Meta data file, Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/crispr_metadata.txt
Export PNG
Views: 2364 Downloads: 33
Created: 23rd Jan 2019 at 13:38
Last updated: 19th Feb 2019 at 10:26
This item has not yet been tagged.
None
Version History
Version 1 (earliest) Created 23rd Jan 2019 at 13:38 by Sahar Hassani
No revision comments
Related items
Projects: GenoSysFat, DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-9551-9280Projects: DigiSal, GenoSysFat, SEEK tutorial for DigiSal, FAIRDOM Community Workers
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0002-3980-8782I am the data and model manager for the Digital Salmon
Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal
Institutions: Norwegian University of Life Sciences
https://orcid.org/0000-0001-5597-8397Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...
Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal, DigiSal-BT8121
Web page: http://tinyurl.com/digisal
Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)
Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...
Programme: The Digital Salmon
Public web page: http://tinyurl.com/digisal
Organisms: Danio rerio, Salmo salar, Oncorhynchus mykiss
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.
Submitter: Sahar Hassani
Studies: ELOVL2 Knockout, FADS Knockout
Assays: Differential expression analysis of genes between FADS-KO and WT, Fatty Acid Analysis, RNAseq, RNAseq-splicing, RNAseq_CountTable, Sanger sequencing
Snapshots: Snapshot 1, Snapshot 2
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.
Submitter: Sahar Hassani
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Assays: Fatty Acid Analysis, RNAseq, RNAseq-splicing, Sanger sequencing
Snapshots: Snapshot 1
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 ...
Submitter: Sahar Hassani
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Knockout omega-3 genes to perturb LC-PUFA metab...
Study: ELOVL2 Knockout
Organisms: No organisms
SOPs: No SOPs
Data files: Combined.counts, Crispr_metadata
Snapshots: No snapshots