Raj B, Wagner DW, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA*, Schier AF*. Nature Biotechnology, 2018. *co-corresponding authors
We merged single cell RNA sequencing with CRISPR-Cas lineage tracing to determine relationships between cells in a large single cell atlas of the juvenile zebrafish brain.
Detailed protocol available at Nature Protocols.
Gagnon JA, Obbad K, Schier AF. Development, 2018.
We discovered that the transcription factor Nanog is required primarily for extraembryonic tissue development, and is not required in embryonic or germ cells.
McKenna A*, Findlay G*, Gagnon JA*, Horwitz M, Schier AF, Shendure J. Science, 2016. * co-first authors
We developed GESTALT - a tool for lineage tracing in animals using CRISPR-Cas genome editing.
Highlighted by The Atlantic, BBC World Service, The Scientist, New Scientist, Science, Science Daily, HHMI News, Biotechniques, Harvard MCB News, Nature Reviews Genetics, Nature Biotechnology, Nature Methods, Cell Systems, Benchling, Epigenie, Faculty of 1000, and a finalist for Nature Methods Method of the Year 2017.
Gagnon JA, Valen E, Thyme SB, Huang P, Akhmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. PLoS One, 2014.
We determined rules that increase CRISPR-Cas activity in zebrafish, and found biases in DNA repair outcomes.
A (somewhat out of date) detailed protocol is available.