How to understand the TruSeq Stranded mRNA?

How is strandedness maintained after DNA amplification?

Strandedness is maintained via the directionality of the adapters. The p7 adapter will be on the 3' end of the cDNA strand. As a consequence, the cDNA strand is sequenced. Second strand synthesis is performed using dUTP in place of dUTP and a high fidelity polymerase that cannot process through dUTP template is used for PCR enrichment. As a result, only the first strand product is amplified and the strand information is retained based on the p5 and p7 adapter orientation.

The P5 end is sequenced first, then the P7; another name for the P5 is the "Universal adapter" (UNad) and P7 is "Index-containing adapter" (IndexAd), because it has the index for de-multiplexing multiple libraries run on the same lane.

For example, the strand of the gene is "+", read1 should be mapped to the reverse strand of the reference genome.

http://nextgen.mgh.harvard.edu/IlluminaChemistry.html

http://seqanswers.com/forums/showthread.php?t=9303&page=3

http://support.illumina.com/sequencing/sequencing_kits/truseq_stranded_mrna_lt_sample_prep_kit/questions.html
http://nextgen.mgh.harvard.edu/CustomPrimer.html