猪瘟病毒基因表达谱芯片的可靠性研究

通过同种组织RNA自身比较实验及不同组织RNA的差异分析实验对猪瘟病毒(classic swine fever virus, CSFV)cDNA芯片实验的重复性进行检验.利用相关系数(correlationcoefficient, R)、变异系数(coefficientofvariation, CV)和假阳性率(falsepositiverate, FPR)分析猪瘟病毒cDNA芯片数据的可靠程度,对cDNA芯片实验数据作了整体的评估.结果证实,该芯片系统得到的猪瘟病毒cDNA表达谱数据相关系数一般大于0.9,假阳性率控制在2 %以内.另外,通过比较猪瘟病毒芯片制备中点样浓度、mRNA和总RNA以及不同标记过程对实验的影响,来分析猪瘟病毒芯片数据的系统误差来源,得出结果:重复两次实验,可以克服绝大部分实验系统引入的假阳性.     

一种用于基因芯片可靠的RNA线性扩增技术

基因芯片是大规模表达谱分析的有力工具 ,有助于阐明疾病发生的分子机制及发现新的诊治靶标。但常规方法需要大量RNA ,每张芯片需要 5 0～ 2 0 0 μg总RNA ,2～ 5 μgmRNA。许多珍贵难得样本都不能满足这一要求 ,成为限制芯片广泛应用的瓶颈。结合模板转移效应 ,优化了基于T7的RNA线性扩增技术 ,可从 3μg以下总RNA得到足量的反义RNA ,克服了这一难题。同一RNA样本的自身比较试验结果显示反义RNA标记的芯片与总RNA、mRNA标记的芯片假阳性率相似。同一对RNA样本的表达谱分析也显示反义RNA标记的芯片与总RNA、mRNA标记的芯片无明显差异。     

鲤鱼垂体mRNA反转录模板活性的研究

 本实验用不同方法研究鲤鱼垂体mRNA反转录为互补DNA的活性。用硫氰酸胍法,从垂体中提取总RNA,经过Oligo(dT)-纤维素柱层析,得到poly(A)~+RNA。 以mRNA为模板,30％反转录成单链cDNA。利用RNaseH-DNA聚合酶Ⅰ-E.coli DNA连接酶合成双链cDNA。单链cDNA拷贝成双链cDNA。经放射自显影分析,证明合成了全长cDNA。用水解法合成双链cDNA,大多数为不完整的双链cDNA。平末端的双链cDNA连接上Eco RI-linker经Sepharose-4B分离,收集大片段cDNA,与pUC 19载体相连接,经转化构建成10~5克隆/μg mRNA的cDNA文库。     

利用表达谱芯片数据筛选不同表达丰度的内参基因

目的基于表达谱芯片的检测结果,筛选多个内参基因,用于小家鼠肝脏组织中具有不同表达丰度基因的定量检测。方法应用表达谱芯片技术,完成小鼠肝脏组织的表达谱检测;依据基因表达丰度将基因分为3组,并进一步通过变异系数(coefficient of variation,CV)组内筛选候选内参基因;采用实时荧光定量PCR技术(realtime quantitative polymerase chain reaction,q PCR)和ge Norm软件确定内参基因。结果表达谱芯片成功采集超过60000个小鼠肝脏组织中转录本的表达量数据,并将之分为低、中、高3个组合。最终筛选了低表达Casp2和Lrrc14、中表达Nrd1和Trpc4ap、高表达Atp5a1和Clu,共6个内参基因。结论基于表达谱芯片数据筛选的6个内参基因,可适用于q PCR技术准确定量小家鼠肝组织转录组中不同表达丰度基因的表达量。     

差异显示反转录PCR技术研究进展

分析一对细胞或组织在不同状态下基因表达的差异,已成为分子生物学研究领域的热点之一.近年来,用于识别差异表达基因的方法已发展起来多种.DDRT-PCR是近年来较为广泛应用的一种技术.理论上,DDRT-PCR技术比较简单,但实施起来却存在着假阳性率高,凝胶中单条cDNA带成分不均一, 所获cDNA仅代表着mRNA 3′UT区(约300 bp)以及一些低拷贝数mRNA不能有效被呈现等问题.对DDRT-PCR技术的改良也主要集中在解决这些问题方面.     

降低差异显示-PCR假阳性和提高重复性的几种策略

简要介绍了几种提高mRNA差异显示重复性和降低假阳性的策略. mRNA差异显示技术从建立时起就引起了科学家的广泛兴趣, 是克隆不同生理或病理过程中差异表达基因的一种高灵敏度、简单、有效的方法.但mRNA差异显示因其假阳性率高和重复性低,限制了其在生命科学中的应用.     

犬SLAM受体mRNA荧光定量PCR检测方法的建立和初步应用

目的建立荧光定量PCR方法,检测犬不同组织中SLAM受体mRNA的表达水平。方法以犬GAPDH为内参基因采用△△ct法,分析SLAM受体mRNA在犬体内不同组织中的表达。结果此方法有较高的重复性,变异系数在0．89％-2．35％。以SLAM受体在心脏的表达为1倍值,结果显示受体mRNA在脾脏中表达最高,为38．49倍;肺门淋巴结、肠系膜淋巴结、腹股沟淋巴结中表达次之,分别为9．13、8．58、6．24倍;膀胱中表达最低。结论成功建立了检测SLAM受体mRNA在不同组织中表达水平的荧光定量PCR检测方法。     

BDV核蛋白FQ RT-PCR试剂盒的评价与应用

为评价博尔纳病病毒(Borna disease virus,BDV)核蛋白荧光定量PCR(FQRT-PCR)试剂盒的各项指标,比较分子信标探针相对普通探针的优势,并了解其实际检测效果,本课题组使用BDVOL持续感染细胞株、非BDV病毒序列转染的OL细胞、正常的OL细胞,对BDVRT-PCR试剂盒的敏感性、特异性、重复性和稳定性进行评估,同时检测部分临床病人和动物外周血液RNA。实验结果显示:试剂盒可以检测出的病毒RNA最低浓度为2.5×101,相当于1个病毒拷贝数,无非特异检出;不同批次的试剂盒的检测结果变异系数小于0.7;加速破坏的试剂盒和正常试剂盒检测结果之间变异系数在2以内;对临床病人检测阳性率为3.6%,对动物检测阳性率为4.2%(猪)和1.5%(马)。可见该试剂盒重复性和稳定性均好;敏感性、特异性优于普通探针试剂盒,是BDV基础研究、流行病学调查和临床检测的良好工具。     

原核细胞mRNA差异显示技术的引物设计

由于原核细胞mRNA3'端不存在ploy(A)结构,因而原核细胞DDRT-PCR引物设计不同于真核细胞。尽管不能根据oligo(dT)设计引物,但利用全基因中高度分散重复的短序列或回文序列却能有效克服mRNA分子结构的影响,最大限度地扩增全长cDNA;并且这2种引物设计方法还可以提高RNA指纹图谱的重复性,降低反应的假阳性,从而为原核细胞DDRT-PCR引物设计提供新的思路。     

Spearman's footrule as a measure of cDNA microarray reproducibility

Replication is a crucial aspect of microarray experiments, due to various sources of errors that persist even after systematic effects are removed. It has been confirmed that replication in microarray studies is not equivalent to duplication, and hence it is not a waste of scientific resources. Replication and reproducibility are the most important issues for microarray application in genomics. However, little attention has been paid to the assessment of reproducibility among replicates. Here we develop, using Spearman's footrule, a new measure of the reproducibility of cDNA microarrays, which is based on how consistently a gene's relative rank is maintained in two replicates. The reproducibility measure, termed index.R, has an R2-type operational interpretation. Index.R assesses reproducibility at the initial stage of the microarray data analysis even before normalization is done. We first define three layers of replicates, biological, technical, and hybridizational, which refer to different biological units, different mRNAs from the same tissue, and separate cDNAs from a cDNA pool. As the replicate layer moves down to a lower level, the experiment has fewer sources of errors and thus is expected to be more reproducible. To validate the method we apply index.R to two sets of controlled cDNA microarray experiments, each of which has two or three layers of replicates. Index.R shows a uniform increase as the layer of the replicates moves into a more homogeneous environment. We also note that index.R has a larger jump size than Pearson's correlation or Spearman's rank correlation for each replicate layer move, and therefore, it has greater expandability as a measure in [0,1] than these two other measures.     

A quality-controlled microarray method for gene expression profiling

Gene expression profiling on microarrays is widely used to measure the expression of large numbers of genes in a single experiment. Because of the high cost of this method, feasible numbers of replicates are limited, thus impairing the power of statistical analysis. As a step toward reducing technically induced variation, we developed a procedure of sample preparation and analysis that minimizes the number of sample manipulation steps, introduces quality control before array hybridization, and allows recovery of the prepared mRNA for independent validation of results. Sample preparation is based on mRNA separation using oligo(dT) magnetic beads, which are subsequently used for first-strand cDNA synthesis on the beads. cDNA covalently bound to the magnetic beads is used as template for second-strand cDNA synthesis, leaving the intact mRNA in solution for further analysis. The quality of the synthesized cDNA can be assessed by quantitative polymerase chain reaction using 3'- and 5'-specific primer pairs for housekeeping genes such as glyceraldehyde-3-phosphate dehydrogenase. Second-strand cDNA is chemically labeled with fluorescent dyes to avoid dye bias in enzymatic labeling reactions. After hybridization of two differently labeled samples to microarray slides, arrays are scanned and images analyzed automatically with high reproducibility. Quantile-normalized data from five biological replica display a coefficient of variation 45% for 90% of profiled genes, allowing detection of twofold changes with false positive and false negative rates of 10% each. We demonstrate successful application of the procedure for expression profiling in plant leaf tissue. However, the method could be easily adapted for samples from animal including human or from microbial origin.     

Apparently low reproducibility of true differential expression discoveries in microarray studies

MOTIVATION: Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is often believed that current small microarray studies will largely introduce false discoveries. RESULTS: Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low reproducibility of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall reproducibility of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the reproducibility of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.     

An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression

The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12–14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.     

Cross-species hybridisation of pig RNA to human nylon microarrays

Background

The objective of this research was to investigate the reproducibility of cross-species microarray hybridisation. Comparisons between same- and cross-species hybridisations were also made. Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed. Three replicate hybridisations of two different amounts of pig RNA, and of human skeletal muscle RNA were completed on three additional microarrays.

Results

Reproducibility of microarray hybridisations of pig cDNA to human microarrays was high, as determined by Spearman and Pearson correlation coefficients and a Kappa statistic. Variability among replicate hybridisations was similar for human and pig data, indicating the reproducibility of results were not compromised in cross-species hybridisations. The concordance between data generated from hybridisations using pig and human skeletal muscle RNA was high, further supporting the use of human microarrays for the analysis of gene expression in the pig. No systematic effect of stripping and re-using nylon microarrays was found, and variability across microarrays was minimal.

Conclusion

The majority of genes generated highly reproducible data in cross-species microarray hybridisations, although approximately 6% were identified as highly variable. Experimental designs that include at least three replicate hybridisations for each experimental treatment will enable the variability of individual genes to be considered appropriately. The use of cross-species microarray analysis looks promising. However, additional validation is needed to determine the specifiCity of cross-species hybridisations, and the validity of results.     

Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis

We have constructed cDNA microarrays for soybean (Glycine maxL. Merrill), containing approximately 4,100 Unigene ESTs derived from axenic roots, to evaluate their application and utility for functional genomics of organ differentiation in legumes. We assessed microarray technology by conducting studies to evaluate the accuracy of microarray data and have found them to be both reliable and reproducible in repeat hybridisations. Several ESTs showed high levels (50 fold) of differential expression in either root or shoot tissue of soybean. A small number of physiologically interesting, and differentially expressed sequences found by microarray analysis were verified by both quantitative real-time RT-PCR and Northern blot analysis. There was a linear correlation (r² = 0.99, over 5 orders of magnitude) between microarray and quantitative real-time RT-PCR data. Microarray analysis of soybean has enormous potential not only for the discovery of new genes involved in tissue differentiation and function, but also to study the expression of previously characterised genes, gene networks and gene interactions in wild-type, mutant or transgenic plants.     

Classification of DNA methylation patterns in tumor cell genomes using a CpG island microarray

Our group has initiated experiments to epigenetically profile CpG island hypermethylation in genomic DNA from tissue specimens of head and neck squamous cell carcinoma (HNSCC) using a microarray of 12,288 CpG island clones. Our technique, known as a methylation-specific restriction enzyme (MSRE) analysis, is a variation of the differential methylation hybridization (DMH) technique, in that it is not an array comparison of two DNA samples using methylation-specific restriction enzymes. Instead, it is a comparison of a single DNA sample's response to a methylation-sensitive restriction enzyme (HpaII) and its corresponding methylation-insensitive isoschizomer (MspI). Estimation of the reproducibility of this microarray assay by intraclass correlation (ICC) demonstrated that in four replicate experiments for three tumor specimens, the ICC observed for a given tumor specimen ranged from 0.68 to 0.85 without filtering of data. Repeated assays achieved 87% concordance or greater for all tumors after filtering of array data by fluorescence intensity. We utilized hierarchical clustering on a population of 37 HNSCC samples to cluster tumor samples with similar DNA methylation profiles. Supervised learning techniques are now being utilized to allow us to identify associations between specific epigenetic signatures and clinical parameters. Such techniques will allow us to identify select groups of CpG island loci that could be used as epigenetic markers for both diagnosis and prognosis in HNSCC.