Identification of Reference Genes in Chordoma Cells Allows Cross-Comparison of Expression Studies Across Subtypes

Didem SEVEN; Nehir KIZILILSOLEY; Emrah NIKEREL; Omer Faruk BAYRAK; Ugur TURE

doi:10.5137/1019-5149.JTN.42049-22.3

Issue release date: 08.03.2024

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Turkish Neurosurgery 2024 , Vol 34 , Num 1

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Identification of Reference Genes in Chordoma Cells Allows Cross-Comparison of Expression Studies Across Subtypes

Didem SEVEN¹,Nehir KIZILILSOLEY²,Emrah NIKEREL²,Omer Faruk BAYRAK¹,Ugur TURE³

¹Yeditepe University, Faculty of Medicine, Department of Medical Genetics, Istanbul, Türkiye
²Yeditepe University, Faculty of Engineering, Department of Genetics of Bioengineering, Istanbul, Türkiye
³Yeditepe University, Faculty of Medicine, Department of Neurosurgery, Istanbul, Türkiye DOI : 10.5137/1019-5149.JTN.42049-22.3 AIM: To present the best housekeeping genes including clival/sacral based chordoma, and the nucleus pulposus cells.

MATERIAL and METHODS: We investigated 13 candidate reference genes in public chordoma array transcriptome datasets, validated these genes by using RT-PCR, and evaluated their stability with NormFinder, geNorm, and Bestkeeper.

RESULTS: YWHAZ, TBP and PGK1 genes were identified as the most stable reference genes as confirmed with three different approaches. Conversely, KRT8, KRT19 and GAPDH genes are less stable and not appropriate for use in chordoma research.

CONCLUSION: For normalization of RT-PCR experiments in gene profiling of chordoma, we recommend the use of the stable genes YWHAZ, TBP and PGK1. Keywords : Chordoma cell lines, Reference genes, YWHAZ, TBP, PGK1

Corresponding author : Omer Faruk BAYRAK, ofbayrak@yeditepe.edu.tr