By Andy Pereira
This publication describes equipment for the research of high-throughput genome series information, the identity of noncoding RNA from series details, the excellent research of gene expression by way of microarrays, and metabolomic research, all of that are supported by way of scripts to assist their computational use.
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Extra info for Plant Reverse Genetics: Methods and Protocols (Methods in Molecular Biology)
Recent reviews contain more rigorous discussions of other potential analysis methods and issues (8–10). Here, we concentrate on one simple series of steps for the analysis of gene expression data produced using a standard singlechannel microarray platform (Affymetrix GeneChip). Similar steps can be extended to the data from other platforms. We will be using bioconductor tools (11) within R statistical computing environment (12) for the analysis. It is assumed that RNA extracted from some samples has been hybridized onto microarrays and the machine-output data are available for analysis.
And Zhu, T. (2006) Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J. 45: 630–650. 9. Allison, D. , Page, G. , and Sabripour, M. (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. 7: 55–65. 10. , and Calogero, R. A. (2007) Microarray data analysis and mining approaches. Brief Funct Genomic Proteomic. 6: 265–281. 11. Gentleman, R. , Carey, V. , Bates, D.
The second step involves real-time PCR, in which the expression levels of miRNAs are monitored and quantified using qRT-PCR that includes miRNA-specific forward primer, reverse primer and FAM dyelabeled TaqMan probes (28). Allow the TaqMan MicroRNA Reverse Transcription Kit reagents and Reverse Transcription Primers (RT primers) to thaw on ice. Briefly centrifuge to bring the reagents and primers to the bottom of the tubes. 00 mL Reverse Transcriptase enzyme. Mix the reagents gently by flicking the tube and briefly centrifuge.
Plant Reverse Genetics: Methods and Protocols (Methods in Molecular Biology) by Andy Pereira