Bioproject ID: PRJNA657617

bioproject id PRJNA657617      to NCBI
key word Baseline, strain, high growth rates, immune performance, life stages
experiment type baseline
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 critical early life stages (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 is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains; 2 developmental stages; 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages. Overall design: An all-female cohort of the select and commercial strains of rainbow trout were reared in flow-through spring water (15°C) starting from eggs. From first feeding to the conclusion of the experiment, both strains received a commercial trout starter diet. Intestinal samples were collected from both groups after ten days of feeding which occurred at 20 days post hatch (dph), and at 65 dph, which is just prior to the time when we traditionally switch the fish to an all plant protein diet. RNAseq libraries were prepared for five intestinal samples per experimental group for a total of 20 samples.

Sample Information

sample id sample name tissue strain treatment description
1. SRR12463372 GSM4729700 intestine nan Commercial Strain 20dph Biological Rep1 nan
2. SRR12463373 GSM4729701 intestine nan Commercial Strain 20dph Biological Rep2 nan
3. SRR12463374 GSM4729702 intestine nan Commercial Strain 20dph Biological Rep3 nan
4. SRR12463375 GSM4729703 intestine nan Commercial Strain 20dph Biological Rep4 nan
5. SRR12463376 GSM4729704 intestine nan Commercial Strain 20dph Biological Rep5 nan
6. SRR12463377 GSM4729705 intestine nan Select Strain 20dph Biological Rep1 nan
7. SRR12463378 GSM4729706 intestine nan Select Strain 20dph Biological Rep2 nan
8. SRR12463379 GSM4729707 intestine nan Select Strain 20dph Biological Rep3 nan
9. SRR12463380 GSM4729708 intestine nan Select Strain 20dph Biological Rep4 nan
10. SRR12463381 GSM4729709 intestine nan Select Strain 20dph Biological Rep5 nan
11. SRR12463382 GSM4729710 intestine nan Commercial Strain 65dph Biological Rep1 nan
12. SRR12463383 GSM4729711 intestine nan Commercial Strain 65dph Biological Rep2 nan
13. SRR12463384 GSM4729712 intestine nan Commercial Strain 65dph Biological Rep3 nan
14. SRR12463385 GSM4729713 intestine nan Commercial Strain 65dph Biological Rep4 nan
15. SRR12463386 GSM4729714 intestine nan Commercial Strain 65dph Biological Rep5 nan
16. SRR12463387 GSM4729715 intestine nan Select Strain 65dph Biological Rep1 nan
17. SRR12463388 GSM4729716 intestine nan Select Strain 65dph Biological Rep2 nan
18. SRR12463389 GSM4729717 intestine nan Select Strain 65dph Biological Rep3 nan
19. SRR12463390 GSM4729718 intestine nan Select Strain 65dph Biological Rep4 nan
20. SRR12463391 GSM4729719 intestine nan Select Strain 65dph Biological Rep5 nan