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

Toby P Aicher; Shaina Carroll; Gianmarco Raddi; Todd Gierahn; Marc H Wadsworth 2nd; Travis K Hughes; Chris Love; Alex K Shalek

doi:10.1007/978-1-4939-9240-9_8

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

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

Authors

Toby P Aicher^{1

2

3}, Shaina Carroll^{4

5

6}, Gianmarco Raddi^{7

8

9

10}, Todd Gierahn¹¹, Marc H Wadsworth 2nd^{4

5

6}, Travis K Hughes^{4

5

6}, Chris Love^{4

6

11

12}, Alex K Shalek^{4

5

6

11}

Affiliations

¹ Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA. [email protected].
² Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), MIT, Cambridge, MA, USA. [email protected].
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA. [email protected].
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.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Equipment Design
Gene Expression Profiling / economics
Gene Expression Profiling / instrumentation
Gene Expression Profiling / methods
Gene Library
High-Throughput Nucleotide Sequencing / economics
High-Throughput Nucleotide Sequencing / instrumentation
High-Throughput Nucleotide Sequencing / methods*
Humans
Membranes, Artificial
Polymerase Chain Reaction / economics
Polymerase Chain Reaction / instrumentation
Polymerase Chain Reaction / methods
RNA, Messenger / genetics*
Reverse Transcription
Sequence Analysis, RNA / economics
Sequence Analysis, RNA / instrumentation
Sequence Analysis, RNA / methods
Single-Cell Analysis / economics
Single-Cell Analysis / instrumentation
Single-Cell Analysis / methods*

Substances

Membranes, Artificial
RNA, Messenger

Abstract

Publication types

MeSH terms

Substances

Grants and funding