Bioproject ID: PRJDB3412

bioproject id PRJDB3412      to NCBI
key word Temperature; Oncorhynchus mykiss; Thermally selected strain; Next generation sequencing; Gill;Global gene expression; HSP gene; c-fos gene; HEAT-SHOCK PROTEINS; UPPER TEMPERATURE TOLERANCE; QUANTITATIVE TRAIT LOCI; ONCORHYNCHUS-MYKISS; MOLECULAR CHAPERONES; DNA-SEQUENCES; C-FOS; TRANSCRIPTOME; GENERATION; STRESS
experiment type temperature
publication Tan E et al., "Global gene expression analysis of gill tissues from normal and thermally selected strains of rainbow trout", Fisheries Science, 2012;78(5):1041-1049
description Different gene expression profiles between normal and thermally selected strains of rainbow trout, Oncorhynchus mykiss, as revealed by comprehensive transcriptome analysis
abstract The objective of the study reported here was to investigate genes related to upper temperature tolerance in rainbow trout Oncorhynchus mykiss, a cold-water species with considerable economic importance, by global gene expression analysis using a next generation sequencing system. Fifty million paired sequences were collected from the gill tissues of each of five individuals of a thermally selected strain developed by selective breeding and from the gilltissues of a standard Donaldson strain and assembled into transcripts. The data of both strains were integrated, and a BLASTX search identified 13,092 independent, known genes. A back-mapping of raw reads from both strains onto the genes, conducted to investigate their frequency of expression, revealed that 324 genes showed at least a twofold higher expression in the thermally selected strain than in the Donaldson strain. In addition, 44.4 % of commonly expressed genes were categorized into 38 functional groups by annotation. Genes encoding heat shock proteins and c-fos-related proteins were highly expressed in the thermally selected strain. Our strategy to employ next generation sequencing proved to be very useful to find genes responsible for upper temperature tolerance of rainbow trout.

Sample Information

sample id sample name tissue strain treatment description
1. DRR046629 SAMD00041049 Brain nan High-temperature selected strain(HT)_Brain_Before heat exposure nan
2. DRR046630 SAMD00041049 Brain nan High-temperature selected strain(HT)_Brain_After heat exposur nan
3. DRR046633 SAMD00041049 Heart nan High-temperature selected strain(HT)_Heart_Before heat exposure nan
4. DRR046635 SAMD00041049 Muscle nan High-temperature selected strain(HT)_Muscle_Before heat exposure nan
5. DRR046636 SAMD00041049 Muscle nan High-temperature selected strain(HT)_Muscle_After heat exposure nan
6. DRR046640 SAMD00041048 Brain nan Donaldson strain(DS)_Brain_After heat exposure nan
7. DRR046645 SAMD00041048 Muscle nan Donaldson strain(DS)_Muscle_Before heat exposure nan
8. DRR046646 SAMD00041048 Muscle nan Donaldson strain(DS)_Muscle_After heat exposure nan
9. DRR046639 SAMD00041048 Brain nan Donaldson strain(DS)_Brain_Before heat exposure nan
10. DRR046648 SAMD00041048 Gill nan Donaldson strain(DS)_Gill_After heat exposure nan
11. DRR046632 SAMD00041049 Liver nan High-temperature selected strain(HT)_Liver_After heat exposure nan
12. DRR046644 SAMD00041048 Heart nan Donaldson strain(DS)_Heart_After heat exposure nan
13. DRR046634 SAMD00041049 Heart nan High-temperature selected strain(HT)_Heart_After heat exposure nan
14. DRR046637 SAMD00041049 Gill nan High-temperature selected strain(HT)_Gill_Before heat exposure nan
15. DRR046638 SAMD00041049 Gill nan High-temperature selected strain(HT)_Gill_After heat exposure nan
16. DRR046647 SAMD00041048 Gill nan Donaldson strain(DS)_Gill_Before heat exposure nan
17. DRR046641 SAMD00041048 Liver nan Donaldson strain(DS)_Liver_Before heat exposure nan
18. DRR046642 SAMD00041048 Liver nan Donaldson strain(DS)_Liver_After heat exposure nan
19. DRR046643 SAMD00041048 Heart nan Donaldson strain(DS)_Heart_Before heat exposure nan
20. DRR046631 SAMD00041049 Liver nan High-temperature selected strain(HT)_Liver_Before heat exposure nan