title: RNAseq of Doryteuthis pealeii lens: core region
design: RNA was extracted from tissue samples using the Qiagen RNeasy Mini Kit (Cat. No. 74104) according to manufacturer instructions and normalized to 25 ng/_L.  Library construction and sequencing for 100% layer and 60% layer was performed by the University of Utah High Throughput Genomics Core Facility. Libraries were prepared from total RNA using the Illumina truSeq stranded mRNA kit (cat# RS-122-2101, RS-122-2102), with polyA selection to remove ribosomal RNA. Libraries were assessed for fragment length, concentration, and molarity with a NanoDrop spectrophotometer, Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) assay and KapaBiosystems Kapa Library Quant Kit (cat# KK4824). Libraries were sequenced with the HiSeq 101 cycle paired-end sequencing protocol using read adapters AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2). The samples were pooled with one other samples in a single lane, using barcodes TAGCTT (100% layer) and GGCTAC (60% layer).  Illumina data were assembled with Trinity (version r20140413p1), using Transdecoder to generate putative amino acid sequences. Predicted S-crystallins were identified with HMMER using a hidden Markov model constructed from known S-crystallins . Only gene candidates were retained for further analysis.