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Sample GSM305893 Query DataSets for GSM305893
Status Public on Jul 06, 2009
Title zebrafish brain3 control
Sample type RNA
 
Source name brain
Organism Danio rerio
Characteristics Wild type zebrafish (Danio rerio, ABC strain) were obtained from the University of Oregon, Zebrafish International Resource Center (Eugene, OR, USA) and maintained at the Northwest Fisheries Science Center in a self-contained re-circulating aquaculture ZMOD system (Marine Biotech Inc.). The facility is operated according to standard procedures for zebrafish husbandry and research (Westerfield 1995). Fish were maintained at 26°C, kept on a 14:10 h light-dark cycle, and fed daily with purified ground salmon feed and brine shrimp. Fish were not fed on the morning of each exposure experiment.
Biomaterial provider University of Washington
Treatment protocol To quantify DA-induced neurobehavioral excitotoxicity in zebrafish, adult fish were exposed to DA via intracoelomic (IC) injection at several doses. For injection, fish were netted individually, placed into Ziplock bags and injected through the bag at a point midway between the pectoral fins and the anus. Contents (10 ml) were slowly injected into the IC cavity. IC injections consisted of a vehicle control (phosphate buffered saline (PBS) only) or DA dissolved in PBS. Eight exposure doses (0.21 ± 0.01, 0.25 ± 0.03, 0.32 ± 0.04, 0.47 ± 0.07, 0.82 ± 0.09, 1.2 ± 0.15, 1.6 ± 0.1, and 3.2 ± 0.5 µg DA/g body weight; n = 4 fish per treatment) were used. After injection, four fish from each treatment were placed in 1-liter clear plastic tanks and observed for 6 h. Behavioral toxicity was quantified by the presence or absence of circle or spiral swimming. Time to the onset of excitotoxicity and the number of fish affected were recorded for each treatment. Percentages of fish affected at each dose were used to generate a dose-response curve and an EC50 for behavioral toxicity using Graphpad Prism® software (San Diego, CA). All DA exposure doses were confirmed by HPLC-UV analysis (see HPLC verification of DA exposure doses below). All animal studies were carried out under approved IACUC protocols at the University of Washington.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from individual snap frozen zebrafish brains using a standard TRIzol procedure with the inclusion of 1 µl RNAse inhibitor/sample.
Label biotin
Label protocol Total RNA (2 ug) was labeled and hybridized to the Zebrafish Genome Arrays and hybridized according to manufacurer’s instructions.
 
Hybridization protocol The standard hybridization protocol was used as recommended by Affymterix.
Scan protocol GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.
Description Wild type zebrafish (Danio rerio, ABC strain) were obtained from the University of Oregon, Zebrafish International Resource Center (Eugene, OR, USA) and maintained at the Northwest Fisheries Science Center in a self-contained re-circulating aquaculture ZMOD system (Marine Biotech Inc.). The facility is operated according to standard procedures for zebrafish husbandry and research (Westerfield 1995). Fish were maintained at 26°C, kept on a 14:10 h light-dark cycle, and fed daily with purified ground salmon feed and brine shrimp. Fish were not fed on the morning of each exposure experiment.
Data processing Bioconductor GCRMA normalization log2
 
Submission date Jul 17, 2008
Last update date Sep 05, 2017
Contact name James William MacDonald
E-mail(s) jmacdon@uw.edu
Organization name University of Washington
Department Environmental and Occupational Health Sciences
Street address 4225 Roosevelt Way NE
City Seattle
State/province WA
ZIP/Postal code 98105-6099
Country USA
 
Platform ID GPL1319
Series (1)
GSE12140 Gene expression profiles in zebrafish brain after acute exposure to domoic acid at symptomatic and asymptomatic doses

Data table header descriptions
ID_REF
VALUE GCRMA normalized signal log2

Data table
ID_REF VALUE
AFFX-BioB-3_at 5.58580679932961
AFFX-BioB-5_at 5.89065683532018
AFFX-BioB-M_at 6.86363979465261
AFFX-BioC-3_at 7.49429747894371
AFFX-BioC-5_at 7.84717987011343
AFFX-BioDn-3_at 10.3265043241812
AFFX-BioDn-5_at 9.64257362667831
AFFX-CreX-3_at 13.1487180051339
AFFX-CreX-5_at 12.5518492928353
AFFX-DapX-3_at 8.72433319413842
AFFX-DapX-5_at 2.68242790473918
AFFX-DapX-M_at 7.00590055483637
AFFX-Dr-AB076373-1_at 2.15718812448667
AFFX-Dr-acta1-3_at 2.14692784039234
AFFX-Dr-acta1-5_at 1.05427827301894
AFFX-Dr-acta1-5_x_at 2.94446028014034
AFFX-Dr-acta1-M_at 2.31633305310686
AFFX-Dr-AF292559-1_at 1.84665095767348
AFFX-Dr-AF292559-2_s_at 3.90651041614565
AFFX-Dr-AF292559-3_s_at 2.99268217049683

Total number of rows: 15617

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM305893.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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