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Full-Text Articles in Computational Biology
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Dan Nettleton
Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the …
Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable
Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable
Dan Nettleton
The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of …
Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle
Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle
Dan Nettleton
The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of …