scholarly journals Quality Evaluation of Reference Gene Expression on Different Tissues in Adults of Tropical Gar Atractosteus tropicus

2021 ◽  
Author(s):  
Luis Daniel Jimenez Martinez
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Quality Evaluation ◽  
Reference Gene Expression ◽  
Tropical Gar ◽  
Different Tissues ◽  
Atractosteus Tropicus

scholarly journals Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca’s response to salinity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Meng Wang ◽  
Tingting Ren ◽  
Prince Marowa ◽  
Haina Du ◽  
Zongchang Xu
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Reference Gene ◽  
Reference Genes ◽  
Suitable Reference Gene ◽  
Normalize Gene Expression ◽  
Suaeda Glauca ◽  
Suitable Reference ◽  
Germinating Seeds ◽  
Different Tissues

AbstractQuantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives under high-salt conditions, which promote the accumulation of high-value secondary metabolites. However, a suitable reference gene has not been identified for gene expression standardization in S. glauca under saline conditions. Here, 10 candidate reference genes, ACT7, ACT11, CCD1, TUA5, UPL1, PP2A, DREB1D, V-H+-ATPase, MPK6, and PHT4;5, were selected from S. glauca transcriptome data. Five statistical algorithms (ΔCq, geNorm, NormFinder, BestKeeper, and RefFinder) were applied to determine the expression stabilities of these genes in 72 samples at different salt concentrations in different tissues. PP2A and TUA5 were the most stable reference genes in different tissues and salt treatments, whereas DREB1D was the least stable. The two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with MYB and AP2 in germinating seeds of S. glauca exposed to different NaCl concentrations. Our study provides a foundational framework for standardizing qPCR analyses, enabling accurate gene expression profiling in S. glauca.

scholarly journals Selection and Validation of Appropriate Reference Genes for Gene Expression Studies in Schima Superba

2021 ◽  
Author(s):  
Zhongyi Yang ◽  
Rui Zhang ◽  
Zhichun Zhou
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Reference Genes ◽  
Geometric Mean ◽  
Gene Transcript ◽  
Expression Stability ◽  
Schima Superba ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Different Tissues

Abstract Background Quantitative real-time PCR (qRT-PCR) is a reliable and high-throughput technique for gene expression studies, but its accuracy depends on the expression stability of reference genes. Schima superba is a strong resistance and fast-growing timber specie. However, so far, reliable reference gene identifications have not been reported in S. superba. In this study, we screened and verified the stably expressed reference genes in different tissues of S. superba.Results Nineteen candidate reference genes were selected and evaluated for their expression stability in different tissues. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the reference gene transcript stabilities, and comprehensive stability ranking was generated by the geometric mean method. Our results identified that SsuACT was the most stable reference gene, SsuACT + SsuRIB was the best reference genes combination for different tissues. Finally, the stable and less stable reference genes were verified using the SsuSND1 expression in different tissues.Conclusions This is the first report to verify the appropriate reference genes for normalizing gene expression in S. superba for different tissues, which will facilitate future elucidation of gene regulations in this species, and useful references for relative species.

scholarly journals Selecting Suitable Reference Genes for qPCR Normalization: A Comprehensive Analysis in MCF-7 Breast Cancer Cell Line

2020 ◽  
Author(s):  
Nityanand Jain ◽  
Dina Nitisa ◽  
Valdis Pirsko ◽  
Inese Cakstina
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Reference Gene ◽  
Reference Genes ◽  
Cancer Cell Line ◽  
Internal Controls ◽  
Reference Gene Expression ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Mcf 7

Abstract BackgroundMCF-7 breast cancer cell line is undoubtedly amongst the most extensively studied patient-derived research models, providing pivotal results that have over the decades translated to constantly improving patient care. Many research groups, have previously identified suitable reference genes for qPCR normalization in MCF-7 cell line. However, over the course of identification of suitable reference genes, a comparative analysis comprising these genes together in a single study have not been reported. Furthermore, the expression dynamics of these reference genes within sub-clones cultured over multiple passages (p) has attracted limited attention from research groups. Therefore, we investigated the expression dynamics of 12 previously suggested reference genes within two sub-clones (culture A1 and A2) cultured identically over multiple passages. Additionally, the effect of nutrient stress on reference gene expression was examined to devise an evidence-based recommendation of the least variable reference genes that could be employed in future gene expression studies.ResultsThe analysis revealed the presence of differential reference gene expression within the sub-clones of MCF-7. In culture A1, GAPDH-CCSER2 were identified as the least variable reference gene pair while for culture A2, GAPDH-RNA28S was identified. However, upon validation using genes of interest, both these pairs were found to be unsuitable control pairs. Normalization of AURKA and KRT19 with triplet pair GAPDH-PCBP1-CCSER2 yielded successful results. The triplet also proved its capability to handle variations arising from nutrient stress.ConclusionsThe variance in expression behavior amongst sub-clones highlights the potential need for exercising caution while selecting reference genes for MCF-7. GAPDH-PCBP1-CCSER2 triplet offers a reliable alternative to otherwise traditionally used internal controls for optimizing intra- and inter-assay gene expression differences. Furthermore, we suggest avoiding the use of ACTB, GAPDH and PGK1 as single internal controls.

Trypsin gene expression in adults and larvae of tropical gar Atractosteus tropicus

2019 ◽  
Vol 46 (1) ◽  
pp. 145-155
Author(s):  
Kristal de M. Jesús-De la Cruz ◽  
Ángela Ávila-Fernández ◽  
Emyr Saúl Peña-Marín ◽  
Luis Daniel Jiménez-Martínez ◽  
Dariel Tovar-Ramírez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tropical Gar ◽  
Atractosteus Tropicus

Multiplex qPCR assay for assessment of reference gene expression stability in rat tissues/samples

2020 ◽  
Vol 53 ◽  
pp. 101611 ◽  
Author(s):  
Alexander P. Schwarz ◽  
Daria A. Malygina ◽  
Anna A. Kovalenko ◽  
Alexander N. Trofimov ◽  
Aleksey V. Zaitsev
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Qpcr Assay ◽  
Rat Tissues ◽  
Expression Stability ◽  
Gene Expression Stability ◽  
Multiplex Qpcr ◽  
Reference Gene Expression

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 Effect of β-Glucans in Diets on Growth, Survival, Digestive Enzyme Activity, and Immune System and Intestinal Barrier Gene Expression for Tropical Gar (Atractosteus tropicus) Juveniles

Fishes ◽  
2018 ◽  
Vol 3 (3) ◽  
pp. 27 ◽  
Author(s):  
Karen Nieves-Rodríguez ◽  
Carlos Álvarez-González ◽  
Emyr Peña-Marín ◽  
Fernando Vega-Villasante ◽  
Rafael Martínez-García ◽  
...  
Keyword(s):  
Gene Expression ◽  
Enzyme Activity ◽  
Immune System ◽  
Digestive Enzyme ◽  
Intestinal Barrier ◽  
Digestive Enzyme Activity ◽  
Tropical Gar ◽  
Atractosteus Tropicus

Impact of Thawing on Reference Gene Expression Stability in Renal Cell Carcinoma Samples

2012 ◽  
Vol 21 (3) ◽  
pp. 157-163 ◽  
Author(s):  
Yi Ma ◽  
HuiLi Dai ◽  
XianMing Kong ◽  
LiMin Wang
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Reference Gene ◽  
Renal Cell ◽  
Expression Stability ◽  
Gene Expression Stability ◽  
Reference Gene Expression

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 Reference gene expression in human osteosarcoma cell lines treated by EGB and CTX

2017 ◽  
Vol 41 ◽  
pp. 439-447
Author(s):  
Ming REN ◽  
Qiwei YANG ◽  
Yuanyuan SONG ◽  
Ao WANG ◽  
Qingyu WANG ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Reference Gene ◽  
Osteosarcoma Cell ◽  
Human Osteosarcoma ◽  
Human Osteosarcoma Cell ◽  
Reference Gene Expression
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