Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

January 2007
BMC Genomics;2007, Vol. 8, p344
Academic Journal
No abstract available.


Related Articles

  • Pigeons: A Novel GUI Software for Analysing and Parsing High Density Heterologous Oligonucleotide Microarray Probe Level Data. Hung-Ming Lai; May, Sean T.; Mayes, Sean // Microarrays (2076-3905);Mar2014, Vol. 3 Issue 1, p1 

    Genomic DNA-based probe selection by using high density oligonucleotide arrays has recently been applied to heterologous species (Xspecies). With the advent of this new approach, researchers are able to study the genome and transcriptome of a non-model or an underutilised crop species through...

  • Optimising oligonucleotide array design for ChIP-on-chip. Nielsen, Fiona; Graef, Stefan; Xinmin Zhang; Kurtz, Stefan; Denissov, Sergei; Green, Roland; Birney, Ewan; Flicek, Paul; Huynen, Martijn; Stunnenberg, Henk // BMC Bioinformatics;2007 Supplement 8, Vol. 8, Special section p1 

    The sequencing of whole genomes has allowed for custom- made genome-wide microarray assays such as the ChIP-on-chip. With this technology we can detect e.g. transcription factor binding sites over an entire genome. In principle, an accurate detection is only limited by the resolution of the...

  • Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. Hammond, John P.; Broadley, Martin R.; Craigon, David J.; Higgins, Janet; Emmerson, Zoe F.; Townsend, Henrik J.; White, Philip J.; May, Sean T. // Plant Methods;2005, Vol. 1, p10 

    High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a...

  • Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida. Ping Gong; Pirooznia, Mehdi; Xin Guan; Perkins, Edward J. // PLoS ONE;2010, Vol. 5 Issue 12, p1 

    High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic...

  • Alternative mapping of probes to genes for Affymetrix chips. Gautier, Laurent; Møller, Morten; Friis-Hansen, Lennart; Knudsen, Steen // BMC Bioinformatics;2004, Vol. 5, p1 

    Background: Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible...

  • A simple optimization can improve the performance of single feature polymorphism detection of Affymetrix expression arrays. Horiuchi, Youko; Harushima, Yoshiaki; Fujisawa, Hironori; Mochizuki, Takako; Kawakita, Masanori; Sakaguchi, Takayuki; Kurata, Nori // BMC Genomics;2010, Vol. 11, p315 

    Background: High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript...

  • Combining gene expression data from different generations of oligonucleotide arrays. Kyu-Baek Hwang; Sek Won Kong; Greenberg, Steve A.; Park, Peter J. // BMC Bioinformatics;2004, Vol. 5, p159 

    Background: One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism...

  • Molecular fish on chips. Goffeau, Andre // Nature;1/16/1997, Vol. 385 Issue 6613, p202 

    Provides background and analysis for a series of papers that report the use of high-density oligonucleotide arrays for large-scale analysis of genomic data. The types of gene sequences that are desired by 2005; The variation of molecular hybridization of polynucleotides; Papers published in...

  • High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. Wallace, James C; Korth, Marcus J; Paeper, Bryan; Proll, Sean C; Thomas, Matthew J; Magness, Charles L; Iadonato, Shawn P; Nelson, Charles; Katze, Michael G // BMC Genomics;2007, Vol. 8, p28 

    Background: Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project...

  • Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays. Høvik, Hedda; Tsute Chen // BMC Bioinformatics;2010, Vol. 11, p82 

    Background: Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics