Muhlich, Victoria Dardov, Jouzas Vasiliauskas, Kelly Haston, Caroline E. Shamu, Raymond Terryn, John F. Reichard, Michel Nederlof, David Kilburn, Leslie M. Thompson, Jia-Ren Lin, Vasileios Stathias, Zichen Wang, Behrouz Shamsaei, James E. Korkola, Pamela Milani, Berhan Mandefro, Terri G. Thompson, Laura M. Heiser, Gavin Daigle, Denis Torre, Ron Margolis, Aravind Subramanian, Elmar Bucher, Sean D. Erickson, Ernest Fraenkel, Jaslin Kalra, Mark A. LaBarge, Gordon B. Mills, Peter K. Sorger, Sean M. Gross, Leslie Derr, Mehdi Fazel

Publikováno v: Cell Systems. 6:13-24

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f2e6db8bbc9afc2e0643a000d0253b2b
https://doi.org/10.1016/j.cels.2017.11.001

Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer

Autor: David Kilburn, James E. Korkola, Sean M. Gross, Kaylyn Devlin, Laura M. Heiser, Joe W. Gray, Mark A. Dane, Michel Nederlof, Damir Sudar, Rebecca Smith, Elmar Bucher

Publikováno v: Journal of visualized experiments : JoVE. (147)

Understanding the impact of the microenvironment on the phenotype of cells is a difficult problem due to the complex mixture of both soluble growth factors and matrix-associated proteins in the microenvironment in vivo. Furthermore, readily available

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::46038278be780eb1883168476f4079bc
https://pubmed.ncbi.nlm.nih.gov/31180341