Differential Expression Levels Assessment of Avian E2A Gene in Two Chinese Indigenous Duck Breeds (Anas platyrhynchos) by Semi-Quantitative RT-PCR

2006 ◽  
Vol 5 (9) ◽  
pp. 895-899 ◽  
Author(s):  
Dafaalla M. Mekki . ◽  
Bian Liang-yong . ◽  
Wang Jin-yu . ◽  
Yang Yan . ◽  
Li lin-chuan . ◽  
...  
2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Weitong Cui ◽  
Huaru Xue ◽  
Lei Wei ◽  
Jinghua Jin ◽  
Xuewen Tian ◽  
...  

Abstract Background RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. Results Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. Conclusions High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.


2001 ◽  
Vol 68 (2) ◽  
pp. 109-116 ◽  
Author(s):  
O. Ishibashi ◽  
T. Inui ◽  
Y. Mori ◽  
T. Kurokawa ◽  
T. Kokubo ◽  
...  

2004 ◽  
Vol 114 (2) ◽  
pp. 174-181 ◽  
Author(s):  
Gaëlle Fromont ◽  
Laurent Chene ◽  
Michel Vidaud ◽  
Guy Vallancien ◽  
Philippe Mangin ◽  
...  

2012 ◽  
Vol 7 (12) ◽  
pp. 1934578X1200701 ◽  
Author(s):  
Lili Huang ◽  
Hong Wang ◽  
Hechun Ye ◽  
Zhigao Du ◽  
Yansheng Zhang ◽  
...  

cDNAs encoding Hypericum sampsonii benzophenone synthase (HsBPS) and chalcone synthase (HsCHS) were isolated and functionally characterized. Differential expressions of HsBPS and HsCHS were monitored using quantitative polymerase chain reaction (PCR). In the vegetative stage, HsBPS was highly expressed in the roots; its transcript level was approx. 100 times higher than that of HsCHS. Relatively high transcript amounts of HsBPS were also detected in older leaves, whereas the youngest leaves contained higher transcript amounts of HsCHS. In the reproductive stage, maximum HsCHS expression was detected in flowers, the transcript level being approx. 5 times higher than that of HsBPS. The inversed situation with a 10-fold difference in the expression levels was observed with fruits. High transcript amounts for both proteins were found in roots.


2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Hui Qiu ◽  
Xuemin Liu ◽  
Shenshen Yao ◽  
Jiaren Zhou ◽  
Xue Zhang ◽  
...  

Objectives. To observe the role of miR-518d in pregnant women with gestational diabetes mellitus (GDM) and its adjusting effects on PPARα and to explore the regulatory mechanisms of the NF-κB pathway in the development and progression of GDM. Methods. Placenta tissues and peripheral plasma were obtained from pregnant women with normal pregnancy and GDM, respectively, followed by the detections of miR-518d contents by RT-PCR and the expression levels of inflammatory factors using ELISA. Human placenta trophoblast cells (HTR8/SVneo) were cultured under the conditions of physiological glucose (PG group) and high glucose level (HG group). Cells in the HG group were transfected with miR-518d control, mimics, and inhibitors and were separately administered with a PPARα-specific antagonist (GW6471) and PPARα siRNA, and cells were divided into the following groups: HG+miR-518d control group (HGNC group), HG+miR-518d mimic group (HGM group), HG+miR-518d inhibitor group (HGI group), HGI+PPARα antagonist group, and HGI+PPARα siRNA group. The relative expression levels of miR-518d, PPARα, and its downstream genes and NF-κB signalling pathway-related genes were detected by RT-PCR and Western blotting. The contents of inflammatory factors were examined by Western blotting. A dual-luciferase report assay was performed to validate the correlations between miR-518d and PPARα. In this study, mouse GDM models were established to further prove the previous hypothesis with an in vivo experiment. A total of 40 C57BL/6J mice were randomly divided into the following groups: normal diet group (ControlMs), GDM group (GDMMs group), GDM+miR-518d antagomir group, and GDM+miR-518d antagomir+PPARα antagonist group. The mouse model of GDM was established by feeding with combined high-sugar and high-saturated fat diet and injecting streptozotocin (STZ) after 15-day feeding. Female and male mice were cocaged in the number ratio of 2 : 1, and the evidence of vaginal suppository detected in female mice was marked as D0 of pregnancy. The contents of total cholesterol (CH), triglyceride (TG), fast glucose, and insulin (INS) were examined using ELISA, followed by the evaluation of insulin resistance (IR). The related expression levels were also detected with the above methods shown in the previous cell culture. Results. miR-518d has a high expression level in placentas with GDM. As the target gene of miR-518d, PPARα was downregulated with the increased levels of miR-518d. When GDM occurs, inflammatory responses were elevated, stimulating the nuclear transport process of NF-κB. Activated NF-κB triggered the phosphorylation of IKKβ and IκBα. Conclusions. High expression of miR-518d was observed in the development of GDM. In this study, we validated that miR-518d negatively regulates the expression of PPARα and triggers the nuclear transport process of NF-κB and phosphorylation of pathway-associated proteins leading to an inflammatory response and the development of GDM.


PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e61605 ◽  
Author(s):  
Thais Fernanda de Almeida Galatro ◽  
Miyuki Uno ◽  
Sueli Mieko Oba-Shinjo ◽  
Antonio Nogueira Almeida ◽  
Manoel J. Teixeira ◽  
...  

1988 ◽  
Vol 8 (9) ◽  
pp. 3929-3933 ◽  
Author(s):  
K Tokunaga ◽  
K Takeda ◽  
K Kamiyama ◽  
H Kageyama ◽  
K Takenaga ◽  
...  

We described the structures of mouse cytoskeletal gamma-actin cDNA clones and showed that there is strong conservation of the untranslated regions with human gamma-actin cDNA. In addition, we found that the expression levels of beta- and gamma-actin mRNAs are differentially controlled in various mouse tissues and cell types but are coordinately increased in the cellular growing state. These results suggest that there are multiple regulatory mechanisms of cytoskeletal actin genes and are consistent with the argument that beta- and gamma-actins might have functional diversity in mammalian cells.


2004 ◽  
Vol 32 (2) ◽  
pp. 449-466 ◽  
Author(s):  
S Bauersachs ◽  
S Rehfeld ◽  
SE Ulbrich ◽  
S Mallok ◽  
K Prelle ◽  
...  

The oviduct epithelium undergoes marked morphological and functional changes during the oestrous cycle. To study these changes at the level of the transcriptome we did a systematic gene expression analysis of bovine oviduct epithelial cells at oestrus and dioestrus using a combination of subtracted cDNA libraries and cDNA array hybridisation. A total of 3072 cDNA clones of two subtracted libraries were analysed by array hybridisation with cDNA probes derived from six cyclic heifers, three of them slaughtered at oestrus and three at dioestrus. Sequencing of cDNAs showing significant differences in their expression levels revealed 77 different cDNAs. Thirty-seven were expressed at a higher level at oestrus, for the other 40 genes expression levels were higher at dioestrus. The identified genes represented a variety of functional classes. During oestrus especially genes involved in the regulation of protein secretion and protein modification, and mRNAs of secreted proteins, were up-regulated, whereas during dioestrus particularly transcripts of genes involved in transcription regulation showed a slight up-regulation. The concentrations of seven selected transcripts were quantified by real-time RT-PCR to validate the cDNA array hybridisation data. For all seven transcripts, RT-PCR results were in excellent correlation (r>0.92) with the results obtained by array hybridisation. Our study is the first to analyse changes in gene expression profiles of bovine oviduct epithelial cells during different stages of the oestrous cycle, providing a starting point for the clarification of the key transcriptome changes in these cells.


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