Stranded RNAseq libraries were prepared from 1µg total RNA from liver tissue using TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, USA) using double unique indices (#20022371), according to the manufacturer's instruction (Part 15031057 Rev.E). Libraries were sequenced at the Norwegian Sequencing Centre (NSC). All libraries were pooled, and the same pool was sequenced on 4 flow cell lanes on a HiSeq 3000 machine (Illumina), generating 100bp single-end reads. RNA sequencing files (.fastq) were processed in the following manner: (i) All reads from the same individual were merged into one fastq file. (ii) Reads were mapped to the Atlantic salmon genome (GenBank Accession number: GCA_0002333375.4) using STAR (v 2.6.0c) 50. (iii) Read alignments, recorded in BAM format were subsequently used to count uniquely mapped reads per gene using featurecounts (v1.4.4) 51, with the RefSeq gene_ids. Raw illumina reads as well as gene counts are publicly available through ArrayExpress 52 accession E-MTAB-7220.
SEEK ID: https://testing.sysmo-db.org/assays/98
Experimental assay
Projects: Student test project
Investigation: Test investigation
Study: Laurentiu Nistor
Assay position:
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: No organisms
Creators
Not specifiedSubmitter
Views: 402
Created: 27th Mar 2019 at 15:30
This item has not yet been tagged.