https://biorxiv.org This feed contains articles for bioRxiv Channel "Allen Institute for Cell Science" bioRxiv https://biorxiv.org https://biorxiv.org/cgi/content/short/123042v1?rss=1" Roberts, B. Haupt, A. Tucker, A. Grancharova, T. Arakaki, J. Fuqua, M. A. Nelson, A. Hookway, C. Ludmann, S. A. Mueller, I. M. Yang, R. Horwitz, A. R. Rafelski, S. M. Gunawardane, R. N. 2017-03-31 doi:10.1101/123042 Cold Spring Harbor Laboratory Press 2017-03-31 https://biorxiv.org/cgi/content/short/216606v1?rss=1" Ounkomol, C. Fernandes, D. A. Seshamani, S. Maleckar, M. M. Collman, F. Johnson, G. R. 2017-11-09 doi:10.1101/216606 Cold Spring Harbor Laboratory Press 2017-11-09 https://biorxiv.org/cgi/content/short/238378v1?rss=1" Johnson, G. R. Donovan-Maiye, R. M. Maleckar, M. M. 2017-12-21 doi:10.1101/238378 Cold Spring Harbor Laboratory Press 2017-12-21 https://biorxiv.org/cgi/content/short/289504v1?rss=1" Ounkomol, C. Seshamani, S. Maleckar, M. M. Collman, F. Johnson, G. 2018-03-27 doi:10.1101/289504 Cold Spring Harbor Laboratory Press 2018-03-27 https://biorxiv.org/cgi/content/short/342881v1?rss=1" Roberts, B. Arakaki, J. Gerbin, K. A. Malik, H. Nelson, A. Hendershott, M. C. Hookway, C. Ludmann, S. A. Mueller, I. A. Yang, R. Rafelski, S. M. Gunawardane, R. N. 2018-06-09 doi:10.1101/342881 Cold Spring Harbor Laboratory Press 2018-06-09 https://biorxiv.org/cgi/content/short/2020.12.18.423371v1?rss=1" Coston, M. E. Gregor, B. W. Arakaki, J. Borensztejn, A. Do, T. P. Fuqua, M. A. Haupt, A. Hendershott, M. C. Leung, W. Mueller, I. A. Nelson, A. M. Rafelski, S. M. Swain-Bowden, M. J. Tang, W. J. Thirstrup, D. J. Wiegraebe, W. Yan, C. Gunawardane, R. N. Gaudreault, N. 2020-12-19 doi:10.1101/2020.12.18.423371 Cold Spring Harbor Laboratory Press 2020-12-19 https://biorxiv.org/cgi/content/short/491035v1?rss=1" Chen, J. Ding, L. Viana, M. P. Hendershott, M. C. Yang, R. Mueller, I. A. Rafelski, S. M. 2018-12-08 doi:10.1101/491035 Cold Spring Harbor Laboratory Press 2018-12-08 https://biorxiv.org/cgi/content/short/2020.12.08.415562v1?rss=1" Viana, M. P. Chen, J. Knijnenburg, T. A. Vasan, R. Yan, C. Arakaki, J. E. Bailey, M. Berry, B. Borensztejn, A. Brown, J. M. Carlson, S. Cass, J. A. Chaudhuri, B. Cordes Metzler, K. R. Coston, M. E. Crabtree, Z. J. Davidson, S. DeLizo, C. M. Dhaka, S. Dinh, S. Q. Do, T. P. Domingus, J. Donovan-Maiye, R. M. Foster, T. J. Frick, C. L. Fujioka, G. Fuqua, M. A. Gehring, J. L. Gerbin, K. A. Grancharova, T. Gregor, B. W. Harrylock, L. Haupt, A. Hendershott, M. C. Hookway, C. Horwitz, A. R. Hughes, C. Isaac, E. J. Johnson, G. R. Kim, B. Leonard, A. N. Leung, W. 2020-12-10 doi:10.1101/2020.12.08.415562 Cold Spring Harbor Laboratory Press 2020-12-10 https://biorxiv.org/cgi/content/short/2020.05.26.081083v1?rss=1" View larger version (60K): org.highwire.dtl.DTLVardef@8f89c4org.highwire.dtl.DTLVardef@19dc813org.highwire.dtl.DTLVardef@1ba7c20org.highwire.dtl.DTLVardef@2b3daa_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gerbin, K. A. Grancharova, T. Donovan-Maiye, R. Hendershott, M. C. Brown, J. Dinh, S. Q. Gehring, J. L. Hirano, M. Johnson, G. R. Nath, A. Nelson, A. Roco, C. M. Rosenberg, A. B. Sluzewski, M. F. Viana, M. P. Yan, C. Zaunbrecher, R. J. Cordes Metzler, K. R. Menon, V. Palecek, S. P. Seelig, G. Gaudreault, N. Knijnenburg, T. Rafelski, S. M. Theriot, J. A. Gunawardane, R. N. 2020-05-27 doi:10.1101/2020.05.26.081083 Cold Spring Harbor Laboratory Press 2020-05-27 https://biorxiv.org/cgi/content/short/2021.04.22.441027v1?rss=1" 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. As expected, differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in differentiation population composition and cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables. ]]> Grancharova, T. Gerbin, K. A. Rosenberg, A. B. Roco, C. M. Arakaki, J. DeLizzo, C. Dinh, S. Q. Donovan-Maiye, R. Hirano, M. Nelson, A. Tang, J. Theriot, J. A. Yan, C. Menon, V. Palecek, S. P. Seelig, G. Gunawardane, R. N. 2021-04-23 doi:10.1101/2021.04.22.441027 Cold Spring Harbor Laboratory Press 2021-04-23 https://biorxiv.org/cgi/content/short/2021.04.25.441198v1?rss=1" Hammer, M. Huisman, M. Rigano, A. Boehm, U. Chambers, J. J. Gaudreault, N. North, A. J. Pimentel, J. A. Sudar, D. Bajcsy, P. Brown, C. M. Corbett, A. D. Faklaris, O. Lacoste, J. Laude, A. Nelson, G. Nitschke, R. Farzam, F. Smith, C. Grunwald, D. Strambio-De-Castillia, C. 2021-04-26 doi:10.1101/2021.04.25.441198 Cold Spring Harbor Laboratory Press 2021-04-26