to study the short - term effects of waterborne depleted uranium ( du ) , atlantic salmon parr ( n  =  6 ) were exposed for 48  h to 0 , 0.25 , 0.5 and 1.0  mg / l uranyl acetate ( uo2(ch3coo)22h2o , purity    98.0% , specific activity 1.459    10  bq / g , fluka , sigma - aldrich , buchs , switzerland ) dissolved in lake water collected from lake maridalsvannet , oslo , norway .
fish experiments were approved by the norwegian animal research authority ( nara i d : 3026 ) and conducted at the figaro facility for environmental radioactivity studies ( norwegian university of life sciences , s , norway ) .
all operations strictly followed the norwegian welfare act and research animal legislation . immediately after the exposure
samples were then stored in ultrafreezer (   80  c ) until further analysis . for rna isolation ,
the rneasy plus mini kit ( qiagen , hilden , germany ) was used to extract total rna from 20 to 30  mg frozen liver .
the procedures have been previously described in detail , . the rna yield and purity ( yield  >  200  ng/l , 260/230  >  2.0 , 260/280  >  1.8 ) were determined using nanodrop spectrophotometer ( nd-1000 , nanodrop technologies , wilminton , delaware , usa ) .
the rna integrity ( rin  >  9.0 ) was determined using bioanalyzer rna 6000 nano chips ( agilent technologies , santa clara , california , usa ) following the manufacturer 's manual .
the microarray probes ( totally 55,418 features ) were designed using the consensus sequences of two salmonid fish , salmo salar and oncorhynchus mykiss from the cgrasp 44  k salmonid oligoarray ( 35,920 sequences ) , release 11/09   complimented by ncbi unigenes ( 2995 sequences from s. salar , build 31 and 16503 sequences from o. mykiss , build 27 ) .
the cross - hybridization potential of the array probes was predicted to be less than 7% ( 3587 probes ) .
a high density 60,000-feature ( 60  k ) custom salmonid oligonucleotide array was then manufactured by agilent technologies ( santa clara , ca , usa ) .
the custom salmonid array platform is currently available in gene expression omnibus ( geo i d : gpl18864 ) .
the agilent  one - color microarray - based gene expression analysis ( v6.5 )  protocol ( agilent technologies ) was used in the microarray analysis with small modifications .
two hundred nanogram of liver total rna was used as input material for array experiment ( n  =  3 ) .
the hybridized array slides were scanned using agilent microarray c scanner ( agilent technologies , scan region : 61    21.6  mm , resolution : 3  m , output tiff image : 20 bit ) .
the agilent feature extraction ( fe ) software ( v10.7 ) was used to extract raw data from scanned array images . the quality assessment for extracted data
was based on the quality control ( qc ) files generated by the fe software ( table  1 ) and correlations of signal intensity of control probes between different arrays .
high quality raw data ( signal intensity values ) was further processed using genespring software ( v11.0 , agilent technologies ) .
briefly , raw data were first corrected for background signals , flagged for low quality and missing features and then normalized within- and between - array using 75% quantile method .
values from replicate features were computed for median and merged to a single normalized signal intensity value for each rna source sequence .
after raw data processing , in total 40,267 features were log-2 transformed and used for downstream statistical analysis to determine differentially expressed gene transcripts ( degs ) .
to study the short - term effects of waterborne depleted uranium ( du ) , atlantic salmon parr ( n  =  6 ) were exposed for 48  h to 0 , 0.25 , 0.5 and 1.0  mg / l uranyl acetate ( uo2(ch3coo)22h2o , purity    98.0% , specific activity 1.459    10  bq / g , fluka , sigma - aldrich , buchs , switzerland ) dissolved in lake water collected from lake maridalsvannet , oslo , norway .
fish experiments were approved by the norwegian animal research authority ( nara i d : 3026 ) and conducted at the figaro facility for environmental radioactivity studies ( norwegian university of life sciences , s , norway ) .
samples were then stored in ultrafreezer (   80  c ) until further analysis . for rna isolation ,
the rneasy plus mini kit ( qiagen , hilden , germany ) was used to extract total rna from 20 to 30  mg frozen liver .
the procedures have been previously described in detail , . the rna yield and purity ( yield  >  200  ng/l , 260/230  >  2.0 , 260/280  >  1.8 ) were determined using nanodrop spectrophotometer ( nd-1000 , nanodrop technologies , wilminton , delaware , usa ) .
the rna integrity ( rin  >  9.0 ) was determined using bioanalyzer rna 6000 nano chips ( agilent technologies , santa clara , california , usa ) following the manufacturer 's manual .
the microarray probes ( totally 55,418 features ) were designed using the consensus sequences of two salmonid fish , salmo salar and oncorhynchus mykiss from the cgrasp 44  k salmonid oligoarray ( 35,920 sequences ) , release 11/09   complimented by ncbi unigenes ( 2995 sequences from s. salar , build 31 and 16503 sequences from o. mykiss , build 27 ) .
the cross - hybridization potential of the array probes was predicted to be less than 7% ( 3587 probes )
. a high density 60,000-feature ( 60  k ) custom salmonid oligonucleotide array was then manufactured by agilent technologies ( santa clara , ca , usa ) .
the custom salmonid array platform is currently available in gene expression omnibus ( geo i d : gpl18864 ) .
the agilent  one - color microarray - based gene expression analysis ( v6.5 )  protocol ( agilent technologies ) was used in the microarray analysis with small modifications .
two hundred nanogram of liver total rna was used as input material for array experiment ( n  =  3 ) .
the hybridized array slides were scanned using agilent microarray c scanner ( agilent technologies , scan region : 61    21.6  mm , resolution : 3  m , output tiff image : 20 bit ) .
the agilent feature extraction ( fe ) software ( v10.7 ) was used to extract raw data from scanned array images . the quality assessment for extracted data
was based on the quality control ( qc ) files generated by the fe software ( table  1 ) and correlations of signal intensity of control probes between different arrays .
high quality raw data ( signal intensity values ) was further processed using genespring software ( v11.0 , agilent technologies ) .
briefly , raw data were first corrected for background signals , flagged for low quality and missing features and then normalized within- and between - array using 75% quantile method .
values from replicate features were computed for median and merged to a single normalized signal intensity value for each rna source sequence .
after raw data processing , in total 40,267 features were log-2 transformed and used for downstream statistical analysis to determine differentially expressed gene transcripts ( degs ) .
this article describes high quality transcriptomic datasets generated from an ecotoxicological study on the early stress responses in atlantic salmon after short - term ( 48  h ) exposure to waterborne depleted uranium ( du ) using a custom microarray for salmonid fish .
the full study has recently been published   and these datasets may serve as a platform to understand the toxic mechanisms and ecological hazard of environmental radionuclides such as du in fish .
 potential environmental hazards of radionuclides are often studied at the individual level . 
 sufficient toxicogenomics data at the molecular / cellular level for understanding the effects and modes of toxic action ( moas ) of radionuclide is still lacking . 
 the current article introduces transcriptomic data generated from a recent ecotoxicological study , with the aims to characterize the moas of a metallic radionuclide , deplete uranium ( du ) in an ecologically and commercially important fish species , atlantic salmon ( salmo salar ) . 
 salmon were exposed to three concentrations ( 0.25 , 0.5 and 1.0  mg / l ) of du for 48  h. short - term global transcriptional responses were studied using agilent custom - designed high density 60,000-feature ( 60  k ) salmonid oligonucleotide microarrays ( oligoarray ) . 
 the microarray datasets deposited at gene expression omnibus ( geo i d : gse58824 ) were associated with a recently published study by song et al . 
 ( 2014 ) in bmc genomics . 
 the authors describe the experimental data herein to build a platform for better understanding the toxic mechanisms and ecological hazard of radionuclides such as du in fish . 