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Sample GSM305891 Query DataSets for GSM305891
Status Public on Jul 06, 2009
Title zebrafish brain1 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 5.83640840297611
AFFX-BioB-5_at 5.99517795583664
AFFX-BioB-M_at 6.98519285255805
AFFX-BioC-3_at 7.93926734617046
AFFX-BioC-5_at 8.14178578459361
AFFX-BioDn-3_at 10.5007277376511
AFFX-BioDn-5_at 9.91952525073297
AFFX-CreX-3_at 13.1714801065254
AFFX-CreX-5_at 12.6112159828028
AFFX-DapX-3_at 8.79543400617098
AFFX-DapX-5_at 2.67447416732
AFFX-DapX-M_at 7.01171563042881
AFFX-Dr-AB076373-1_at 2.1322022122758
AFFX-Dr-acta1-3_at 2.11361339316665
AFFX-Dr-acta1-5_at 1.04491016976286
AFFX-Dr-acta1-5_x_at 2.93202123371688
AFFX-Dr-acta1-M_at 2.28985715091004
AFFX-Dr-AF292559-1_at 1.81503748409908
AFFX-Dr-AF292559-2_s_at 3.92797645761913
AFFX-Dr-AF292559-3_s_at 3.00061555573524

Total number of rows: 15617

Table truncated, full table size 512 Kbytes.




Supplementary file Size Download File type/resource
GSM305891.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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