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).
CNVs are defined as deletions, insertions, or duplications of a region of DNA 1 kilobase
or larger in length and have significant impacts on genetic variation in the human genome by altering gene dosage, disrupting coding sequences, or perturbing long-range gene regulation .
Expression levels were calculated as fragments per kilobase
million (FPKM) using read mapping in BowTie2, version 2.2.3 (Langmead and Salzberg, 2012), run on the National Center for Genome Analysis Support (NCGAS) Mason Linux Server (Indiana University, Bloomington, FN).
Paired-end sequencing of short (550 bp) and mate-paired sequencing of long (2-10 kilobase
[kb]) genomic fragments was performed to obtain finished bacterial genomes.
The lead SNP, rs1619661 is on chromosome 10, approximately 132 kilobase
(kb) downstream of CXCL12 (Table 2).
The selection of suitable vector for e.g Libraries containing 2-10 Kilobase
(Kb) can be constructed in plasmids or lambda expression vectors.
Transcript abundances were estimated by Cufflinks in Fragments per Kilobase
per Million mapped reads (FPKM) for paired-end reads.
To determine specific expression of genes, expression profiles were calculated using the reads per kilobase
mapped (FPKM) method (Mortazavi et al.
We observed that SLCP produced small DNA fragments, including lower nucleotides oligomers, which was less than 100 kilobase
pair (kb), whereas similar fragmentation was not observed in the case of Cur-treated or control cells (Figure 5(d)).
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 gene expression FPKM (fragment per kilobase
per million mapped reads) values were calculated.
The RNA-Seq was employed to calculate the FPKM (expected number of fragments per kilobase
of transcript sequence per millions base pairs sequenced), which represented the expression level of each transcript (Trapnell et al., 2010).