RNA-seq of Homo sapiens:MCF7
To quantify the mapped reads on the reference genome in to the gene expression values, Cuffquant in Cufflinks ver 2.2.1[4] with the strand-specific library option, --library-type=fr-firststrand and other default options was used. The gene annotation of the reference genome rn6 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit. The differentially expressed genes between the two selected biological conditions were analyzed by Cuffdiff in Cufflinks package[5] with the strand-specific library option, --library-type=fr-firststrand and other default options was used. To compare the expression profiles among the samples, the normalized expression values of the selected a few hundred of the differentially expressed genes were unsupervised clustered by in-house R scripts. The scatter plots for the gene expression values and the volcano plots for the expression-fold changes and p-values between the two selected samples also were drawn by in-house R scripts.