Single cell RNA-seq of Oncorhynchus mykiss PBLs from infected and healthy fish

Single cell RNA-Seq data generated on a 10x Chromium genomics platform from infected and healthy PBLs from Oncorhynchus mykiss. Overall design: Two rainbow trout were killed by benzocaine overdose. Blood was extracted with a heparinized needle from the caudal vein and diluted 10 times with Leibovitz medium. PBLs were obtained by centrifugation of diluted blood on 51% continuous Percoll density gradients. IPNV (Sp strain, ATCC VR 1318) was propagated in the RTG-2 (Rainbow Trout Gonad-2) cell line. To produce viral stocks, complete culture media was removed from 80% confluent cell cultures in 75 cm2 culture flasks and IPNV inoculated. For the in vitro infection of rainbow trout PBLs, cells resuspended in L-15 containing antibiotics and 5% FCS were disposed in 24-well plates. Cell suspensions (1,000 cells/µl ) from each sample were loaded into the chips of the Chromium™ Single Cell 5' Gel Beads Kit (10x Genomics) and subjected to the Chromium Controller instrument to generate single cell Gel Bead-In Emulsions (GEMs). GEMs were subjected to library construction using the Chromium™ Single Cell 5' Library Kit v1 (10x Genomics). Samples were sequenced using a NextSeq instrument (Illumina) with 150PE chemistry.