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E-GEOD-59756 - Transciptional response to acute thermal stress in Chinook salmon

Status
Released on 25 July 2015, last updated on 19 August 2015
Organism
Oncorhynchus tshawytscha
Samples (15)
Protocols (4)
Description
Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and poses a threat to dwindling salmon populations. In order to better understand how acute thermal stress affects the biology of salmon, we performed a transcriptional analysis of gill tissue from unacclimated Chinook juveniles exposed to short periods at water temperatures ranging from ideal to potentially lethal. Reverse transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. Fifty-five fish were randomly assigned to one of five treatment groups and were allowed to acclimate at 12 degrees C in the experimental chambers overnight. Treatments consisted of a three-hour water bath at 15 degrees C, 18 degrees C, 21 degrees C or 25 degrees C degrees, followed by one hour of recovery at 12 degrees C. The experimental chambers were moved to water baths held at a constant temperature, facilitating very rapid change in the temperature experienced by the fish. Controls were handled identically to the other four treatment groups, but remained at 12 degrees C. Three replicates were performed on consecutive days. RNA from the 11 individuals in each treatment group were proportionally pooled and used to create 15 illumina libraries.
Experiment type
RNA-seq of coding RNA 
Contacts
Bernie May <bpmay@ucdavis.edu>, Bernie P May, Gonzalo Rincon, Katharine M Tomalty, Mariah H Meek, Melinda R Baerwald, Nann A Fangue
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-59756.idf.txt
Sample and data relationshipE-GEOD-59756.sdrf.txt
Additional data (1)E-GEOD-59756.additional.1.zip
Links