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Series GSE216505 Query DataSets for GSE216505
Status Public on Nov 01, 2023
Title Validation of a QTL for Flavobacterium psychrophilum resistance in rainbow trout Oncorhynchus mykiss
Organism Oncorhynchus mykiss
Experiment type Expression profiling by RT-PCR
Summary Rainbow trout (1000 fish) was exposed to the bacterial pathogen F. psychrophilum by simple bath challenge without any pre-treatment with hydrogen peroxide.
Samples (fin clip for Affymetrix QTL analysis) were taken from 167 moribund fish during the course of infection.
When mortality/morbidity ended (day 40) we euthanized a total of 197 specimens of the remaining fish and took samples for DNA (QTL analysis) and assigned the status: Survivor.
For gene expression analysis we took samples from gill, spleen and liver between day 11 and 15 from fish with clinical signs (CS) and no clinical signs (NCS), whereas samples from survivors were taken at day 40.
 
Overall design Rainbow trout (1000 fish) from an outbred batch were used for infection and additionally 1,000 fish were kept as non-infected controls (3.3 ± 0.75 g; 6.9 ± 0.5 cm).
Samples for gene expression (gills, liver and spleen) were taken at three different time-points, at day 0 (before exposure), at day 11-14 (when the mortality rate peaked) and at day 40 (termination of experiment). At day 0, samples were taken from 15 uninfected control fish. At day 11 to 14 we sampled from 15 uninfected control fish, 15 infected fish showing clinical signs (CS) and 15 fish infected fish showing no clinical signs (NCS). The samples at day 40 was from 15 uninfected control and from 15 surviving rainbow trout. All samples were fixed in RNAlater (cat. no. R90901. Sigma-Aldrich, Denmark) and stored at 4°C for 24 h before being placed at -20°C until further analysis.
Web link https://doi.org/10.1016/j.aqrep.2023.101573
 
Contributor(s) Karami AM, Kania PW, Buchmann K, Mathiessen H
Citation Heidi Mathiessen, Yajiao Duan, Moonika H Marana, Shaozhi Zuo, Asma M Karami, Rzgar Jafaar, Louise von Gersdorff Jørgensen, Per W Kania, Inger Dalsgaard, Lone Madsen, Torben Nielsen, Fabian Grammes, Jørgen Ødegård, Valeria Macchia, and Kurt Buchmann. Validation of a QTL for Flavobacterium psychrophilum resistance in rainbow trout Oncorhynchus mykiss. Aquaculture Reports 2023, Vol 30, 101573. doi:10.1016/j.aqrep.2023.101573
Submission date Oct 25, 2022
Last update date Jan 31, 2024
Contact name Per Walter Kania
E-mail(s) pwk@sund.ku.dk
Organization name University of Copenhagen
Department Department of Veterinary and Animal Sciences
Lab Aquatic Pathobiology
Street address Stigbojlen 7
City Frederiksberg
ZIP/Postal code 1870
Country Denmark
 
Platforms (1)
GPL32679 University of Copenhagen, Laboratory of Aquatic Pathobiology - Oncorhynchus mykis TechFish Immunegene PCR Array
Samples (270)
GSM6675155 Gill, Control, Day 0 (Fp_C1_G)
GSM6675156 Gill, Control, Day 0 (Fp_C2_G)
GSM6675157 Gill, Control, Day 0 (Fp_C7_G)
Relations
BioProject PRJNA894124

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE216505_Matrixes_Fold-change.xlsx 257.5 Kb (ftp)(http) XLSX
Processed data are available on Series record

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