Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.
Gene Expression Omnibus
We thank R. Macare, A. Rotem, C. Muus, and E. Drokhlyansky for helpful discussions, T. Habib for babysitting, T. Tickle and A. Bankapur for technical support, and L. Gaffney and A. Hupalowska for help with graphics. Work was supported by the Klarman Cell Observatory, National Institute of Mental Health (NIMH) grant U01MH105960, National Cancer Institute (NCI) grant 1R33CA202820-1 and NIAID grant U24AI118672-01 (to A.R.), and Koch Institute Support (core) grant P30-CA14051 from the NCI. Microfluidic devices were fabricated at the Center for Nanoscale Systems, Harvard University, supported by National Science Foundation award no. 1541959. N.H. is supported by HHMI through the HHWF, A.R. is supported by HHMI, and F.Z. is supported by the New York Stem Cell Foundation. F.Z. is supported by NIMH (5DP1-MH100706 and 1R01-MH110049), NSF, HHMI, and the New York Stem Cell, Simons, Paul G. Allen Family, and Vallee Foundations, and by J. and P. Poitras, R. Metcalfe, and D. Cheng. D.A.W. thanks NSF DMR-1420570, NSF DMR-1310266, and NIH P01HL120839 grants for their support. GTEx is supported by the NIH Common Fund (Contract HHSN268201000029C to K.A.).
Integrated supplementary information
CAD scheme of DroNc-seq microfluidic device.