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In total, we detected 12,453 expressed genes by calculating reads per kilobase million (RPKM) values and analyzed the data from the first 50 highly expressed selected genes in the pooled MM cells (Table 2) and compared the expression levels with the controls (Table 3).
The RPKM method was used to calculate the known expression level using the Cufflinks software package.
Figure 1 shows the temporal evolution of PTGS2 (COX2) expression levels during infection, based on the RPKM values and relative quantification by RT-qPCR.
Figure S1: RPKM distribution and RPKM density distribution of different genes in the DS and CK hemp.
A total of 16.777 genes from our six datasets obtained by RNA-Seq (GSE81265) were inserted in an expression matrix normalized by RPKM and, after that, used for enrichment comparing with expression datasets from collections H and C2.
For RPKM (PDMS) >RPKM (SLIPS), fold change was calculated by RPKM (PDMS)/RPKM (SLIPS).
RPKM = Transcription reads/Transcription length x Total assembly reads in run x 10 9
For each opsin transcript, relative expression was normalized as reads per kilobase transcript per million reads (RPKM).
Gene counts were normalized to the values of Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Uniquely localized reads were used to calculate reads number and RPKM (reads per kilobase of exon model per million mapped reads) value of each gene .
The expression levels are given as reads per kilobase per million (RPKM) values.
The expression of PCGs from the exonic or antisense lncRNA transcripts was determined based on RPKM values as described above.
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