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Sample GSM307095 Query DataSets for GSM307095
Status Public on Jul 23, 2009
Title Danio_rerio_Larvae_MicrocystisAlgae_rep1
Sample type RNA
 
Source name Danio_rerio,Larvae,MicrocystisAlgae_LR,rep1
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 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.
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 630.992 P 0.000146581
AFFX-BioB-M_at 819.038 P 4.42873e-05
AFFX-BioB-3_at 470.118 P 0.000581214
AFFX-BioC-5_at 1577.78 P 4.42873e-05
AFFX-BioC-3_at 1733.86 P 4.42873e-05
AFFX-BioDn-5_at 2969.98 P 4.42873e-05
AFFX-BioDn-3_at 6030.09 P 5.16732e-05
AFFX-CreX-5_at 17466.1 P 4.42873e-05
AFFX-CreX-3_at 23794.5 P 4.42873e-05
AFFX-DapX-5_at 24.5094 A 0.262809
AFFX-DapX-M_at 35.0306 M 0.0542134
AFFX-DapX-3_at 8.33683 A 0.574038
AFFX-LysX-5_at 3.34886 A 0.804734
AFFX-LysX-M_at 6.7374 A 0.772364
AFFX-LysX-3_at 16.3911 A 0.139482
AFFX-PheX-5_at 4.39106 A 0.794288
AFFX-PheX-M_at 1.56956 A 0.989689
AFFX-PheX-3_at 69.3179 A 0.083592
AFFX-ThrX-5_at 10.6598 A 0.686277
AFFX-ThrX-M_at 6.12683 A 0.783476

Total number of rows: 15617

Table truncated, full table size 570 Kbytes.




Supplementary file Size Download File type/resource
GSM307095.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM307095.CHP.gz 5.7 Mb (ftp)(http) CHP
GSM307095.EXP.gz 342 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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