Assessment of an internal reference gene in Rhodobacter sphaeroides grown under cobalt exposure

2010 ◽  
Vol 50 (3) ◽  
pp. 302-305 ◽  
Author(s):  
Luca Losurdo ◽  
Francesca Italiano ◽  
Massimo Trotta ◽  
Raffaele Gallerani ◽  
Ruggiero Ceci Luigi ◽  
...  
Keyword(s):  
Reference Gene ◽  
Rhodobacter Sphaeroides ◽  
Internal Reference ◽  
Internal Reference Gene ◽  
Cobalt Exposure

scholarly journals Validation of internal reference genes for relative quantitation studies of gene expression in human laryngeal cancer

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2763 ◽  
Author(s):  
Xiaofeng Wang ◽  
Jinting He ◽  
Wei Wang ◽  
Ming Ren ◽  
Sujie Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Laryngeal Cancer ◽  
Reference Genes ◽  
Target Gene ◽  
Cancer Tissue ◽  
Internal Reference ◽  
Target Gene Expression ◽  
Internal Reference Gene ◽  
Relative Quantitation

BackgroundThe aim of this study was to determine the expression stabilities of 12 common internal reference genes for the relative quantitation analysis of target gene expression performed by reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) in human laryngeal cancer.MethodsHep-2 cells and 14 laryngeal cancer tissue samples were investigated. The expression characteristics of 12 internal reference gene candidates (18S rRNA, GAPDH, ACTB, HPRT1, RPL29, HMBS, PPIA, ALAS1, TBP, PUM1, GUSB, and B2M) were assessed by RT-qPCR. The data were analyzed by three commonly used software programs: geNorm, NormFinder, and BestKeeper.ResultsThe use of the combination of four internal reference genes was more appropriate than the use of a single internal reference gene. The optimal combination was PPIA + GUSB + RPL29 + HPRT1 for both the cell line and tissues; while the most appropriate combination was GUSB + RPL29 + HPRT1 + HMBS for the tissues.ConclusionsOur recommended internal reference genes may improve the accuracy of relative quantitation analysis of target gene expression performed by the RT-qPCR method in further gene expression research on laryngeal tumors.

scholarly journals β-2 microglobulin is unsuitable as an internal reference gene for the analysis of gene expression in human colorectal cancer

2013 ◽  
Vol 1 (2) ◽  
pp. 193-196 ◽  
Author(s):  
YASUHIRO NIHON-YANAGI ◽  
KENSUKE TERAI ◽  
TAKEYOSHI MURANO ◽  
TAKAYUKI KAWAI ◽  
SHINYA KIMURA ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Reference Gene ◽  
Human Colorectal Cancer ◽  
Internal Reference ◽  
Internal Reference Gene

scholarly journals Internal Reference Gene Selection for Quantitative Real-Time RT-PCR Normalization in Potato Tissues

Phyton ◽  
2020 ◽  
Vol 89 (2) ◽  
pp. 329-344
Author(s):  
Gang Li ◽  
Yao Zhou ◽  
Yaqi Zhao ◽  
Yaxue Liu ◽  
Yuwei Ke ◽  
...  
Keyword(s):  
Real Time ◽  
Reference Gene ◽  
Gene Selection ◽  
Rt Pcr ◽  
Internal Reference ◽  
Reference Gene Selection ◽  
Internal Reference Gene ◽  
Selection For

scholarly journals Internal Reference Gene Selection under Different Hormone Stresses in Multipurpose Timber Yielding Tree Neolamarckia cadamba

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1014
Author(s):  
Deng Zhang ◽  
Jingjian Li ◽  
Buye Li ◽  
Chunmei Li ◽  
Xiaoyang Chen ◽  
...  
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Gene Selection ◽  
Housekeeping Genes ◽  
Gene Families ◽  
Internal Reference ◽  
Qpcr Data ◽  
Reference Gene Selection ◽  
Internal Reference Gene ◽  
Cell Wall Extension

Neolamarckia cadamba, a member of the Rubiaceae family, is widely distributed throughout South Asia and South China. In order to acquire reliable and repeatable results, the use of a suitable internal reference gene to normalize the RT-qPCR data is essential. In this study, we reported the validation of housekeeping genes to identify the most suitable internal reference gene(s) for normalization of qPCR data obtained among different tissues (bud, leaf, cambium region) under different hormone stresses. Here, ΔCt, geNorm, NormFinder, and BestKeeper analyses were carried out to analyze the normalization of qPCR data of twenty-one reference gene families (ACT, CAC, CYP, EF1α, eIF, FPS1, FBK, GAPDH, RAN, PEPKR1, PP2A, RPL, RPS, RuBP, SAMDC, TEF, Tub-α, Tub-β, UBCE, UBQ, UPL) including 43 genes. The results showed that FPS1, RPL, and FBK were the most stable reference genes across all of the tested samples. In addition, the expression of NcEXPA8, one gene of interest that plays an important role in regulating cell wall extension, under different phytohormone stresses was used to further confirm the validated reference genes. Taken together, our results provide guidelines for reference gene selection under different phytohormone stresses and a foundation for more accurate and widespread use of RT-qPCR in N. cadamba.

scholarly journals Selection of internal references for RT-qPCR assays in Neurofibromatosis type 1 (NF1) related Schwann cell lines

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0241821
Author(s):  
Yi-Hui Gu ◽  
Xi-Wei Cui ◽  
Jie-Yi Ren ◽  
Man-Mei Long ◽  
Wei Wang ◽  
...  
Keyword(s):  
Schwann Cell ◽  
Cell Lines ◽  
Reference Gene ◽  
Reference Genes ◽  
Gene Selection ◽  
Neurofibromatosis Type ◽  
Internal Reference ◽  
Real Time Quantitative Pcr ◽  
Internal Reference Gene

Real-time quantitative PCR (RT-qPCR) has been widely applied in uncovering disease mechanisms and screening potential biomarkers. Internal reference gene selection determines the accuracy and reproducibility of data analyses. The aim of this study was to identify the optimal reference genes for the relative quantitative analysis of RT-qPCR in fourteen NF1 related cell lines, including non-tumor, benign and malignant Schwann cell lines. The expression characteristics of eleven candidate reference genes (RPS18, ACTB, B2M, GAPDH, PPIA, HPRT1, TBP, UBC, RPLP0, TFRC and RPL32) were screened and analyzed by four software programs: geNorm, NormFinder, BestKeeper and RefFinder. Results showed that GAPDH, the most frequently used internal reference gene, was significantly unstable between various cell lines. The combinational use of two reference genes (PPIA and TBP) was optimal in malignant Schwann cell lines and the use of single reference genes (PPIA or PRLP0) alone or in combination was optimal in benign Schwann cell lines. These recommended internal reference gene selections may improve the accuracy and reproducibility of RT-qPCR in gene expression analyses of NF1 related tumors.

scholarly journals Expression Stability of Internal Reference Gene in Response to Trichoderma polysporum Infection in Avena fatua L.

2021 ◽  
Author(s):  
Haixia Zhu ◽  
Yongqiang Ma ◽  
Liang Cheng
Keyword(s):  
Gene Expression ◽  
Reference Gene ◽  
Expression Analysis ◽  
Reference Genes ◽  
Gene Expression Analysis ◽  
Avena Fatua ◽  
Expression Stability ◽  
Internal Reference ◽  
Qpcr Analysis ◽  
Suitable Combination

Abstract In order to construct a RT-qPCR system suitable for response of Avena fatua L. to Trichoderma polysporum , and screen stable internal reference genes, GeNorm, NormFinder, BestKeeper and RefFinde were used to perform SYBR Green-based RT-qPCR analysis on 8 candidate internal reference genes ( 18S , 28S , TUA , UBC , ACT , GAPDH , TBP and EF-1 ) in A. fatua samples after inoculation of T. polysporum Strain HZ-31. The results showed that TBP , 18S and UBC were the most stable internal reference genes, TBP and TUA , TBP and GAPDH , 18S and TBP , UBC and 18S were the most suitable combination of the two internal reference genes, which could be used as the internal reference genes for functional gene expression analysis during the interaction between T. polysporum and A. fatua .

scholarly journals Stable Reference Gene Selection for RT-qPCR Analysis inSynechococcus elongatusPCC 7942 under Abiotic Stresses

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Xiao Luo ◽  
Jiaxing Li ◽  
Tianliang Chang ◽  
Hongyan He ◽  
Yi Zhao ◽  
...  
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Time Course ◽  
Light Stress ◽  
Nacl Stress ◽  
High Light ◽  
Stress Conditions ◽  
Internal Reference ◽  
High Light Stress ◽  
Pcc 7942

Synechococcus elongatusPCC 7942 (S. elongatusPCC 7942) is a model cyanobacteria species for circadian clock mechanism studies. It has also been widely used as a bioreactor to produce biofuels and other metabolic products. Quantitative real-time PCR (qPCR) technology is the most commonly used method for studying the expression of specific genes, in which the relative expression level of target genes is calibrated by stably expressed internal reference genes. In this work, we examined the expression of nine candidate reference genes in time-course samples ofS. elongatusPCC 7942 under no treatment (control), NaCl-stress conditions, H2O2-stress conditions, and high light-stress conditions. Based on the qPCR amplification parameters, the stability ranking of these candidate reference genes was established by three statistical software programs, geNorm, NormFinder, and BestKeeper. Considering all the stress conditions or high light stress alone, the results showed that the combination ofprsandsecAwas the best choice for the double reference gene calibration method by qPCR. The combination ofsecAandppc,rimMandrnpA,rnpA,andilvDwas most stable under no treatment, NaCl-stress conditions, and H2O2-stress conditions, respectively.rimMwas stable under only special conditions and should be carefully chosen.16SandrnpBwere not suitable as internal reference genes forS. elongatusPCC 7942 qPCR experiments under all experimental conditions. To validate the above results, a cyanobacterial core clock gene,kaiC, was used to evaluate the actual performance of the optimized reference genes by qPCR, as well as the worst reference genes under different stress conditions. The results indicated that the best reference gene yielded more accurate calibration results for qPCR experiments carried out inS. elongatusPCC 7942 time-course samples.

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