scholarly journals Selection of a reference gene for studies on lipid‐related aquatic adaptations of toothed whales ( Grampus griseus )

2021 ◽  
Author(s):  
Jayan D. M. Senevirathna ◽  
Ryo Yonezawa ◽  
Taiki Saka ◽  
Yoji Igarashi ◽  
Noriko Funasaka ◽  
...  
Keyword(s):  
Reference Gene ◽  
Grampus Griseus ◽  
Selection Of

scholarly journals Selection of Reference Gene Expression in a Schizophrenia Brain Cohort

2010 ◽  
Vol 44 (1) ◽  
pp. 59-70 ◽  
Author(s):  
Cynthia Shannon Weickert ◽  
Donna Sheedy ◽  
Debora A. Rothmond ◽  
Irina Dedova ◽  
Samantha Fung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Reference Gene Expression ◽  
Selection Of

scholarly journals Validation of the Reference Genes for the Gene Expression Studies in Chicken DT40 Cell Line

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 372
Author(s):  
Aleksandra Dunislawska ◽  
Anna Slawinska ◽  
Maria Siwek
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Reference Gene ◽  
Reference Genes ◽  
Gene Expression Analysis ◽  
Relative Gene Expression ◽  
Dt40 Cell ◽  
Relative Gene ◽  
Chicken Dt40 Cell ◽  
Selection Of

The selection of a suitable reference gene assures a reliable gene expression analysis when using the qPCR method. Normalization of the reaction is based on the basic metabolism genes. These genes show a constant, unregulated expression in all cells and function throughout their lifetime. In the current study, seven reference gene candidates were screened using RT-qPCR, to determine the best-matched pair of reference genes in the chicken DT40 cell line. The DT40 was derived from bursal lymphoma cells that were subjected to RAV-1 bird retroviral infection. It is a simplified in vitro model that allows tracking the direct interaction of stimulants on the lymphoid population and profiling of the hepatocellular B cell transcriptome. The reference gene analysis was carried out using statistical tools integrating four independent methods—geNorm, Best Keeper, NormFinder, delta Ct and RefFinder. Based on the selected reference genes, the relative gene expression analysis was done using the ddCt method. Complete relative gene expression study on a panel of the target genes revealed that proper selection of reference genes depending on the tissue eliminate decreases in data quality. The SDHA and RPL4 genes constitute stable internal controls as reference genes when analyzing gene expression in the DT40 cell line.

SELECTION OF REFERENCE GENE EXPRESSION IN A SCHIZOPHRENIA BRAIN COHORT

2010 ◽  
Vol 117 (2-3) ◽  
pp. 372
Author(s):  
Debora A. Rothmond ◽  
Samantha J. Fung ◽  
Jenny Wong ◽  
Carlotta Duncan ◽  
Shan-Yuan Tsai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Reference Gene Expression ◽  
Selection Of

scholarly journals Selection of reference gene in Eucalyptus camaldulensisfor real-time qRT-PCR

2011 ◽  
Vol 5 (S7) ◽  
Author(s):  
Boby Unnikrishnan ◽  
Gurumurthy Demlapura Shankaranarayan ◽  
Navin Sharma
Keyword(s):  
Real Time ◽  
Reference Gene ◽  
Qrt Pcr ◽  
Selection Of

scholarly journals Selection of a reference gene for studies of adipose tissues of toothed whales

2021 ◽  
Author(s):  
Jayan Senevirathna ◽  
Ryo Yonezawa ◽  
Taiki Saka ◽  
Yoji Igarashi ◽  
Kazutoshi Yoshitake ◽  
...  
Keyword(s):  
Reference Gene ◽  
Fat Metabolism ◽  
Housekeeping Gene ◽  
Suitable Reference Gene ◽  
Amplification Efficiency ◽  
Stable Gene ◽  
Reliable Technique ◽  
Toothed Whale ◽  
Suitable Reference ◽  
Selection Of

Fat metabolism in toothed whales is different from other mammals. RT-qPCR is still a reliable technique for studying the relative expressions of various genes involved in metabolism. This study was done for Risso’s dolphin, a toothed whale and information produced here will be important for further transcriptomics studies focused on unrevealed marine mammal fat metabolism. In this study, we sought to identify a suitable reference gene with minimum resources. Seven candidate reference genes ZC3H10, FTL, LGALS1, RPL27A, GAPDH, FTH1 and DCN were initially tested for amplification efficiency using RT-qPCR by producing standard curves. Then, three nearly 100% efficient genes FTL, LGALS1 and GAPDH were selected for the gene stability analysis to determine one stable gene across eight different fat tissues, liver, and muscle of Risso’s dolphins based on four algorithms, provided in geNorm, NormFinder, BestKeeper and Delta Ct. Finally, a RefFinder comprehensive ranking was done based on stability values and the genes were ranked as: FTL>LGALS1>GAPDH. The FTL and LGHLS were identified as the most stable genes; however, GAPDH was third, a well-known housekeeping gene for mammals. Finally, we suggest using FTL as a reliable reference gene for functional genomics studies on toothed whales in the future.

151 EVALUATION OF REFERENCE GENE TRANSCRIPT STABILITY DURING EARLY PRE-IMPLANTATION DEVELOPMENT AND IN SPERMATOGONIAL CELLS IN THE CAT

2012 ◽  
Vol 24 (1) ◽  
pp. 187 ◽  
Author(s):  
M. N. Biancardi ◽  
C. E. Pope ◽  
R. H. Powell ◽  
J. Galiguis ◽  
C. Dumas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Reference Gene ◽  
18S Rrna ◽  
Domestic Cat ◽  
Amplification Efficiency ◽  
Gene Transcript ◽  
Sample Type ◽  
Selection Of

Differences in the stability of commonly used reference genes have been discovered between species and among different tissue types. These inconsistencies underscore the importance of validation and selection of an appropriate reference for normalization of gene expression to an endogenous control in RT-qPCR experiments. Three different reference transcripts (GAPDH, RPS19 and 18S rRNA) of 3 different functional categories were selected for evaluation during pre-implantation embryonic development and in spermatogonial cells in the domestic cat. Amplification efficiency was done by standard curve analysis with 5-fold template dilutions. For pre-implantation analysis, transcripts were assayed at 4 developmental stages: 2- to 6-cell (2–6C), 8- to 16-cell (8–16C), morula (M) and blastocyst (BL). Embryos were from pools of 4 to 10 in vitro matured and fertilized domestic cat embryos. For spermatogonia, isolates of 20 000 to 30 000 cells were assayed from single testis isolates following a collagenase and trypsin with DNase digestion and Percoll gradient separation. Total mRNA was isolated using the Cells-to-cDNA II Kit, with a minimum of 2 biological replicates for each sample type. The RNA quantitation was done by RiboGreen analysis and 47 ng of RNA was used for cDNA synthesis. Transcript abundance was detected in 2 technical replicates per sample by SYBR Green chemistry and data were analysed with NormFinder and one-way ANOVA. Each transcript showed varying levels of expression throughout development and among embryonic stages and in spermatogonial cells. The GADPH and 18S rRNA transcripts were expressed at higher levels in BL than in 2–6C and 8–16C, respectively. Contrarily, transcript levels of RSP19 were lower in BL compared with levels at 2–6C. Even though differences were observed among embryonic stages, analysis with NormFinder indicated that the most stable reference gene throughout early pre-implantation development was RPS19. When each stage was analysed separately, 18S rRNA was the most stable at 2–6C, whereas RPS19 was found to be the most stable at 8–16C, M and BL stages. In spermatogonial samples, GAPDH was the most stably expressed gene. Our results support the selection of an appropriate reference gene based on the needs of the experimental design. We conclude from these findings that when gene expression throughout the duration of early embryonic development is examined, RPS19 is the preferred selection. If gene expression is analysed within discrete time points of development only, it is appropriate to select 18S rRNA at the 2–6C stage and RPS19 for 8–16C, M and BL stage embryos. For spermatogonial samples, if comparing only different biological replicates, GAPDH should be selected for normalization of expression; however if the purpose of the experiment is to assay genes that are also expressed in BL, the most stably expressed reference gene is RPS19.

scholarly journals Selection of Reference Genes for Quantitative Real-Time PCR in Chrysoperla nipponensis (Neuroptera: Chrysopidae) Under Tissues in Reproduction and Diapause

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Xiao Wang ◽  
Xue Kong ◽  
Shaoye Liu ◽  
Haiyi Huang ◽  
Zhenzhen Chen ◽  
...  
Keyword(s):  
Real Time ◽  
Reference Gene ◽  
Reference Genes ◽  
Fat Body ◽  
Model Organism ◽  
Reproductive Diapause ◽  
Genomics Research ◽  
Polymerase Chain ◽  
Selection Of ◽  
Polymerase Chain Reaction Data

Abstract Chrysoperla nipponensis (Okamoto), which has the unique diapause phenotype distinguishable from nondiapause adult, is an ideal model organism for studying the mechanism of reproductive diapause. However, there is no reliable and effective reference genes used for the reproductive diapause study of C. nipponensis. Therefore, in this study, we evaluated the expression stability of 10 candidate reference genes (Tub1, Arpc5, EF1a, 128up, RpS5, RpS26e, GAPDH, Arp3, Actin, α-Tub) in adults under diapause and nondiapause induction conditions using four statistical algorithms including GeNorm, NormFinder, Bestkeeper, and ∆CT method. Results showed that Arp3 and Tub1 were the most stable reference genes in all samples and in the adult tissues group. Arp3 and RpS5 were the most stable reference genes in the development degree group. α-Tub and EF1a were unstable reference genes under the conditions of this study. Meanwhile, to verify the reliability of the reference genes, we evaluated the relative expression levels of Vg and VgR in different treatments. Significant upregulation and downregulation in expression level of two genes in response to diapause termination and diapause fat body tissue was, respectively, observed when using Arp3 as the reference gene but not when using an unstable reference gene. The reference genes identified in this work provided not only the basis for future functional genomics research in diapause of C. nipponensis and will also identify reliable normalization factors for real-time quantitative real-time polymerase chain reaction data for other related insects.

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