C
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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Journal ArticleDOI
Massively multiplex chemical transcriptomics at single-cell resolution
Sanjay Srivatsan,José L. McFaline-Figueroa,Vijay Ramani,Vijay Ramani,Lauren M. Saunders,Junyue Cao,Jonathan S. Packer,Hannah A. Pliner,Dana Jackson,Riza M. Daza,Lena Christiansen,Fan Zhang,Frank J. Steemers,Jay Shendure,Cole Trapnell +14 more
TL;DR: The results with histone deacetylase inhibitors support the view that chromatin acts as an important reservoir of acetate in cancer cells, and reveal substantial intercellular heterogeneity in response to specific compounds, commonalities inresponse to families of compounds, and insight into differential properties within families.
Journal ArticleDOI
Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures.
Akshayalakshmi Sridhar,Akina Hoshino,Connor Finkbeiner,Alex Chitsazan,Li Dai,Alexandra K. Haugan,Kayla M. Eschenbacher,Dana Jackson,Cole Trapnell,Olivia Bermingham-McDonogh,Ian A. Glass,Thomas A. Reh +11 more
TL;DR: The authors' single-cell RNA sequencing comparisons of fetal retina, retinal organoids, and retinospheres provide a resource for developing better in vitro models for retinal disease.
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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,Jay Shendure,Cole Trapnell +9 more
TL;DR: This work optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
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A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition.
José L. McFaline-Figueroa,Andrew J. Hill,Xiaojie Qiu,Xiaojie Qiu,Dana Jackson,Jay Shendure,Cole Trapnell +6 more
TL;DR: Inhibiting the KRAS effector MEK and its upstream activators EGFR and MET demonstrates that interruption of key signaling events reveals regulatory ‘checkpoints’ in the EMT continuum that mimic discrete stages, and reconciles opposing views of the program that controls EMT.
Journal ArticleDOI
Modeling and automation of sequencing-based characterization of RNA structure
Sharon Aviran,Cole Trapnell,Cole Trapnell,Julius B. Lucks,Stefanie Mortimer,Shujun Luo,Gary P. Schroth,Jennifer A. Doudna,Jennifer A. Doudna,Jennifer A. Doudna,Adam P. Arkin,Adam P. Arkin,Lior Pachter +12 more
TL;DR: A novel assay utilizing selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) that can be used to characterize RNA secondary and tertiary structure and is generalized to modeling polymerase drop-off in other sequence census-based experiments.