Bioproject ID: PRJNA658476

bioproject id PRJNA658476      to NCBI
key word Challenge, strain, high growth rates, immune performance, hematopoietic necrosis virus
experiment type challenge
publication nan
description Gene expression analysis comparing a selected strain of rainbow trout with superior growth and immune performance to a commercial reference strain during infection with infectious hematopoietic necrosis virus (rainbow trout)
abstract Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain also shows superior performance in bacterial and viral disease challenges compared to commercial trout strains, and even a strain specifically selected over many generations for viral and bacterial disease resistance. The selection criteria was strictly focused on performance on plant-based diets, and therefore the physiological mechanisms responsible for the strain’s superior disease resistance remain unresolved. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the intestinal gene expression of the select strain to that of a commercial control line of trout during an experimental viral infection using the CSF 220-90 isolate of Infectious Hematopoietic Necrosis virus (IHNv). At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. For both strains of trout, three tanks of fish were experimentally infected with IHNv by static bath and one tank was mock challenged by static bath (Sham). Sampling was conducted at 4 days post challenge (dpc) (Early Infection) and 20 dpc (Late/Recovered Infection). Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. Infections were mild with mortality rates near 50% over the 21 day trial and no significant difference in mortality rates between the two strains of trout. Reads from the RNAseq samples were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the strains of trout, infection time points, and disease status. Overall design: At 65 days post hatch, all female rainbow trout from the select and commercial strain were stocked separately into four 150L tanks each, at a density of 45 fish per tank. There were three infected tanks and one mock challenged tank per strain. Intestinal samples were collected from all groups at 4 days post challenge (dpc) and 20 dpc. Two intestinal samples from each tank were pooled and two pools from each tank were utilized for RNAseq library preparation. At each time point, there are 6 pooled samples of infected fish and 2 pooled samples of mock challenged fish per strain.

Sample Information

sample id sample name tissue strain treatment description
1. SRR12491281 GSM4734541 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI1 BiologicalRep1 nan
2. SRR12491282 GSM4734542 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI1 BiologicalRep2 nan
3. SRR12491283 GSM4734543 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI2 BiologicalRep1 nan
4. SRR12491284 GSM4734544 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI2 BiologicalRep2 nan
5. SRR12491285 GSM4734545 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI3 BiologicalRep1 nan
6. SRR12491286 GSM4734546 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV TI3 BiologicalRep2 nan
7. SRR12491287 GSM4734547 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV_Sham TIControl BiologicalRep1 nan
8. SRR12491288 GSM4734548 intestine Hematopoietic Necrosis virus (IHNv) Commercial 20dpc IHNV_Sham TIControl BiologicalRep2 nan
9. SRR12491289 GSM4734549 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI1 BiologicalRep1 nan
10. SRR12491290 GSM4734550 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI1 BiologicalRep2 nan
11. SRR12491291 GSM4734551 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI2 BiologicalRep1 nan
12. SRR12491292 GSM4734552 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI2 BiologicalRep2 nan
13. SRR12491293 GSM4734553 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI3 BiologicalRep1 nan
14. SRR12491294 GSM4734554 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV CI3 BiologicalRep2 nan
15. SRR12491295 GSM4734555 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV_Sham CIControl BiologicalRep1 nan
16. SRR12491296 GSM4734556 intestine Hematopoietic Necrosis virus (IHNv) Select 20dpc IHNV_Sham CIControl BiologicalRep2 nan
17. SRR12491297 GSM4734557 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI1 BiologicalRep1 nan
18. SRR12491298 GSM4734558 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI1 BiologicalRep2 nan
19. SRR12491299 GSM4734559 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI2 BiologicalRep1 nan
20. SRR12491300 GSM4734560 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI2 BiologicalRep2 nan
21. SRR12491301 GSM4734561 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI3 BiologicalRep1 nan
22. SRR12491302 GSM4734562 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV TI3 BiologicalRep2 nan
23. SRR12491303 GSM4734563 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV_Sham TIControl BiologicalRep1 nan
24. SRR12491304 GSM4734564 intestine Hematopoietic Necrosis virus (IHNv) Commercial 4dpc IHNV_Sham TIControl BiologicalRep2 nan
25. SRR12491305 GSM4734565 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI1 BiologicalRep1 nan
26. SRR12491306 GSM4734566 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI1 BiologicalRep2 nan
27. SRR12491307 GSM4734567 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI2 BiologicalRep1 nan
28. SRR12491308 GSM4734568 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI2 BiologicalRep2 nan
29. SRR12491309 GSM4734569 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI3 BiologicalRep1 nan
30. SRR12491310 GSM4734570 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV CI3 BiologicalRep2 nan
31. SRR12491311 GSM4734571 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV_Sham CIControl BiologicalRep1 nan
32. SRR12491312 GSM4734572 intestine Hematopoietic Necrosis virus (IHNv) Select 4dpc IHNV_Sham CIControl BiologicalRep2 nan