Rotylenchuls reniformis GAIIx reads
Starting with 5 μg total DNA (A260/280 = 1.78) from a pooled population of R. reniformis, library construction was performed using the NEBNext DNA sample prep kit (New England Biolabs).  Fragmentation was carried out using an Illumina (San Diego, CA) nebulizer according to the Illumina protocol.  DNA was end-repaired and ‘A’ overhangs were added.  Illumina index paired-end sequence adaptors were ligated to the cDNA fragments.  Fragments of approximately 250 and 350 bp were isolated from a 2% agarose gel and amplified (15 cycles) according to the Illumina protocol (Illumina Genomic DNA Sample Prep Guide #1003806).  An Agilent bioanalyzer was used to quantify and confirm the fragment size of each library.  For each library, one flow cell lane was sequenced on a GAIIx sequencer (2 x 100 bp).  One nanomole of each mRNA-seq library sample prepared for sequencing on the Illumina GAIIx was denatured and diluted to 6 picomoles for clustering (v2) according to the manufacturer’s protocol.  Paired-end sequencing (2x100 bp) of the clustered flow cell was performed using Illumina’s SBS chemistry (v3) and its SCS data analysis pipeline v2.4.  Flow-cell image analysis and cluster intensity calculations were carried out by Illumina Real Time Analysis (RTA v1.4.15.0) software.  Subsequent base-calling was performed using the Illumina GA Pipeline v1.5.1 software.