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Pipeline publication

[…] million reads for each library) to the candidate LEA genes and the mapped read number was normalized based on the Z-score method for heatmap (heatmap2 of R package)., We mapped the SOLiD RNA-Seq reads generated from P. dactylifera samples at seven distinct fruit developmental stages (0, 15, 30, 60, 90, 120 and 135 DPP) to the gene models using Bioscope v1.3 with default parameters. The uniquely mapped reads for gene expression were defined with a threshold of >5 and normalized to per kb of genes per million reads (RPKM). We annotated genes using InterProScan, KAAS (KAAS, http://www.genome.ad.jp/tools/kaas/) and KEGG basic metabolic pathway. We identified DEGs during fruit ripening using edgeR and clustered all them based on RPKM values using the R hclust function. We also conducted gene ontology enrichment analysis of the two major clusters using AGRIGO. On the basis of gene annotation and transcriptome analysis, we estimated gene expression levels of each pathway in the KEGG ‘metabolism’ category according to the following protocol. First, expression levels for each KEGG ortholog (KO) were calculated as the sum of all RPKM values for each gene. This value at seven distinct fruit development stages was defined as the KO expression value. All KO expression values in a single pathway were then averaged, giving the pathway expression value. Finally, the average value of pathway expression values for each subcategory of the KEGG ‘metabolism’ category was calculated., We mapped the SOLiD mate-pair reads from Khalas, Agwa, Sukry and Fahal […]

Pipeline specifications

Software tools edgeR, Hclust, agriGO