A quick search in Illumina website: http://www.illumina.com/applications/sequencing/rna.ilmn#strand_specific_rna_seq, it was mentioned that: "The Directional mRNA-Seq Sample Prep protocol is an experimental application of Illumina technology, requiring Illumina small RNA sequencing primers and the mRNA-Seq Sample Prep kit. This protocol is compatible with single-read flow cells only."
I am not sure if this means that the directional mRNA-seq experiment only applicable for single-end read?
After searching through the website, I bumped into this website: http://microarrays.nki.nl/index.php?page=samples-seq. It was mentioned that:
"4) Single read libraries cannot be used on Paired End flowcells."
"5) Paired End libraries can be read on Single read flowcells for the first read only."