Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

Hanni Willenbrock; Jesper Salomon; Rolf Søkilde; Kim Bundvig Barken; Thomas Nøhr Hansen; Finn Cilius Nielsen; Søren Møller; Thomas Litman

doi:10.1261/rna.1699809

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

Hanni Willenbrock, Jesper Salomon, Rolf Søkilde, Kim Bundvig Barken, Thomas Nøhr Hansen, Finn Cilius Nielsen, Søren Møller, Thomas Litman

119 Citations (Scopus)

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Abstract

Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.

Original language	English
Journal	RNA: A publication of the RNA Society
Volume	15
Issue number	11
Pages (from-to)	2028-34
Number of pages	6
ISSN	1355-8382
DOIs	https://doi.org/10.1261/rna.1699809
Publication status	Published - 2009

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Quantitative microRNA expression analysis: comparing microarrays with next-generation sequencing.Final published version, 488 KBLicence: Unspecified

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title = "Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing",

abstract = "Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.",

author = "Hanni Willenbrock and Jesper Salomon and Rolf S{\o}kilde and Barken, {Kim Bundvig} and Hansen, {Thomas N{\o}hr} and Nielsen, {Finn Cilius} and S{\o}ren M{\o}ller and Thomas Litman",

note = "Keywords: Gene Expression; MicroRNAs; Oligonucleotide Array Sequence Analysis; Reproducibility of Results; Sequence Analysis, RNA",

year = "2009",

doi = "10.1261/rna.1699809",

language = "English",

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T1 - Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

AU - Willenbrock, Hanni

AU - Salomon, Jesper

AU - Søkilde, Rolf

AU - Barken, Kim Bundvig

AU - Hansen, Thomas Nøhr

AU - Nielsen, Finn Cilius

AU - Møller, Søren

AU - Litman, Thomas

N1 - Keywords: Gene Expression; MicroRNAs; Oligonucleotide Array Sequence Analysis; Reproducibility of Results; Sequence Analysis, RNA

PY - 2009

Y1 - 2009

N2 - Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.

AB - Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing data. In addition, microarrays appear highly sensitive and perform equivalently to next-generation sequencing in terms of reproducibility and relative ratio quantification.

U2 - 10.1261/rna.1699809

DO - 10.1261/rna.1699809

M3 - Journal article

C2 - 19745027

SN - 1355-8382

VL - 15

SP - 2028

EP - 2034

JO - RNA

JF - RNA

IS - 11

ER -

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing

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