Listed below are highlighted papers from the lab. Stay tuned to this page for more publications as they are released.
For a complete set of publications please see google scholar
This study presents a novel semi-permeable capsule (SPC) that isolates single cells while allowing small molecules to diffuse in and out, enabling efficient biochemistry on encapsulated cells.
Dustin B. Mullaney†, Samantha R. Sgrizzi†, David Mai†, Ian Campbell†, Yuqi Huang, Andrius Šinkūnas, D. Lucas Kerr, Valentino E. Browning, Helen E. Eisenach, Jeremiah Sims, Eva K. Nichols, Christopher P. Lapointe, Yasuhiro Arimura, Kelley Harris, Rapolas Žilionis, Sanjay R. Srivatsan
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Spatial genomic sequencing-based approaches are limited by the complexities of associating DNA barcodes with spatial coordinates. We developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free method inspired by DNA microscopy.
Hanna Liao*, Sanjay Kottapalli*, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, Riza M. Daza, Frederick A. Matsen IV, Cole Trapnell, Jay Shendure, Sanjay Srivatsan
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A new framework for the use of single cell sequencing as a tool for whole organism phenotyping. We sequenced over 2 million single cells from zebrafish embryos to understand development.
Lauren M. Saunders*, Sanjay R. Srivatsan*, Madeleine Duran, Michael W. Dorrity, Brent Ewing, Tor Linbo, Jay Shendure, David W. Raible, Cecilia B. Moens, David Kimelman, Cole Trapnell
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Single-cell RNA sequencing can provide information about cellular relationships based on shared transcriptional programs. We developed sci-Space to add spatial context to single-cell transcriptomics.
Sanjay R Srivatsan*, Mary C Regier*, Eliza Barkan, Jennifer M Franks, Jonathan S Packer, Parker Grosjean, Madeleine Duran, Sarah Saxton, Jon J Ladd, Malte Spielmann, Carlos Lois, Paul D Lampe, Jay Shendure, Kelly R Stevens, Cole Trapnell
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First proof-of-concept experiment for showing that single cell sequencing can be used as a high content phenotyping modality to ascertain the effects of a library of chemicals on cancer cell lines.
Sanjay R Srivatsan*, José L McFaline-Figueroa*, Vijay Ramani*, Lauren Saunders, Junyue Cao, Jonathan Packer, Hannah A Pliner, Dana L Jackson, Riza M Daza, Lena Christiansen, Fan Zhang, Frank Steemers, Jay Shendure, Cole Trapnell
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