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Sample GSM307085 Query DataSets for GSM307085
Status Public on Jul 23, 2009
Title Danio_rerio_Larvae_Control_fishwateronly_rep3
Sample type RNA
 
Source name Danio_rerio,Larvae,fishwateronly,rep3
Organism Danio rerio
Characteristics Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained in the Center for Environmental Biotechnology at the University of Tennessee. Fish husbandry, spawning, and experimental procedures were conducted with approval from the University of Tennessee Institutional Animal Care and Use Committee (Protocol #1690-1007). Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl. Embryos were obtained by spawning adult fish with no history of contaminant exposure. Fertilization of embryos took place at the same time (± 15 min.), such that larvae used in experiments were of similar age at the time of exposure. All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27± 1 ºC and 14:10h light:dark photoperiod.
Biomaterial provider Emily Rodgers
Treatment protocol Preparation of Exposure Solutions No Exposure for Fish Water Only Controls
The Microcystis treatment was prepared using lyophilized cells of Microcystis aeruginosa. M. aeruginosa PCC-7806 was cultured in BG-11 media. Live cultures of Microcystis were centrifuged to concentrate cells into a pellet, and pellets obtained after centrifuging 6 L of culture were combined. Cells were lyophilized for 48 hours using a freeze-dry system (Labconco, Kansas City, MO) and the total mass of algal cells obtained was 300 mg (50 mg lyophilized cells/L of live culture). For the exposure of larval zebrafish, lyophilized Microcystis was reconstituted to a nominal concentration of 50 mg lyophilized cells/L.
Solutions for microcystin-LR (MC-LR) treatments were prepared by dissolving 1mg of purified MC-LR (Alexis Biochemicals, San Diego, CA) in 0.5 mL ethanol and diluting to appropriate concentrations using fish water. The concentration of ethanol in all treatments was = 0.05%, and a treatment of 0.05% ethanol was used as a vehicle control. Fish water served as the negative control.
Growth protocol Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained in the Center for Environmental Biotechnology at the University of Tennessee. Fish husbandry, spawning, and experimental procedures were conducted with approval from the University of Tennessee Institutional Animal Care and Use Committee (Protocol #1690-1007). Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl. Embryos were obtained by spawning adult fish with no history of contaminant exposure. Fertilization of embryos took place at the same time (± 15 min.), such that larvae used in experiments were of similar age at the time of exposure. All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27± 1 ºC and 14:10h light:dark photoperiod.
Extracted molecule total RNA
Extraction protocol Total RNA Extraction Larvae were centrifuged for 10 min. at 13,000 rpm to separate larvae from exposure water, and pellets containing larvae were stored at –80ºC until RNA extraction was performed. Total larval RNA was extracted using the RNeasy mini extraction kit for animal tissues (Qiagen, Valencia, CA) and quantified using a spectrophotometer (Nanodrop, Wilmington, DE).
Label Biotin
Label protocol Ambion Message Amp II-Biotin Enhanced Method with 1µg Total RNA
 
Hybridization protocol Protocol follows the Affymetrix Hybridization, Wash and Stain kit for Eukaryotic Target Hybridization for 49Format array using 15µg fragmented cRNA and 45°C hyb temp for 16 hours at 60rpm. Washed with Affymetrix 450 Fluidics using FS450_001.
Scan protocol Affymetrix 7G GeneChip Scanner standard parameters for Zebrafish Array
Description Emily D. Rogers, Theodore B. Henry, Julia S. Gouffon, Jackson McPherson, Gregory L. Boyer, Gary S. Sayler, Steven W. Wilhelm
Data processing Affymetrix GCOS MAS5.0 Algorithm
 
Submission date Jul 22, 2008
Last update date Jul 23, 2008
Contact name Julia Gouffon
Organization name Univ. of TN
Department Nutrition
Lab Affymetrix Core Lab
Street address 1215 West Cumberland Ave, RM 229
City Knoxville
State/province TN
ZIP/Postal code 37996
Country USA
 
Platform ID GPL1319
Series (1)
GSE12214 Microcystin Genomic Effects on Zebrafish Larvae

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 850.58 P 0.000146581
AFFX-BioB-M_at 807.268 P 5.16732e-05
AFFX-BioB-3_at 539.013 P 0.000389797
AFFX-BioC-5_at 1901.84 P 4.42873e-05
AFFX-BioC-3_at 1692.51 P 5.16732e-05
AFFX-BioDn-5_at 3541.79 P 4.42873e-05
AFFX-BioDn-3_at 7022.47 P 5.16732e-05
AFFX-CreX-5_at 17114.4 P 4.42873e-05
AFFX-CreX-3_at 23925.2 P 4.42873e-05
AFFX-DapX-5_at 37.8919 A 0.0894781
AFFX-DapX-M_at 33.6576 A 0.13134
AFFX-DapX-3_at 27.6935 A 0.165861
AFFX-LysX-5_at 21.5795 A 0.382599
AFFX-LysX-M_at 12.5659 A 0.783476
AFFX-LysX-3_at 6.87522 A 0.425962
AFFX-PheX-5_at 1.67939 A 0.910522
AFFX-PheX-M_at 2.7527 A 0.994435
AFFX-PheX-3_at 34.9392 A 0.185131
AFFX-ThrX-5_at 12.8094 A 0.52976
AFFX-ThrX-M_at 27.1493 A 0.48511

Total number of rows: 15617

Table truncated, full table size 572 Kbytes.




Supplementary file Size Download File type/resource
GSM307085.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM307085.CHP.gz 5.7 Mb (ftp)(http) CHP
GSM307085.EXP.gz 344 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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