Knockout omega-3 genes to perturb LC-PUFA metabolism in Salmon

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The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.

DOI: None

Zenodo URL: None

Created at: 20th Oct 2020 at 20:54

Contents

ELOVL2 Knockout

By generating CRISPR-mediated elovl2 knockout, we are planning to study the crucial role of elovl2 for multi-tissue synthesis of 22:6n-3 in vivo. Endogenously synthesized PUFAs are important for transcriptional regulation of lipogenic genes in Atlantic salmon. This study demonstrates key roles of elovl2 at two penultimate steps of PUFA synthesis in vivo and suggests Srebp-1 as a main regulator of endogenous PUFA synthesis in Atlantic salmon.

RNAseq

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
...

Combined.counts

RNAseq data file, source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/final/2018-06-25_samples_ELOVL2/combined.counts

  • combined.counts

Crispr_metadata

Meta data file,
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/crispr_metadata.txt

  • crispr_metadata.txt

Fatty Acid Analysis

Total lipids are extracted from tissues of white muscle, liver and whole brain from three fish per dietary treatment.

Initial FAD KO_Liver phospholipid fatty acid profile

Lipid data file
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/Lipid_data

  • Initial FAD KO_Liver phospholipid fatty acid profile.xlsx

Initial FAD KO_White muscle phospholipid fatty acid profile

Lipid data file
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/Lipid_data

  • Initial FAD KO_White muscle phospholipid fatty acid profile.xlsx

Sanger sequencing

The three different CRISPR target sites within the elovl2 gene (T1-3) were characterised by Sanger sequencing, sequencing on average 8 clones per individual.

FT1KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT1KO1.fq

FT1KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT1KO2.fq

FT1KO3.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT1KO3.fq

FT2KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT2KO1.fq

FT2KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT2KO2.fq

FT2KO5.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT2KO5.fq

FT3KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT3KO1.fq

FT3KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT3KO2.fq

FT3KO5.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT3KO5.fq

FT4KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT4KO1.fq

FT4KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT4KO2.fq

FT4KO3.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • FT4KO3.fq

T1KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T1KO2.fq

T1KO3.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T1KO3.fq

T1KO4.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T1KO4.fq

T2KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T2KO1.fq

T2KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T2KO2.fq

T2KO4.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T2KO4.fq

T3KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T3KO1.fq

T3KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T3KO2.fq

T3KO3.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T3KO3.fq

T4KO1.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T4KO1.fq

T4KO2.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T4KO2.fq

T4KO3.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T4KO3.fq

T4KO4.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T4KO4.fq

T4KO5.fq

FASTQ file made from AB1 files.
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/sanger/data/fq

  • T4KO5.fq

RNAseq-splicing

RNAseq is utilised to validate the SnpEff annotation predictions for aberrant splicing. For this purpose the percentage exon retention for exons 4, 6 and 7 are calculated using RNAseq data.

RNAseq data

RNAseq data file,
Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/splicing/elovl2.splicing.txt

  • elovl2.splicing.txt
Fingerprints

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MD5: 6ae63a2cb45628ac54941f9fd9293a97

SHA1: 721810bbd26aa92fb064ea29b4f3fb8d73a3e070

Snapshots
Snapshot 2 (20th Oct 2020)
Snapshot 1 (20th Oct 2020)
Activity

Views: 620   Downloads: 5

Created: 20th Oct 2020 at 20:54

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