Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

Abstract Reverse transcription—quantitative real-time PCR (RT-qPCR) is a ubiquitously used method in biological research, however, finding appropriate reference genes for normalization is challenging. We aimed to identify genes characterized with low expression variability among human cancer and nor...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Gergely Attila Rácz, Nikolett Nagy, József Tóvári, Ágota Apáti, Beáta G. Vértessy
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/75fd21e5bc2547d4bfcc35d5f61d861c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:75fd21e5bc2547d4bfcc35d5f61d861c
record_format	dspace
spelling	oai:doaj.org-article:75fd21e5bc2547d4bfcc35d5f61d861c2021-12-02T19:17:05ZIdentification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines10.1038/s41598-021-98869-x2045-2322https://doaj.org/article/75fd21e5bc2547d4bfcc35d5f61d861c2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98869-xhttps://doaj.org/toc/2045-2322Abstract Reverse transcription—quantitative real-time PCR (RT-qPCR) is a ubiquitously used method in biological research, however, finding appropriate reference genes for normalization is challenging. We aimed to identify genes characterized with low expression variability among human cancer and normal cell lines. For this purpose, we investigated the expression of 12 candidate reference genes in 13 widely used human cancer cell lines (HeLa, MCF-7, A-549, K-562, HL-60(TB), HT-29, MDA-MB-231, HCT 116, U-937, SH-SY5Y, U-251MG, MOLT-4 and RPMI-8226) and, in addition, 7 normal cell lines (HEK293, MRC-5, HUVEC/TERT2, HMEC, HFF-1, HUES 9, XCL-1). In our set of genes, we included SNW1 and CNOT4 as novel candidate reference genes based on the RNA HPA cell line gene data from The Human Protein Atlas. HNRNPL and PCBP1 were also included along with the „classical” reference genes ACTB, GAPDH, IPO8, PPIA, PUM1, RPL30, TBP and UBC. Results were evaluated using GeNorm, NormFiner, BestKeeper and the Comparative ΔCt methods. In conclusion, we propose IPO8, PUM1, HNRNPL, SNW1 and CNOT4 as stable reference genes for comparing gene expression between different cell lines. CNOT4 was also the most stable gene upon serum starvation.Gergely Attila RáczNikolett NagyJózsef TóváriÁgota ApátiBeáta G. VértessyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gergely Attila Rácz Nikolett Nagy József Tóvári Ágota Apáti Beáta G. Vértessy Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
description	Abstract Reverse transcription—quantitative real-time PCR (RT-qPCR) is a ubiquitously used method in biological research, however, finding appropriate reference genes for normalization is challenging. We aimed to identify genes characterized with low expression variability among human cancer and normal cell lines. For this purpose, we investigated the expression of 12 candidate reference genes in 13 widely used human cancer cell lines (HeLa, MCF-7, A-549, K-562, HL-60(TB), HT-29, MDA-MB-231, HCT 116, U-937, SH-SY5Y, U-251MG, MOLT-4 and RPMI-8226) and, in addition, 7 normal cell lines (HEK293, MRC-5, HUVEC/TERT2, HMEC, HFF-1, HUES 9, XCL-1). In our set of genes, we included SNW1 and CNOT4 as novel candidate reference genes based on the RNA HPA cell line gene data from The Human Protein Atlas. HNRNPL and PCBP1 were also included along with the „classical” reference genes ACTB, GAPDH, IPO8, PPIA, PUM1, RPL30, TBP and UBC. Results were evaluated using GeNorm, NormFiner, BestKeeper and the Comparative ΔCt methods. In conclusion, we propose IPO8, PUM1, HNRNPL, SNW1 and CNOT4 as stable reference genes for comparing gene expression between different cell lines. CNOT4 was also the most stable gene upon serum starvation.
format	article
author	Gergely Attila Rácz Nikolett Nagy József Tóvári Ágota Apáti Beáta G. Vértessy
author_facet	Gergely Attila Rácz Nikolett Nagy József Tóvári Ágota Apáti Beáta G. Vértessy
author_sort	Gergely Attila Rácz
title	Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
title_short	Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
title_full	Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
title_fullStr	Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
title_full_unstemmed	Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
title_sort	identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/75fd21e5bc2547d4bfcc35d5f61d861c
work_keys_str_mv	AT gergelyattilaracz identificationofnewreferencegeneswithstableexpressionpatternsforgeneexpressionstudiesusinghumancancerandnormalcelllines AT nikolettnagy identificationofnewreferencegeneswithstableexpressionpatternsforgeneexpressionstudiesusinghumancancerandnormalcelllines AT jozseftovari identificationofnewreferencegeneswithstableexpressionpatternsforgeneexpressionstudiesusinghumancancerandnormalcelllines AT agotaapati identificationofnewreferencegeneswithstableexpressionpatternsforgeneexpressionstudiesusinghumancancerandnormalcelllines AT beatagvertessy identificationofnewreferencegeneswithstableexpressionpatternsforgeneexpressionstudiesusinghumancancerandnormalcelllines
_version_	1718376919804674048

Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines

Ejemplares similares