检索结果-内蒙古大学图书馆

A methodical microarray design enables surveying of expression of a broader range of genes in Ciona intestinalis

GENE 2013年第1期519卷 82-90页

作者： Matsumae, Hiromi Hamada, Mayuko Fujie, Manabu Niimura, Yoshihito Tanaka, Hiroshi Kawashima, Takeshi Tokyo Med & Dent Univ Med Res Inst Dept Bioinformat Bunkyo Ku Tokyo 1138510 Japan Okinawa Inst Sci & Technol Grad Univ Marine Genom Unit Kunigami Okinawa 9040495 Japan Okinawa Inst Sci & Technol Grad Univ Genome Sequencing Ctr Kunigami Okinawa 9040495 Japan

We provide a new oligo-microarray for Ciona intestinalis, based on the NimbleGen 12-plex x 135k format. The array represents 106,285 probes, which is more than double the probe number of the currently available 44k microarray. These probes cover 99.2% of the transcripts in the KyotoHoya (KH) models, published in 2008, and they contain 81.1% of the entries in the UniGene database that are not included in the KH models. In this paper, we show that gene expression levels measured by this new 135k microarray are highly correlated with those obtained by the existing 44k microarray for genes common to both arrays. We also investigated gene expression using samples obtained from the ovary and the neural complex of adult C intestinalis, showing that the expression of tissue-specific genes is consistent with previous reports. Approximately half of the highly expressed genes identified in the 135k microarray are not included in the previous microarray. The high coverage of gene models by this microarray made it possible to identify splicing variants for a given transcript. The 135k microarray is useful in investigating the functions of genes that are not yet well characterized. Detailed information about this 135k microarray is accessible at no charge from supplemental materials, NCBI Gene Expression Omnibus (GEO), and http://***. (c) 2013 Elsevier B.V. All rights reserved.

关键词： microarray design Gene expression analysis Ciona intestinalis Tissue specific analysis Cross-platform analysis

来源：评论

学校读者我要写书评

暂无评论

Randomized probe selection algorithm for microarray design

引用

JOURNAL OF THEORETICAL BIOLOGY 2007年第3期248卷 512-521页

作者： Gasieniec, Leszek Li, Cindy Y. Sant, Paul Wong, Prudence W. H. Univ Liverpool Dept Comp Sci Liverpool L69 3BX Merseyside England

DNA microarray technology, originally developed to measure the level of gene expression, has become one of the most widely used tools in genomic study. The crux of microarray design lies in how to select a unique probe that distinguishes a given genomic sequence from other sequences. Due to its significance, probe selection attracts a lot of attention. Various probe selection algorithms have been developed in recent years. Good probe selection algorithms should produce a small number of candidate probes. Efficiency is also crucial because the data involved are usually huge. Most existing algorithms are usually not sufficiently selective and quite a large number of probes are returned. We propose a new direction to tackle the problem and give an efficient algorithm based on randomization to select a small set of probes and demonstrate that such a small set of probes is sufficient to distinguish each sequence from all the other sequences. Based on the algorithm, we have developed probe selection software RANDPS, which runs efficiently in practice. The software is available on our website (http://***/similar to cindy/RandPS/***). We test our algorithm via experiments on different genomes (Escherichia coli, Saccharamyces cercvisiae, etc.) and our algorithm is able to output unique probes for most of the genes efficiently. The other genes can be identified by a combination of at most two probes. (C) 2007 Elsevier Ltd. All rights reserved.

关键词： randomized algorithm probe selection microarray design

来源：评论

学校读者我要写书评

暂无评论

ArrayD: A general purpose software for microarray design

引用

BMC BIOINFORMATICS 2004年第1期5卷 142-142页

作者： Sharma, A Srivastava, GP Sharma, VK Ramachandran, S CSIR Inst Genom & Integrat Biol Delhi 110007 India

Background: microarray is a high-throughput technology to study expression of thousands of genes in parallel. A critical aspect of microarray production is the design aimed at space optimization while maximizing the number of gene probes and their replicates to be spotted. Results: We have developed a software called 'ArrayD' that offers various alternative design solutions for an array given a set of user requirements. The user feeds the following inputs: type of source plates to be used, number of gene probes to be printed, number of replicates and number of pins to be used for printing. The solutions are stored in a text file. The choice of a design solution to be used will be governed by the spotting chemistry to be used and the accuracy of the robot. Conclusions: ArrayD is a software for standard cartesian robots. The software aids users in preparing a judicious and elegant design. ArrayD is universally applicable and is available at http://***/scientists/arrayd/***.

关键词： Gene Probe design Solution Space Optimization microarray design Executable File

来源：评论

学校读者我要写书评

暂无评论

Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization

引用

BMC GENOMICS 2008年第1期9卷 497-497页

作者： Flibotte, Stephane Moerman, Donald G. BC Canc Agcy Canadas Michael Smith Genome Sci Ctr Vancouver BC V5Z 4S6 Canada Univ British Columbia Dept Zool Vancouver BC V6T 1Z4 Canada Univ British Columbia Michael Smith Labs Vancouver BC V6T 1Z4 Canada

Background: microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans) the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. Results: We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10 C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data quality when varying the oli

关键词： Comparative Genomic Hybridization design Recommendation Standard Filter microarray design microarray Comparative Genomic Hybridization

来源：评论

学校读者我要写书评

暂无评论

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum)

引用

BMC GENOMICS 2013年第1期14卷 1-19页

作者： Lee, Yang Ping Giorgi, Federico M. Lohse, Marc Kvederaviciute, Kotryna Klages, Sven Usadel, Bjoern Meskiene, Irute Reinhardt, Richard Hincha, Dirk K. Max Planck Inst Mol Pflanzenphysiol D-14476 Potsdam Germany FELDA Agr Serv Sdn Bhd Kuala Lumpur 54000 Malaysia Columbia Univ Ctr Computat Biol & Bioinformat New York NY 10032 USA Univ Vilnius Inst Biotechnol LT-02241 Vilnius Lithuania Max Planck Inst Mol Genet D-14195 Berlin Germany Rhein Westfal TH Aachen Inst Biol D-52056 Aachen Germany Forschungszentrum Julich IBG 2 Pflanzenwissensch D-52425 Julich Germany Univ Vienna Max F Perutz Labs A-1030 Vienna Austria Med Univ Vienna Max F Perutz Labs A-1030 Vienna Austria

Background: Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has attracted interest as an alternative plant model species with high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still incomplete and transcriptomic information is scarce. In addition, functional genomics investigations in this species are severely hampered by a lack of affordable tools for genome-wide gene expression studies. Results: Here, we report the results of Thellungiella de novo transcriptome assembly and annotation based on 454 pyrosequencing and development and validation of a T. salsuginea microarray. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from samples covering different tissues and abiotic stress conditions. Both libraries yielded partially unique sequences, indicating their necessity to obtain comprehensive transcriptome coverage. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. These unigenes were compared to all available Thellungiella genome sequence information. In addition, the groups of Late Embryogenesis Abundant (LEA) proteins, Mitogen Activated Protein (MAP) kinases and protein phosphatases were annotated in detail. We also predicted the target genes for 384 putative miRNAs. From the sequence information, we constructed a 44 k Agilent oligonucleotide microarray. Comparison of same-species and cross-species hybridization results showed superior performance of the newly designed array for T. salsuginea samples. The developed microarrays were used to investigate transcriptional responses of T. salsuginea and Arabidopsis during cold acclimation using the MapMan software. C

关键词： Arabidopsis thaliana Cold acclimation Gene annotation LEA proteins MAP kinases microarray design microRNAs Protein phosphatases Thellungiella salsuginea Transcriptome sequencing

来源：评论

学校读者我要写书评

暂无评论

Resequencing microarray probe design for typing genetically diverse viruses: human rhinoviruses and enteroviruses

引用

BMC GENOMICS 2008年第1期9卷 577-577页

作者： Wang, Zheng Malanoski, Anthony P. Lin, Baochuan Kidd, Carolyn Long, Nina C. Blaney, Kate M. Thach, Dzung C. Tibbetts, Clark Stenger, David A. Naval Res Lab Ctr Biomol Sci & Engn Washington DC 20375 USA Nova Res Inc Alexandria VA 22308 USA Tessarae LLC Potomac Falls VA 20165 USA

Background: Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results: Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen microarray RPM-Flu v. 30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion: This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v. 30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.

关键词： Reverse Transcription Polymerase Chain Reaction Base Call microarray design Febrile Respiratory Illness Prototype Sequence

来源：评论

学校读者我要写书评

暂无评论

A diffusion-reaction model for DNA microarray assays

引用

JOURNAL OF BIOTECHNOLOGY 2004年第1-2期114卷 31-45页

作者： Gadgil, C Yeckel, A Derby, JJ Hu, WS Univ Minnesota Dept Chem Engn & Mat Sci Minneapolis MN 55455 USA

DNA microarrays are extensively used for the quantification of the degree of differential mRNA expression. The assay involves hybridization of mobile DNA strands with immobilized complementary DNA strands to form duplexes. The overall duplex formation rate depends on the rate of transport of strands in solution to the corresponding spot on the surface, and the rate of the hybridization reaction. We present a theoretical model that incorporates both kinetics of the reversible hybridization reaction and diffusional transport of the labeled strands, and analyze DNA microarray hybridization using this model. Simulations are carried out in a geometrically realistic domain for labeled DNA concentrations corresponding to rare and abundant transcripts for typical assay conditions. The rate of strand diffusion in solution is shown to strongly affect the overall hybridization rate. We compute the minimum inter-spot spacing for replicate spots to enhance sensitivity. We also determine the hybridization time for which reliable estimates of the relative mRNA abundance of two species can be obtained using total fluorescence intensities. An analytical solution for the concentration distribution of mobile strands at intermediate hybridization times provides a convenient tool to calculate the mobile strand concentration profiles. This model provides a framework for the process analysis of all microarray assays currently used for genomic transcriptional analysis. (C) 2004 Elsevier B.V. All rights reserved.

关键词： diffusion-reaction hybridization kinetics microarray design mathematical model

来源：评论

学校读者我要写书评

暂无评论

CEM-designer: design of custom expression microarrays in the post-ENCODE Era

引用

JOURNAL OF BIOTECHNOLOGY 2014年 189卷 154-156页

作者： Arnold, Christina Externbrink, Fabian Hackermueller, Joerg Reiche, Kristin Univ Leipzig Dept Comp Sci Bioinformat Grp D-04109 Leipzig Germany UFZ Helmholtz Ctr Environm Res Dept Prote Young Investogators Grp Leipzig Germany Fraunhofer Inst Cell Therapy & Immunol Dept Diagnost RNom Grp Leipzig Germany

microarrays are widely used in gene expression studies, and custom expression microarrays are popular to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes uncovered recently make custom expression microarray design a non-trivial task. Pervasive transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that requires well-considered probe design strategies and is largely neglected in existing approaches. We developed the web server CEM-designer that facilitates microarray platform independent design of custom expression microarrays for complex transcriptomes. CEM-designer covers (i) the collection and generation of a set of unique target sequences from different sources and (ii) the selection of a set of sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to third party software to ensure that probes meet provider-specific constraints. (C) 2014 Elsevier B.V. All rights reserved.

关键词： Transcriptomics Pervasive transcription Non-coding RNA Custom expression microarray microarray design

来源：评论

学校读者我要写书评

暂无评论

design, optimization and validation of genomic DNA microarrays for examining the Clostridium acetobutylicum transcriptome

引用

BIOTECHNOLOGY AND BIOPROCESS ENGINEERING 2005年第5期10卷 432-443页

作者： Alsaker, KV Paredes, CJ Papoutsakis, ET Northwestern Univ Dept Chem & Biol Engn Evanston IL 60208 USA

microarray technology has contributed significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that signal quality is significantly improved by increasing the hybridization volume, possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that 40 similar to 55% of the C acetobutylicum genome is expressed at any time during batch culture, similar to estimates made for Bacillus subtilis.

关键词： gram-positive solvent-production gene-expression sporulation heat-shock butanol degenerate strain extrachromosomal number-of-expressed-genes Spo0A AbrB diffusion limitation microarray design

来源：评论

学校读者我要写书评

暂无评论

Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses

引用

NEW PHYTOLOGIST 2008年第4期180卷 766-786页

作者： Pavy, Nathalie Boyle, Brian Nelson, Colleen Paule, Charles Giguere, Isabelle Caron, Sebastien Parsons, Lee S. Dallaire, Nancy Bedon, Frank Berube, Hugo Cooke, Janice Mackay, John Univ Laval Ctr Etude Foret Quebec City PQ G2K 7P4 Canada BC Array Lab Ctr Vancouver BC V6H 3Z6 Canada Univ Minnesota Ctr Computat Genom & Bioinformat Minneapolis MN 55455 USA Univ Alberta Dept Biol Sci Edmonton AB T6G 2E9 Canada

One approach for investigating the molecular basis of wood formation is to integrate microarray profiling data sets and sequence analyses, comparing tree species with model plants such as Arabidopsis. Conifers may be included in comparative studies thanks to large-scale expressed sequence tag (EST) analyses, which enable the development of cDNA microarrays with very significant genome coverage. A microarray of 10 400 low-redundancy sequences was designed starting from white spruce (Picea glauca (Moench.) Voss) cDNAs. Computational procedures that were developed to ensure broad transcriptome coverage and efficient PCR amplification were used to select cDNA clones, which were re-sequenced in the microarray manufacture process. White spruce transcript profiling experiments that compared secondary xylem to phloem and needles identified 360 xylem-preferential gene sequences. The functional annotations of all differentially expressed sequences were highly consistent with the results of similar analyses carried out in angiosperm trees and herbaceous plants. Computational analyses comparing the spruce microarray sequences and core xylem gene sets from Arabidopsis identified 31 transcripts that were highly conserved in angiosperms and gymnosperms, in terms of both sequence and xylem expression. Several other spruce sequences have not previously been linked to xylem differentiation (including genes encoding TUBBY-like domain proteins (TLPs) and a gibberellin insensitive (gai) gene sequence) or were shown to encode proteins of unknown function encompassing diverse conserved domains of unknown function. New Phytologist (2008) 180: 766-786 (c) The Authors (2008). Journal compilation (c) New Phytologist (2008) doi: 10.1111/j.1469-8137.2008.02615.x.

关键词： computational analysis microarray design transcript profiling vascular tissues white spruce (Picea glauca)

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：