Subtraction was performed by using the RiboMinus Transcriptome Isolation Kit (Invitrogen) following the manufacturer's protocol.
We have addressed the cross platform/cross species comparison by using the zebrafish transcriptome as a reference.
RNA, 1 μg, was used as starting material, and the rRNA was reduced by using the RiboMinus Transcriptome Isolation Kit (Invitrogen), as per Affymetrix recommendations.
Contigs showing up two or more tryptic peptides were identified by using the P. albipes transcriptome database.
cDNA was synthesized by using the TransPlex® Complete Whole Transcriptome Amplification Kit according to the manufacturer's protocol (SIGMA).
After eliminating read with adaptors, read with unknown nucleotides larger than 5% and low quality read, 51,198,090 paired-end reads from total nucleotide of 4,607,828,100 were generated by using the SOAP de novo transcriptome assembly program.
The full length of α-2 was subsequently identified using the transcriptome reported earlier by Whelan et al.8, confirming that the difference is confined to a single amino acid substitution of a Val to Phe.
LncRNAs were related to the genes of the developmental transcriptome by using the GENCODE v22 long noncoding RNA annotations.
The reads were analyzed by using the ABI BioScope v1.3 whole-transcriptome analysis (WTA) pipeline.
In this study, grouper kidney cell (GK cell) was used to establish a transcriptome library by using the NGS technology.
In the present study, we mapped these unique sRNA sequences to S. europaea transcriptome database by using the computational software SOAP (http://soap.genomics.org.cn) [ 29].
