TY - JOUR T1 - Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable? JF - bioRxiv DO - 10.1101/2020.12.08.415562 SP - 2020.12.08.415562 AU - Matheus P. Viana AU - Jianxu Chen AU - Theo A. Knijnenburg AU - Ritvik Vasan AU - Calysta Yan AU - Joy E. Arakaki AU - Matte Bailey AU - Ben Berry AU - Antoine Borensztejn AU - Jackson M. Brown AU - Sara Carlson AU - Julie A. Cass AU - Basudev Chaudhuri AU - Kimberly R. Cordes Metzler AU - Mackenzie E. Coston AU - Zach J. Crabtree AU - Steve Davidson AU - Colette M. DeLizo AU - Shailja Dhaka AU - Stephanie Q. Dinh AU - Thao P. Do AU - Justin Domingus AU - Rory M. Donovan-Maiye AU - Tyler J. Foster AU - Christopher L. Frick AU - Griffin Fujioka AU - Margaret A. Fuqua AU - Jamie L. Gehring AU - Kaytlyn A. Gerbin AU - Tanya Grancharova AU - Benjamin W. Gregor AU - Lisa Harrylock AU - Amanda Haupt AU - Melissa C. Hendershott AU - Caroline Hookway AU - Alan R. Horwitz AU - Chris Hughes AU - Eric J. Isaac AU - Gregory R. Johnson AU - Brian Kim AU - Andrew N. Leonard AU - Winnie Leung AU - Jordan J. Lucas AU - Susan A. Ludmann AU - Blair M. Lyons AU - Haseeb Malik AU - Ryan McGregor AU - Gabe E. Medrash AU - Sean L. Meharry AU - Kevin Mitcham AU - Irina A. Mueller AU - Timothy L. Murphy-Stevens AU - Aditya Nath AU - Angelique M. Nelson AU - Luana Paleologu AU - T. Alexander Popiel AU - Megan M. Riel-Mehan AU - Brock Roberts AU - Lisa M. Schaefbauer AU - Magdalena Schwarzl AU - Jamie Sherman AU - Sylvain Slaton AU - M. Filip Sluzewski AU - Jacqueline E. Smith AU - Youngmee Sul AU - Madison J. Swain-Bowden AU - W. Joyce Tang AU - Derek J. Thirstrup AU - Daniel T. Toloudis AU - Andrew P. Tucker AU - Veronica Valencia AU - Winfried Wiegraebe AU - Thushara Wijeratna AU - Ruian Yang AU - Rebecca J. Zaunbrecher AU - Allen Institute for Cell Science AU - Graham T. Johnson AU - Ruwanthi N. Gunawardane AU - Nathalie Gaudreault AU - Julie A. Theriot AU - Susanne M. Rafelski Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/12/10/2020.12.08.415562.abstract N2 - Despite the intimate link between cell organization and function, the principles underlying intracellular organization and the relation between organization, gene expression and phenotype are not well understood. We address this by creating a benchmark for mean cell organization and the natural range of cell-to-cell variation. This benchmark can be used for comparison to other normal or abnormal cell states. To do this, we developed a reproducible microscope imaging pipeline to generate a high quality dataset of 3D, high-resolution images of over 200,000 live cells from 25 isogenic human induced pluripotent stem cell (hiPSC) lines from the Allen Cell Collection. Each line contains one fluorescently tagged protein, created via endogenous CRISPR/Cas9 gene editing, representing a key cellular structure or organelle. We used these images to develop a new multi-part generalizable analysis approach of the locations, amounts, and variation of the 25 cellular structures. Taking an integrated approach, we found that both the extent to which a structure’s individual location varied (“stereotypy”) and the extent to which the structure localized relative to all the other cellular structures (“concordance”) were robust to a wide range of cell shape variation, from flatter to taller, smaller to larger, or less to more polarized cells. We also found that these cellular structures varied greatly in how their volumes scaled with cell and nuclear size. These analyses create a data-driven set of quantitative rules for the locations, amounts, and variation of 25 cellular structures within the hiPSC as a normal baseline for cell organization.Competing Interest StatementThe authors have declared no competing interest. ER -