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Pipeline publication

[…] by the National Animal Research Authority (Utvalg for forsøk med dyr, forsøksdyrutvalget, Norway) General License for Fish Maintenance and Breeding (Godkjenning av avdeling for forsøksdyr) no. 17. To collect tissues, animals were anesthetized with 1% MS-222 (3-aminobenzoate methanesulfonic acid, Sigma Aldrich) and sacrificed thereafter according to standard procedure., Atlantic halibut genomic DNA was extracted from ovarian tissue of a 5-years-old individual using MagMAX™ DNA Multi-Sample Kit (AB Applied Biosystems, Foster City, California, USA) and sequenced using Roche 454 GS FLX titanium sequencer, according to the manufacturer's instructions. The genomic DNA sequence was examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and de novo assembled using CLC (CLC Genomics Workbench 4.9)., We used small RNA transcriptome data generated previously using Sequencing by Oligonucleotide Ligation and Detection (SOLiD) , . Data analysis strategy is shown in . Atlantic halibut SOLiD sequence reads were mapped to zebrafish genome sequences (Zv9.62) and hairpins were extracted using wapRNA tools in default setting . miRBase 18 hairpin sequences were mapped to the 454 sequences to identify conserved pre-miRNAs. Novel pre-miRNAs were identified by extracting hairpins from 454 reads using srnaloop using the parameters described previously , and mapping them to miRBase 18 (http://www.mirbase.org/) using CLC. Assuming the average length of fish pre-miRNAs and mature miRNAs at ∼86 nts and ∼22 nts, respectively, and taking into account non-conserved region of pre-miRNA, mapping was performed with 80% similarity in half of the length with 2 mismatches and 3 indels costs. All positively mapped sequences were checked manually and tandem repeat sequences were removed. The two map […]

Pipeline specifications

Software tools FastQC, CLC Genomics Workbench, wapRNA
Databases miRBase