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Sample GSM787296 Query DataSets for GSM787296
Status Public on Sep 06, 2012
Title Control_rep2
Sample type RNA
 
Source name Danio rerio Larvae exposed to Control Fish Water for 96 h
Organism Danio rerio
Characteristics developmental stage: larval
Treatment protocol Larval zebrafish (72 hpf) were exposed for 96 h in 200ml fish water containing appropirate amount of SSRI stock (i.e. fluoxetine or sertraline). There were four SSRIs treatments (25 and 250 ug/L fluoxetine and 25 and 250 ug/L sertraline) and one control (no SSRIs) with triplicate beakers and each beaker contained about 100 larval fish. During exposure for 96 hours, beakers were kept covered to prevent water evaporation and fish were not fed (i.e., fish consumed their yolk sac).
Growth protocol Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained at the Center for Environmental Biotechnology at the University of Tennessee. Fish husbandry, spawning, and experimental procedures were conducted with approval from the UT Insititutional 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. Embroyos were obtained by spawning adult fish with no history of contaminant exposure. Fertilization of embryos took place at the same time (<15 minutes), 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 C and 14:10h light:dark photoperiod.
Extracted molecule total RNA
Extraction protocol Larvae were centrifuged for 10 min. at 13,000 rpm to separate larvae from exposure water, and pellets containing larvae were stored at <-80C 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 Affymetrix 3' labeling kit 5 ug total RNA
 
Hybridization protocol Protocol follows the Affymetrix Hybridization, Wash and Stain kit for Eukaryotic Target Hybridization for 49 Format Array using 15 ug fragmented cRNA and 45C hyb temp for 16 hours at 60 rpm. Washed with Affymetrix 450 Fluidics Station using FS450_001 script.
Scan protocol Affymetrix 7G Scanner/GCOS
Description TBH065_Control_14
Data processing Partek Genomics Suite GCRMA Algorithm
 
Submission date Aug 29, 2011
Last update date Sep 06, 2012
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)
GSE31712 Danio rerio larvae exposed to SSRIs Fluoxetine and Sertraline

Data table header descriptions
ID_REF
VALUE Log2 GCRMA Signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 4.5027
AFFX-BioB-5_at 5.98306
AFFX-BioB-M_at 6.31864
AFFX-BioC-3_at 7.54551
AFFX-BioC-5_at 7.3425
AFFX-BioDn-3_at 9.27816
AFFX-BioDn-5_at 8.55168
AFFX-CreX-3_at 12.6357
AFFX-CreX-5_at 11.7602
AFFX-DapX-3_at 2.15989
AFFX-DapX-5_at 2.33157
AFFX-DapX-M_at 2.31187
AFFX-Dr-AB076373-1_at 1.77691
AFFX-Dr-AF292559-1_at 2.09364
AFFX-Dr-AF292559-2_s_at 3.88049
AFFX-Dr-AF292559-3_s_at 2.97486
AFFX-Dr-AF292559-4_s_at 2.02016
AFFX-Dr-AF292560-1_s_at 2.71491
AFFX-Dr-AF298789-1_at 1.9273
AFFX-Dr-AF323980-1_at 2.37623

Total number of rows: 15617

Table truncated, full table size 375 Kbytes.




Supplementary file Size Download File type/resource
GSM787296.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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