Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package

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Standard

Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package. / Petersen, Patrick H.D.; Lopacinska-Jørgensen, Joanna; Høgdall, Claus K.; Høgdall, Estrid V.

I: Bio-protocol, Bind 13, Nr. 17, e4801, 2023.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Petersen, PHD, Lopacinska-Jørgensen, J, Høgdall, CK & Høgdall, EV 2023, 'Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package', Bio-protocol, bind 13, nr. 17, e4801. https://doi.org/10.21769/BioProtoc.4801

APA

Petersen, P. H. D., Lopacinska-Jørgensen, J., Høgdall, C. K., & Høgdall, E. V. (2023). Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package. Bio-protocol, 13(17), [e4801]. https://doi.org/10.21769/BioProtoc.4801

Vancouver

Petersen PHD, Lopacinska-Jørgensen J, Høgdall CK, Høgdall EV. Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package. Bio-protocol. 2023;13(17). e4801. https://doi.org/10.21769/BioProtoc.4801

Author

Petersen, Patrick H.D. ; Lopacinska-Jørgensen, Joanna ; Høgdall, Claus K. ; Høgdall, Estrid V. / Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package. I: Bio-protocol. 2023 ; Bind 13, Nr. 17.

Bibtex

@article{057f702e4d844bf6a64ac91ed21193ef,
title = "Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package",
abstract = "When performing expression analysis either for coding RNA (e.g., mRNA) or non-coding RNA (e.g., miRNA), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used method. To normalize these data, one or more stable endogenous references must be identified. RefFinder is an online web-based tool using four almost universally used algorithms for assessing candidate endogenous references—delta-Ct, BestKeeper, geNorm, and Normfinder. However, the online interface is presently cumbersome and time consuming. We developed an R package, RefSeeker, which performs easy and straightforward RefFinder analysis by enabling raw data import and calculation of stability from each of the algorithms and provides data output tools to create graphs and tables. This protocol uses RefSeeker R package for fast and simple RefFinder stability analysis.",
keywords = "Coding and non-coding RNA expression, Expression stability, Normalization, R package, RefFinder, RT-qPCR",
author = "Petersen, {Patrick H.D.} and Joanna Lopacinska-J{\o}rgensen and H{\o}gdall, {Claus K.} and H{\o}gdall, {Estrid V.}",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors; exclusive licensee Bio-protocol LLC.",
year = "2023",
doi = "10.21769/BioProtoc.4801",
language = "English",
volume = "13",
journal = "Bio-protocol",
issn = "2331-8325",
publisher = "bio-protocol",
number = "17",

}

RIS

TY - JOUR

T1 - Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package

AU - Petersen, Patrick H.D.

AU - Lopacinska-Jørgensen, Joanna

AU - Høgdall, Claus K.

AU - Høgdall, Estrid V.

N1 - Publisher Copyright: © 2023 The Authors; exclusive licensee Bio-protocol LLC.

PY - 2023

Y1 - 2023

N2 - When performing expression analysis either for coding RNA (e.g., mRNA) or non-coding RNA (e.g., miRNA), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used method. To normalize these data, one or more stable endogenous references must be identified. RefFinder is an online web-based tool using four almost universally used algorithms for assessing candidate endogenous references—delta-Ct, BestKeeper, geNorm, and Normfinder. However, the online interface is presently cumbersome and time consuming. We developed an R package, RefSeeker, which performs easy and straightforward RefFinder analysis by enabling raw data import and calculation of stability from each of the algorithms and provides data output tools to create graphs and tables. This protocol uses RefSeeker R package for fast and simple RefFinder stability analysis.

AB - When performing expression analysis either for coding RNA (e.g., mRNA) or non-coding RNA (e.g., miRNA), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used method. To normalize these data, one or more stable endogenous references must be identified. RefFinder is an online web-based tool using four almost universally used algorithms for assessing candidate endogenous references—delta-Ct, BestKeeper, geNorm, and Normfinder. However, the online interface is presently cumbersome and time consuming. We developed an R package, RefSeeker, which performs easy and straightforward RefFinder analysis by enabling raw data import and calculation of stability from each of the algorithms and provides data output tools to create graphs and tables. This protocol uses RefSeeker R package for fast and simple RefFinder stability analysis.

KW - Coding and non-coding RNA expression

KW - Expression stability

KW - Normalization

KW - R package

KW - RefFinder

KW - RT-qPCR

U2 - 10.21769/BioProtoc.4801

DO - 10.21769/BioProtoc.4801

M3 - Journal article

C2 - 37719076

AN - SCOPUS:85171547948

VL - 13

JO - Bio-protocol

JF - Bio-protocol

SN - 2331-8325

IS - 17

M1 - e4801

ER -

ID: 396719549