ArrayExpress

Last updated on 16 April 2020, released on 30 April 2020

Esox lucius, Oncorhynchus kisutch, Salvelinus alpinus

The aim of this sequencing experiment was to make available liver tissue expression for selected fish species, northern pike (Esox lucius, Eluc), coho salmon (Oncorhynchus kisutch, Okis) and Arctic charr (Salvelinus alpinus, Salp), for comparative expression studies between the species. Samples in replicate of four were sacrificed according to protocols at each of the facilities from where samples were obtained. RNA was extracted from samples and Illumina TruSeq Stranded mRNA libraries were built. Sequencing was performed in two passes on an Illumina HiSeq2500, paired-end 125bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the NCBI genomes of the respective species using STAR and gene level counting using RSEM and NCBI gene annotation.

RNA-seq of coding RNA, organism part comparison design, species design

Gareth B Gillard <gareth.gillard@nmbu.no>, Ben Koop <bkoop@uvic.ca>, Eric B Rondeau <erondeau@uvic.ca>, Simen R Sandve <simen.sandve@nmbu.no>