ELOVL2 Knockout

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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.

DOI: None

Zenodo URL: None

Created at: 19th Feb 2019 at 12:00

Contents

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: a407aa22c03d4e26c495a901f0866eb7

SHA1: 9b2352c0532f93a365f19cdb9e71ba0eff3456a4

Snapshots
Snapshot 1 (19th Feb 2019)
Activity

Views: 1172   Downloads: 13

Created: 19th Feb 2019 at 12:00

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