Hi,
I have been working on RNA-seq data from Blueberry for a while and couple of day ago I came across this article. It describes developmental stages of grape berry using gene expression data.
Similar to blueberry, grape is also a berry producing plant so it makes more sense to compare blueberry against the grape rather than comparing against the Arabidopsis. Both blueberry and grape produce anthocyanins responsible for ripening red color. Here authors motivate the use of RNA-seq against microarray for finding the genes controlling the biological process involved during the berry development. Authors here sequenced a single lane of Illumina HiSeq 2000, getting around 16 billion bases. They do not have any replicates and all four sample types have about 40 million reads. For transcript reconstruction, they have used something called GAZE, which I have no idea about but I wonder why not using well established TopHat/Cufflinks. In particular, I liked the clustering in figure using Cluter3.0.
I have been working on RNA-seq data from Blueberry for a while and couple of day ago I came across this article. It describes developmental stages of grape berry using gene expression data.
Similar to blueberry, grape is also a berry producing plant so it makes more sense to compare blueberry against the grape rather than comparing against the Arabidopsis. Both blueberry and grape produce anthocyanins responsible for ripening red color. Here authors motivate the use of RNA-seq against microarray for finding the genes controlling the biological process involved during the berry development. Authors here sequenced a single lane of Illumina HiSeq 2000, getting around 16 billion bases. They do not have any replicates and all four sample types have about 40 million reads. For transcript reconstruction, they have used something called GAZE, which I have no idea about but I wonder why not using well established TopHat/Cufflinks. In particular, I liked the clustering in figure using Cluter3.0.
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I intend not to break any copyrights rules.
Please find article at: http://www.biomedcentral.com/1471-2164/13/691
Authors: Crystal Sweetman, Darren CJ Wong, Christopher M Ford and Damian P Drew
journal: BMC Genomics
Publishers: BioMed Central Ltd.
If you would like review to be removed, please write me at vikas0633@gmail.com
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