How the RNA isolation method can affect microRNA microarray results

Agnieszka Podolska; Bogumil Kaczkowski; Thomas Litman; Merete Fredholm; Susanna Cirera Salicio

How the RNA isolation method can affect microRNA microarray results

Agnieszka Podolska, Bogumil Kaczkowski, Thomas Litman, Merete Fredholm, Susanna Cirera Salicio

Computational and RNA Biology

25 Citations (Scopus)

Abstract

The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.

Original language	English
Journal	Acta Biochimica Polonica
Volume	58
Issue number	4
Pages (from-to)	535-540
Number of pages	6
ISSN	0001-527X
Publication status	Published - 2011

Keywords

Animals
Gene Expression Profiling
MicroRNAs
Oligonucleotide Array Sequence Analysis
RNA
RNA Stability
Reagent Kits, Diagnostic
Reproducibility of Results
Sensitivity and Specificity
Sequence Analysis, RNA
Swine

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title = "How the RNA isolation method can affect microRNA microarray results",

abstract = "The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana{\texttrademark} microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.",

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author = "Agnieszka Podolska and Bogumil Kaczkowski and Thomas Litman and Merete Fredholm and {Cirera Salicio}, Susanna",

year = "2011",

language = "English",

volume = "58",

pages = "535--540",

journal = "Acta Biochimica Polonica",

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TY - JOUR

T1 - How the RNA isolation method can affect microRNA microarray results

AU - Podolska, Agnieszka

AU - Kaczkowski, Bogumil

AU - Litman, Thomas

AU - Fredholm, Merete

AU - Cirera Salicio, Susanna

PY - 2011

Y1 - 2011

N2 - The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.

AB - The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.

KW - Animals

KW - Gene Expression Profiling

KW - MicroRNAs

KW - Oligonucleotide Array Sequence Analysis

KW - RNA

KW - RNA Stability

KW - Reagent Kits, Diagnostic

KW - Reproducibility of Results

KW - Sensitivity and Specificity

KW - Sequence Analysis, RNA

KW - Swine

M3 - Journal article

C2 - 22146134

SN - 0001-527X

VL - 58

SP - 535

EP - 540

JO - Acta Biochimica Polonica

JF - Acta Biochimica Polonica

IS - 4

ER -

How the RNA isolation method can affect microRNA microarray results

Abstract

Keywords

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