检索结果-内蒙古大学图书馆

Identification of Stable housekeeping genes for miRNA Expression Studies in a Mouse Unilateral Ureteral Obstruction Model

引用

BIOCHEMICAL GENETICS 2025年 1-17页

作者： Bronel, Bruno Aristides dos Santos Anauate, Ana Carolina Novaes, Antonio da Silva Boim, Mirian Aparecida Maquigussa, Edgar Univ Fed Sao Paulo Renal Div Dept Med Rua Pedro Toledo 781 BR-04039032 Sao Paulo SP Brazil

Recently, several studies have aimed to establish the role of microRNAs (miRNAs) in the unilateral ureteral obstruction (UUO) model. Therefore, it is essential to identify the best housekeeping genes (HKG) to correctly estimate the expression levels of miRNAs. The present study aimed to identify suitable HKG to normalize the expression of miRNAs by RT-qPCR in kidney samples from the UUO mice model. We analyzed the stability of twelve endogenous reference genes of small non-coding RNAs (Snord61, Snord68, Snord72, Snord95, Snord96a, U6, let-7e-5p, let-7i-3p, miR-15b-5p, miR-16a-5p, miR-26a-5p, and miR-30c-5p) by using four software packages: NormFinder, GeNorm, Delta Ct method, and BestKeeper. The optimal number of genes was calculated using GenEx software analysis. To validate the best HKG, we normalized the expression of miR-18a-5p, miR-21a-3p, and miR-29b-3p. In silico analysis revealed that Snord61, Snord68, and Snord72 were the most stable HKG between the groups. Using GenEX software and Pearson's correlation, we determined that the combination of Snord61 and Snord68 or the combination of Snord68 and Snord72, provided the best HKG association. These results along with the correlation analyses establish that the association of Snord68 and Snord72 is the best choice for miRNA expression analysis by RT-qPCR in the UUO model.

关键词： housekeeping genes miRNAs Gene expression analysis Unilateral ureteral obstruction model Renal fibrosis

来源：评论

学校读者我要写书评

暂无评论

housekeeping genes as internal standards: use and limits

引用

JOURNAL OF BIOTECHNOLOGY 1999年第2-3期75卷 291-295页

作者： Thellin, O Zorzi, W Lakaye, B De Borman, B Coumans, B Hennen, G Grisar, T Igout, A Heinen, E Univ Liege Inst Human Histol B-4020 Liege Belgium Univ Liege Lab Biochem Endocrinol B-4020 Liege Belgium Univ Liege Biochem Lab Res Grp Neurochem B-4020 Liege Belgium

Quantitative studies are commonly realised in the biomedical research to compare RNA expression in different experimental or clinical conditions. These quantifications are performed through their comparison to the expression of the housekeeping gene transcripts like glyceraldehyde-3-phosphate dehydrogenase (G3PDH), albumin, actins, tubulins, cyclophilin, hypoxantine phosphoribosyltransferase (HRPT), L32. 28S and 18S rRNAs are also used as internal standards. In this paper, it is recalled that the commonly used internal standards can quantitatively vary in response to various factors. Possible variations are illustrated using three experimental examples. Preferred types of internal standards are then proposed for each of these samples and thereafter the general procedure concerning the choice of an internal standard and the way to manage its used are discussed. (C) 1999 Elsevier Science B.V. All rights reserved.

关键词： internal standards housekeeping genes RNase protection RT-PCR

来源：评论

学校读者我要写书评

暂无评论

housekeeping genes and death genes in the Penna aging model

引用

INTERNATIONAL JOURNAL OF MODERN PHYSICS C 2000年第4期11卷 775-783页

作者： Niewczas, E Kurdziel, A Cebrat, S Univ Wroclaw Inst Microbiol Dept Genet PL-54148 Wroclaw Poland

The Penna model of aging predicts the accumulation of defective genes expressed after the organism reaches the minimum reproduction age in the genetic pool of the population. The accumulation of defects in the genomes implicates the specific age structure of the modeled populations. Nevertheless, the fraction of defective alleles at loci switched on before the reproduction period does not depend on exact age when precisely they are switched on, it may be just after conception or after birth. We have modeled the mortality of a population in the period before the minimum reproduction age, even before birth, assuming that sets of genes of different size are switched on in different periods of the life span.

关键词： biological aging Monte Carlo simulation death genes housekeeping genes

来源：评论

学校读者我要写书评

暂无评论

housekeeping genes revisited:: Different expressions depending on gender, brain area and stressor

引用

NEUROSCIENCE 2008年第2期156卷 305-309页

作者： Derks, N. M. Muller, M. Gaszner, B. Tilburg-Ouwens, D. T. W. M. Roubos, E. W. Kozicz, L. T. Radboud Univ Nijmegen Dept Cellular Anim Physiol NL-6500 GL Nijmegen Netherlands

housekeeping gene (HKG) mRNAs are used to normalize expression data of genes of interest in quantitative reverse transcriptase polymerase chain reaction studies. Such normalization assumes constant HKG gene expression under all circumstances. Although sporadic evidence suggests that HKG expression may not always fulfill this requirement and, therefore, such normalization may lead readily to erroneous results, this fact is generally not sufficiently appreciated by investigators. Here, we have systematically analyzed the expression of three common HKGs, glyceraldehyde-3-phosphate dehydrogenase, ribosomal subunit 18S and beta-actin, in two different stress paradigms, in various brain areas, in male and in female rats. HKG expressions differed considerably with respect to brain area, type of stressor and gender, in an HKG-specific manner. Therefore, we conclude that before final experimentation, pilot expression studies are necessary to select an HKG which expression is unaffected by the experimental factor(s), allowing reliable interpretation of expression data of genes of interest. (C) 2008 IBRO. Published by Elsevier Ltd. All rights reserved.

关键词： q-RT-PCR housekeeping genes brain area gender stressor adaptation

来源：评论

学校读者我要写书评

暂无评论

3′-UTR Shortening Contributes to Subtype-Specific Cancer Growth by Breaking Stable ceRNA Crosstalk of housekeeping genes

引用

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY 2020年 8卷 334-334页

作者： Fan, Zhenjiang Kim, Soyeon Bai, Yulong Diergaarde, Brenda Park, Hyun Jung Univ Pittsburgh Dept Comp Sci Pittsburgh PA 15260 USA Univ Pittsburgh Sch Med Dept Pediat Pittsburgh PA 15261 USA Childrens Hosp Pittsburgh UPMC Div Pulm Med Pittsburgh PA USA Univ Pittsburgh Grad Sch Publ Hlth Dept Human Genet Pittsburgh PA 15261 USA Univ Pittsburgh Med Canc Hillman Canc Ctr Pittsburgh PA USA

Shortening of 3 ' UTRs (3 ' US) through alternative polyadenylation is a post-transcriptional mechanism that regulates the expression of hundreds of genes in human cancers. In breast cancer, different subtypes of tumor samples, such as estrogen receptor positive and negative (ER+ and ER-), are characterized by distinct molecular mechanisms, suggesting possible differences in the post-transcriptional regulation between the subtype tumors. In this study, based on the profound tumorigenic role of 3 ' US interacting with competing-endogenous RNA (ceRNA) network (3 ' US-ceRNA effect), we hypothesize that the 3 ' US-ceRNA effect drives subtype-specific tumor growth. However, we found that the subtypes are available in different sample sizes, biasing the ceRNA network size and disabling the fair comparison of the 3 ' US-ceRNA effect. Using normalized Laplacian matrix eigenvalue distribution, we addressed this bias and built tumor ceRNA networks comparable between the subtypes. Based on the comparison, we identified a novel role of housekeeping (HK) genes as stable and strong miRNA sponges (sponge HK genes) that synchronize the ceRNA networks of normal samples (adjacent to ER+ and ER- tumor samples). We further found that distinct 3 ' US events in the ER- tumor break the stable sponge effect of HK genes in a subtype-specific fashion, especially in association with the aggressive and metastatic phenotypes. Knockdown of NUDT21 further suggested the role of 3 ' US-ceRNA effect in repressing HK genes for tumor growth. In this study, we identified 3 ' US-ceRNA effect on the sponge HK genes for subtype-specific growth of ER- tumors.

关键词： competing-endogenous RNA housekeeping genes breast cancer subtypes RNA regulation alternative polyadenylation (APA)

来源：评论

学校读者我要写书评

暂无评论

Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis

引用

PLANT CELL TISSUE AND ORGAN CULTURE 2020年第2期141卷 417-433页

作者： Cukovic, Katarina Dragicevic, Milan Bogdanovic, Milica Paunovic, Danijela Giurato, Giorgio Filipovic, Biljana Subotic, Angelina Todorovic, Sladana Simonovic, Ana Univ Belgrade Natl Inst Republ Serbia Inst Biol Res Sinisa Stankovic Dept Plant Physiol Bul Despota Stefana 142 Belgrade 11060 Serbia Univ Salerno Dept Med Surg & Dent Scuola Med Salernitana Dept Med Lab Mol Med & Genom I-84081 Baronissi SA Italy Genomix4Life Srl Baronissi SA Italy

Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites. Key message De novo assembled and fully annotated Centaurim erythraea transcriptome is publically available along with validated housekeeping genes with stable expression during in vitro development and mechanical injury.

关键词： Centaury housekeeping genes RNA-seq Somatic embryogenesis Transcriptome Wounding

来源：评论

学校读者我要写书评

暂无评论

Effect of Scrapie on the Stability of housekeeping genes

引用

ANIMAL BIOTECHNOLOGY 2010年第1期21卷 1-13页

作者： Lyahyai, J. Serrano, C. Ranera, B. Badiola, J. J. Zaragoza, P. Martin-Burriel, I. Univ Zaragoza Fac Vet LAGENBIO E-50013 Zaragoza Spain Univ Zaragoza Fac Vet Dept Patol Anim E-50013 Zaragoza Spain

Scrapie is the archetype of prion diseases, fatal neurodegenerative disorders that affect humans and animals. Gene expression analysis of normal and infected sheep may provide clues to clarify the molecular mechanisms involved in the neuropathology of these diseases. Real time quantitative PCR has become a powerful and accurate technique for examination of transcription patterns in different biological conditions. One of the critical steps in the comparison of transcription profiles is the selection of stable genes for normalization of expression data. In this work, we have investigated the effect of scrapie on the stability of eight commonly used housekeeping genes in the central nervous system of sheep. We found that their stability decreased in scrapie-infected tissues, with the effect of the disease most evident in the medulla oblongata, a highly affected area of the brain stem. The risk of choosing inappropriate housekeeping genes for expression analysis was evaluated. Although the stability of each reference gene was suitable, a wide variation in expression of target genes (BAX and BCL2) was observed when only one or two housekeeping genes were used to normalize. However, reliable results were obtained with a normalization factor based on three reference genes, regardless of their position in a stability ranking.

关键词： housekeeping genes Prion Quantitative Real Time PCR Scrapie Stability

来源：评论

学校读者我要写书评

暂无评论

Identification of genes from flat oyster Ostrea edulis as suitable housekeeping genes for quantitative real time PCR

引用

FISH & SHELLFISH IMMUNOLOGY 2010年第6期29卷 937-945页

作者： Morga, Benjamin Arzul, Isabelle Faury, Nicole Renault, Tristan IFREMER LGP F-17390 La Tremblade France

Bonamia ostreae is an intrahaemocytic protozoan affecting Ostrea edulis. The parasite multiplies within haemocytes without being degraded and involves changes in cellular activities. Studies aiming at better understanding host response to a pathogen at the transcriptome levels are frequently based on the use of real time PCR assays, which require some reference genes. However, very few sequence data is available for O. edulis in public databases. Subtracted cDNA libraries were constructed from the O. edulis haemocytes in order to identify genes involved in host reactions against the parasite and quantitative real time PCR assays were developed to study expression of these genes. In this context, identification of reference genes and study of their relative expression stability were required for quantitative real time PCR normalization. The expression of 5 potential candidate reference genes from O. edulis (ie elongation factor 1 alpha (EF1-alpha), 605 ribosomal protein L5 (L5), glyceraldehyde 3-phosphate-dehydrogenase (GAPDH), polyubiquitin (Ubiq) and beta-actin (ACT)) was studied using RNAs extracted from pools of haemocytes in contact with the parasite B. ostreae and haemocytes alone. Gene expression was quantified by real time PCR and expression stability was analysed with two analytical approaches GeNorm and NormFinder. GAPDH and EF1-alpha were identified as the most stable genes with the GeNorm analysis. Whatever were the tested conditions, EF1-alpha was also found as the most stable gene using Normfinder. The less stable gene was beta-actin although this gene is commonly used as housekeeping gene in many studies. Our results suggest using GAPDH and EF1-alpha combined as reference genes when studying expression levels in haemocytes of O. edulis. In addition, the complete ORF of these two genes was characterized. (C) 2010 Elsevier Ltd. All rights reserved.

关键词： Real time PCR housekeeping genes Haemocytes Ostrea edulis Bonamia ostreae

来源：评论

学校读者我要写书评

暂无评论

Selecting a set of housekeeping genes for quantitative real-time PCR in normal and tetraploid haemocytes of soft-shell clams, Mya arenaria

引用

FISH & SHELLFISH IMMUNOLOGY 2008年第3期25卷 202-207页

作者： Siah, A. Dohoo, C. McKenna, P. Delaporte, M. Berthe, F. C. J. Univ Prince Edward Isl Atlantic Vet Coll Dept Pathol & Microbiol Charlottetown PE C1A 4P3 Canada EFSA I-43100 Parma Italy Univ Strasbourg Inst Virol F-67000 Strasbourg France

The transcripts involved in the molecular mechanisms of haemic neoplasia in relation to the haemocyte ploidy status of the soft-shell clam, Mya arenaria, have yet to be identified. For this purpose, real-time quantitative RT-PCR constitutes a sensitive and efficient technique, which can help determine the gene expression involved in haemocyte tetraploid status in clams affected by haemic neoplasia. One of the critical steps in comparing transcription profiles is the stability of selected housekeeping genes, as well as an accurate normalization. In this study, we selected five reference genes, S18, L37, EF1, EF2 and actin, generally used as single control genes. Their expression was analyzed by real-time quantitative RT-PCR at different levels of haemocyte ploidy status in order to select the most stable genes. Using the geNorm software, our results showed that L37, EF1 and S18 represent the most stable gene expressions related to various ploidy status ranging from 0 to 78% of tetraploid haemocytes in clams sampled in North River (Prince Edward Island, Canada). However, actin gene expression appeared to be highly regulated. Hence, using it as a housekeeping gene in tetraploid haemocytes can result in inaccurate data. To compare gene expression levels related to haemocyte ploidy status in Mya arenaria, using L37, EF1 and S18 as housekeeping genes for accurate normalization is therefore recommended. Crown Copyright (c) 2008 Published by Elsevier Ltd. All rights reserved.

关键词： Mya arenaria tetraploidy haemocytes housekeeping genes normalization

来源：评论

学校读者我要写书评

暂无评论

Screening and Stability Analysis of housekeeping genes for Transcriptomic Studies in Danio rerio (Zebrafish) at Early Developmental Stages

引用

MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2024年第2期39卷 131-136页

作者： Partevian, S. A. Safina, D. R. Rybolovlev, I. N. Rudenok, M. M. Kostrov, S. V. Shadrina, M. I. Slominsky, P. A. Alieva, A. Kh. Kurchatov Inst Natl Res Ctr Moscow 123182 Russia

The zebrafish (Danio rerio) is one of the promising objects for modeling pathological conditions. A large number of such works are carried out at the transcriptomic level. Transcriptomic studies require the use of stable housekeeping genes (HKGs), and so we selected candidate HKGs and analyzed their stability in D. rerio under normal conditions. The work was carried out using D. rerio of the AB line whose embryos were sampled at three time points: the hatching stage (2 days postfertilization, dpf), and early larval stages (5 and 9 dpf). Analysis of HKG expression levels was performed using real-time polymerase chain reaction. Further analysis of the obtained Ct results was carried out in the RefFinder program. Different HKGs are suitable for assessing changes in gene expression at different stages of D. rerio development. When assessing changes in gene expression at the hatching stage (2 dpf), the optimal pair of HKGs is aars1 and polr2f;for the early larval stage (5 dpf), it is aars1 and psmd6;and for 9 dpf, it is bcat2 and actb1. During transcriptomic studies conducted at several developmental stages simultaneously, it is necessary to use a single selected pair of HKGs for all the studied stages of zebrafish development: aars1 and lsm12b. According to the data obtained, aars1 and lsm12b are the most stable HKGs for all the early developmental stages of D. rerio studied. At the same time, we first showed that aars1 is the most stable HKG for the early stages of the development. The second most stable HKG is lsm12b. Our data on the stability of the lsm12b gene are consistent with previously published data.

关键词： Danio rerio transcriptome analysis real-time polymerase chain reaction housekeeping genes gene expression

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：