The Illumina next generation sequencing platform and its associated mRNA-Seq protocols will be used for analysis. In summary, messenger RNA with polyA tails will be purified from the total RNA samples. The mRNA will be fragmented and transcribed into ds cDNA for library preparation. Sequencing of the library will be done in a paired-end mode with a read length of 75 cycles. The paired-end reads will be mapped to the genome, and the potential splicing pattern will be analyzed. When applicable, expression levels of transcripts, genes, CDSs will be estimated, in RPKM, and reported.
- Extraction of raw sequencing data (in FASTA or FASTQ format)
- Alignment of sequencing reads to genome
- Report of splice junctions
- Annotation of known transcripts
- Report of potential new transcripts
- Report of relative expression levels for transcripts and genes