title: RNA-Seq of Penaeus monodon: adult female ovary
design: We carried out the de novo transcriptome sequencing and assembling by Illumina TruSeq platform. 3 ug pooled RNA from the adult female ovary in Penaeus monodon was used as mRNA library construction using Illumina TruSeq RNA Sample Preparation Kit (Illumina) following manufacturer  s recommendations. Then, cDNA fragments with length >200 bp were purified with AMPure XP system (Beckman), and those ligated with adapters on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 10 cycles PCR reaction, and the products were purified again by AMPure XP system and quantified by Agilent 2100 bioanalyzer. Subsequently, the cluster of indexcoded samples was generated using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) and sequenced on an Illumina Hiseq 2000 platform. Finally, 100 bp paired-end reads were generated. After removing the reads with adapters, any reads containing   N   (>10%), low quality reads (sQ  5) and the redundant reads, the remaining clean reads were assembled by TRINITY method, and then the redundant contigs were screened by CAP3. Finally, the unigenes were searched against Nr database (NCBI non-redundant protein sequences) by Blast2GO, and the orthologs were used as the reference sequences.