BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Daniel Alpern; Vincent Gardeux; Julie Russeil; Bastien Mangeat; Antonio C.A. Meireles-Filho; Romane Breysse; David Hacker; Bart Deplancke

doi:10.1186/s13059-019-1671-x

BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Daniel Alpern, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio C.A. Meireles-Filho, Romane Breysse, David Hacker, Bart Deplancke

Medicine

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

Abstract

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.

Original language	English (US)
Article number	71
Journal	Genome biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1671-x
State	Published - Apr 19 2019

Keywords

Barcoding
Gene expression
RNA-seq
Transcriptomics
qPCR

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Access to Document

10.1186/s13059-019-1671-x

Fingerprint Dive into the research topics of 'BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing'. Together they form a unique fingerprint.

Cite this

BRB-seq : Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. / Alpern, Daniel; Gardeux, Vincent; Russeil, Julie; Mangeat, Bastien; Meireles-Filho, Antonio C.A.; Breysse, Romane; Hacker, David; Deplancke, Bart.

In: Genome biology, Vol. 20, No. 1, 71, 19.04.2019.

Research output: Contribution to journal › Article › peer-review

@article{41c850ceb2bb4c6989884e9788de242b,

title = "BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing",

abstract = "Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.",

keywords = "Barcoding, Gene expression, RNA-seq, Transcriptomics, qPCR",

author = "Daniel Alpern and Vincent Gardeux and Julie Russeil and Bastien Mangeat and Meireles-Filho, {Antonio C.A.} and Romane Breysse and David Hacker and Bart Deplancke",

note = "Funding Information: This work was supported by a grant from the Commission for Technology and Innovation (17945.2 PFLS-LS) and the Precision Health & related Technologies Initiative (PHRT-502), by funds from the Swiss National Science Foundation (#31003A_162735 and #IZLIZ3_156815), and by Institutional Support from the Swiss Federal Institute of Technology in Lausanne (EPFL). Publisher Copyright: {\textcopyright} 2019 The Author(s).",

year = "2019",

month = apr,

day = "19",

doi = "10.1186/s13059-019-1671-x",

language = "English (US)",

volume = "20",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - BRB-seq

T2 - Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

AU - Alpern, Daniel

AU - Gardeux, Vincent

AU - Russeil, Julie

AU - Mangeat, Bastien

AU - Meireles-Filho, Antonio C.A.

AU - Breysse, Romane

AU - Hacker, David

AU - Deplancke, Bart

N1 - Funding Information: This work was supported by a grant from the Commission for Technology and Innovation (17945.2 PFLS-LS) and the Precision Health & related Technologies Initiative (PHRT-502), by funds from the Swiss National Science Foundation (#31003A_162735 and #IZLIZ3_156815), and by Institutional Support from the Swiss Federal Institute of Technology in Lausanne (EPFL). Publisher Copyright: © 2019 The Author(s).

PY - 2019/4/19

Y1 - 2019/4/19

N2 - Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.

AB - Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.

KW - Barcoding

KW - Gene expression

KW - RNA-seq

KW - Transcriptomics

KW - qPCR

UR - http://www.scopus.com/inward/record.url?scp=85064528030&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85064528030&partnerID=8YFLogxK

U2 - 10.1186/s13059-019-1671-x

DO - 10.1186/s13059-019-1671-x

M3 - Article

C2 - 30999927

AN - SCOPUS:85064528030

VL - 20

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 71

ER -

BRB-seq: Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this