Transcriptome analysis of a nematode resistant and susceptible upland cotton line

We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. Overall design: Replicated set of cDNA libraries were constructed from M120 and C201 plants at 12, 30 DAI and untreated plants. All libraries were constructed using the NEBNext Ultra RNA library Prep Kit for Illumina (New England BioLabs Inc.) following the manufacturers protocol. The NEBNext Multiplex Oligos for Illumina (Index Primers Set 2, New England BioLabs Inc.) containing adaptors and primers were used to label libraries facilitating pooling.