Identification of reference genes for normalization of gene expression in thoroughbred and Jeju native horse(Jeju pony) tissues

Ahn, Kung; Bae, Jin-Han; Nam, Kyu-Hwi; Lee, Chong-Eon; Park, Kyung-Do; Lee, Hak-Kyo; Cho, Byung-Wook; Kim, Heui-Soo

doi:10.1007/s13258-010-0114-6

Cited by 17 publications

(13 citation statements)

References 25 publications

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“…According to the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, reference genes are now selected based on their specificity in interactions between a species or tissue subjected to different experimental treatments. Several studies have reported evaluations of reference gene in animals such as cattle [ 5 ], pig [ 6 ], sheep [ 7 ], goat [ 8 ], horse [ 9 ], fish [ 10 ], and birds [ 11 ]. However, a limited number of studies have investigated identification of reference genes used in chicken ( Gallus gallus ).…”

Section: Introductionmentioning

confidence: 99%

Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus )

et al. 2015

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Thirteen reference genes were investigated to determine their stability to be used as a housekeeping in gene expression studies in skeletal muscle of chickens. Five different algorithms were used for ranking of reference genes and results suggested that individual rankings of the genes differed among them. The stability of the expression of reference genes were validated using samples obtained from the Pectoralis major muscle in chicken. Samples were obtained from chickens in different development periods post hatch and under different nutritional diets. For gene expression calculation the ΔΔCt approach was applied to compare relative expression of pairs of genes within each of 52 samples when normalized to mitochondrially encoded cytochrome c oxidase II (MT-CO2) target gene. Our findings showed that hydroxymethylbilane synthase (HMBS) and hypoxanthine phosphoribosyl transferase 1 (HPRT1) are the most stable reference genes while transferrin receptor (TFRC) and beta-2-microglobulin (B2M) ranked as the least stable genes in the Pectoralis major muscle of chickens. Moreover, our results revealed that HMBS and HPRT1 gene expression did not change due to dietary variations and thus it is recommended for accurate normalization of RT-qPCR data in chicken Pectoralis major muscle.

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Section: Introductionmentioning

confidence: 99%

Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus )

et al. 2015

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“…For comparison four traditional RGs, two universal RGs and one expressed repetitive element were selected. The traditional RGs were selected just by educated guess-work and tradition ( ACTB and GAPDH , [ 30 ]) or based on stable expression across a panel of equine tissues ( UBB and B2M , [ 31 , 32 ]). The universal RGs, OAZ1 and RPS29 , exhibited highly uniform expression in men and mice across a plenitude of conditions [ 33 – 35 ].…”

Section: Methodsmentioning

confidence: 99%

The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data

et al. 2015

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BackgroundVertebrate evolution is accompanied by a substantial conservation of transcriptional programs with more than a third of unique orthologous genes showing constrained levels of expression. Moreover, there are genes and exons exhibiting excellent expression stability according to RNA-seq data across a panel of eighteen tissues including the ovary (Human Body Map 2.0).ResultsWe hypothesized that orthologs of these exons would also be highly uniformly expressed across neonatal ovaries of the horse, which would render them appropriate reference genes (RGs) for normalization of reverse transcription quantitative PCR (RT-qPCR) data in this context. The expression stability of eleven novel RGs (C1orf43, CHMP2A, EMC7, GPI, PSMB2, PSMB4, RAB7A, REEP5, SNRPD3, VCP and VPS29) was assessed by RT-qPCR in ovaries of seven neonatal fillies and compared to that of the expressed repetitive element ERE-B, two universal (OAZ1 and RPS29) and four traditional RGs (ACTB, GAPDH, UBB and B2M). Expression stability analyzed with the software tool RefFinder top ranked the normalization factor constituted of the genes SNRPD3 and VCP, a gene pair that is not co-expressed according to COEXPRESdb and GeneMANIA. The traditional RGs GAPDH, B2M, ACTB and UBB were only ranked 3rd and 12th to 14th, respectively.ConclusionsThe functional diversity of the novel RGs likely facilitates expression studies over a wide range of physiological and pathological contexts related to the neonatal equine ovary. In addition, this study augments the potential for RT-qPCR-based profiling of human samples by introducing seven new human RG assays (C1orf43, CHMP2A, EMC7, GPI, RAB7A, VPS29 and UBB).

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“…The melting curves were determined by increasing the temperature from 55°C to 99°C over a period of 30 s. All samples were amplified in triplicate to ensure reproducibility. As a standard control, the UBB gene was amplified with the primer pair described by Ahn et al (2011).…”

Section: Quantitative Rt-pcr Analysismentioning

confidence: 99%

Identification of ORF sequences and exercise-induced expression change in thoroughbred horse OXCT1 gene

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et al. 2012

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Identification of reference genes for normalization of gene expression in thoroughbred and Jeju native horse(Jeju pony) tissues

Cited by 17 publications

References 25 publications

Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus )

Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus )

The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data

Identification of ORF sequences and exercise-induced expression change in thoroughbred horse OXCT1 gene

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