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Cole Trapnell
Researcher at University of Washington
Publications - 148
Citations - 101469
Cole Trapnell is an academic researcher from University of Washington. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 57, co-authored 123 publications receiving 84590 citations. Previous affiliations of Cole Trapnell include Iowa State University & Massachusetts Institute of Technology.
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On the design of CRISPR-based single cell molecular screens
Andrew J. Hill,José L. McFaline-Figueroa,Lea M. Starita,Molly Gasperini,Kenneth A. Matreyek,Jonathan S. Packer,Dana Jackson,Jay Shendure,Cole Trapnell +8 more
TL;DR: It is demonstrated that vector designs for single cell molecular screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity.
Journal ArticleDOI
The continuum of Drosophila embryonic development at single-cell resolution
D. Calderon,Ronnie Blecher-Gonen,Xingfan Huang,Stefano Secchia,James Kentro,Riza M. Daza,Beth Martin,Alessandro Dulja,C. D. Schaub,Cole Trapnell,Erica Larschan,Kate M. O'Connor-Giles,Eileen E. M. Furlong,Jay Shendure +13 more
TL;DR: This Drosophila embryonic atlas broadly informs the orchestration of cellular states during the most dynamic stages in the life cycle of metazoan organisms, with continuous, multimodal views of molecular and cellular transitions in absolute time.
Posted ContentDOI
Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
Lauren M. Saunders,Abhishek Kumar Mishra,Andy Aman,Victor M Lewis,Matthew B. Toomey,Jonathan S. Packer,José L. McFaline-Figueroa,Xiaojie Qiu,Joseph C. Corbo,Cole Trapnell,David M. Parichy +10 more
TL;DR: It is found that thyroid hormone promotes the maturation of both melanophores and xanthophores in distinct ways, promoting cellular senescence and carotenoid accumulation, respectively.
Journal ArticleDOI
Optimized single-nucleus transcriptional profiling by combinatorial indexing
Beth Martin,Chengxiang Qiu,Eva Nichols,M. Phung,Rula Green-Gladden,Sanjay Srivatsan,Ronnie Blecher-Gonen,Brian J. Beliveau,Cole Trapnell,Junyue Cao,Jay Shendure +10 more
TL;DR: In this article , a simplified version of the Sci-RNA-seq protocol with three rounds of split-pool indexing was proposed, which is faster, more robust and more sensitive than the original protocol.
Posted ContentDOI
Dynamics of gene expression in single root cells of A. thaliana
Ken Jean-Baptiste,José L. McFaline-Figueroa,Cristina M. Alexandre,Michael W. Dorrity,Lauren M. Saunders,Kerry L. Bubb,Cole Trapnell,Stanley Fields,Christine Queitsch,Josh T. Cuperus +9 more
TL;DR: In this article, the authors apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells and use machine learning to reconstruct single-cell developmental trajectories along pseudotime.