RNA-seq of Stygichthys typhlops, transcriptome
The libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit. The mRNA was purified using poly-T oligo-attached magnetic beads to pull down the poly-A mRNA. After purification, the mRNA was fragmented and copied into first strand cDNA using reverse transcriptase. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase. The concentration of the cDNA libraries was measured with the qubit dsDNA high-sensitivity (HS) assay kit using the qubit fluorometer (Invitrogen). Concentrations of sequencing runs were normalized based on final concentrations of the fragmented cDNA. Next-generation sequencing (NGS) was carried out using the Illumina HiSeq 2000 platform (Illumina Inc., San Diego, CA) at the University of Chicago Genomics Facility. Raw red sequenced paired-end reads were 101 bp.