BLAST

Yoder Lab BLAST databases

RNAseq from a double-haploid CG2 zebrafish

A single CG2 zebrafish was euthanized and the kidney, intestine, gills and spleen were dissected and combined for RNA extraction. RNA was prepared for sequencing with the TruSeq RNA kit (Illumina) and sequenced (2 x 100 bp paired end reads) on a single lane of a HiSeq2000 (Illumina). In an effort to detect rare transcripts, a normalization procedure also was employed. Normalized cDNA was achieved with the MINT-Universal cDNA synthesis and TRIMMER-DIRECT cDNA normalization kits (Evrogen) which was then prepared for sequencing with the TruSeq DNA kit (Illumina). The normalized library was sequenced (2 x 100 bp paired end reads) on a single HiSeq2000 lane. The Trinity Assembler was used to create a de novo transcriptome assembly from the raw RNA-seq data, and the transcriptome was formatted into a BLAST database using the formatdb command for the stand-alone NCBI BLAST software. The BLAST database is available here. Raw sequence data has been deposited in the NCBI short read archives (SRA) with accession number SRP057116.