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Methods Mol Biol. 2019;1979:111-132. doi: 10.1007/978-1-4939-9240-9_8.

Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing.

Aicher TP1,2,3, Carroll S4,5,6, Raddi G7,8,9,10, Gierahn T11, Wadsworth MH 2nd4,5,6, Hughes TK4,5,6, Love C4,6,11,12, Shalek AK4,5,6,11.

Author information

1
Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA. tpaicher@gmail.com.
2
Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA, USA. tpaicher@gmail.com.
3
Broad Institute of MIT and Harvard, Cambridge, MA, USA. tpaicher@gmail.com.
4
Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA.
5
Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA, USA.
6
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
7
Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
8
University of Cambridge, Cambridge, UK.
9
NIAID, National Institutes of Health, Bethesda, MD, USA.
10
David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
11
Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
12
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

Abstract

Seq-Well is a low-cost picowell platform that can be used to simultaneously profile the transcriptomes of thousands of cells from diverse, low input clinical samples. In Seq-Well, uniquely barcoded mRNA capture beads and cells are co-confined in picowells that are sealed using a semipermeable membrane, enabling efficient cell lysis and mRNA capture. The beads are subsequently removed and processed in parallel for sequencing, with each transcript's cell of origin determined via the unique barcodes. Due to its simplicity and portability, Seq-Well can be performed almost anywhere.

KEYWORDS:

Picowells; RNA-Seq; Seq-Well; Single-cell RNA sequencing; Single-cell genomics; Systems biology; Transcriptomics

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