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Sample GSM256781 Query DataSets for GSM256781
Status Public on Jan 01, 2010
Title DMSO exposed embryos, replicate 1
Sample type RNA
 
Channel 1
Source name Universal RNA Reference Sample
Organism Danio rerio
Characteristics Strain: TL
Age: 1-6 days post-fertilization
Biomaterial provider M.E. Hahn (Woods Hole Oceanographic Institution)
Treatment protocol Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 1, 2, 3, 4, 5, and 6-dpf were exposed for 6 hr to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) (4 groups per compound per time point). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis. The Universal RNA Reference Sample was created by mixing equal amounts of total RNA from 2 replicates each from all toxicants (TCDD, tBHQ, DMSO) and timepoints (1, 2, 3, 4, 5, 6-dpf).
Growth protocol Adult fish were maintained according to the guidelines set forth by the zebrafish handbook. Embryos were kept in egg water (60 μg/ml Instant Ocean Salts) in a 28°C incubator with no light.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from pooled tissues using RNA STAT-60.
Label Cy3
Label protocol RNA samples were checked for quality using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 BioAnalyzer. cDNA synthesis from 600 ng of total RNA was performed using the Agilent Low RNA Input Linear Fluorescent Amplification Plus kit, following the manufacturer’s instructions. cRNA was synthesized from the cDNA template, with incorporation of cyanine-3-CTP (Perkin Elmer). Labeled cRNA was purified using the Qiagen RNeasy Mini kit with quantity and quality was assessed by NanoDrop spectrophotometer and Agilent BioAnalyzer.
 
Channel 2
Source name 4 days post-fertilization DMSO exposed Danio rerio embryos, replicate 1
Organism Danio rerio
Characteristics Strain: TL
Age: 4 days post-fertilization
Biomaterial provider M.E. Hahn (Woods Hole Oceanographic Institution)
Treatment protocol Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 4 dpf were exposed for 6 hr to 0.1% dimethyl sulfoxide (DMSO). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis.
Growth protocol Adult fish were maintained according to the guidelines set forth by the zebrafish handbook. Embryos were kept in egg water (60 μg/ml Instant Ocean Salts) in a 28°C incubator with no light.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from pooled tissues using RNA STAT-60.
Label Cy5
Label protocol RNA samples were checked for quality using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 BioAnalyzer. cDNA synthesis from 600 ng of total RNA was performed using the Agilent Low RNA Input Linear Fluorescent Amplification Plus kit, following the manufacturer’s instructions. cRNA was synthesized from the cDNA template, with incorporation of cyanine-5-CTP (Perkin Elmer). Labeled cRNA was purified using the Qiagen RNeasy Mini kit with quantity and quality was assessed by NanoDrop spectrophotometer and Agilent BioAnalyzer.
 
 
Hybridization protocol cRNA samples were hybridized to Agilent 22k zebrafish microarrays using the Agilent Gene Expression Hybridization Kit. Labeled cRNAs were combined with the Agilent 25x fragmentation buffer and incubated at 60°C for 30 minutes. This was followed by mixing with 2x hybridization buffer, after which 100 ul of the product was spread evenly across the surface of an Agilent 22K zebrafish microarray. The loaded microarray was incubated at 60°C for 17 hours with rotation in an Agilent DNA Microarray Hybridization Oven. Post-hybridization, microarray slides were washed, air-dried, and stored in darkness with desiccation.
Scan protocol Raw hybridization results were obtained by laser-excited fluorescence scanning in an Agilent DNA Micorarray Scanner.
Description DMSO exposed embryos, replicate 1
Data processing Analysis of raw microarray data was performed using Agilent’s feature extraction protocol, which includes spot finding, spot analysis, background subtraction (using local background plus global background based on spots along the central tendency line for red versus green intensity), dye normalization (linear and lowess algorithms, using spots along the central tendency line as for background subtraction), and final calculation of Cy5/Cy3 ratios and log2 transformed fold change for each spot. Data were additionally median centered among all microarray results prior to statistical analyses.
 
Submission date Jan 11, 2008
Last update date Jun 24, 2009
Contact name Andrew G. McArthur
E-mail(s) mcarthua@mcmaster.ca
Organization name McMaster University
Department Biochemistry & Biomedical Sciences
Street address 1280 Main Street West
City Hamilton
State/province Ontario
ZIP/Postal code L8S 4K1
Country Canada
 
Platform ID GPL2878
Series (1)
GSE10157 Altered gene expression in zebrafish embryos exposed to tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin

Data table header descriptions
ID_REF
VALUE Normalized log transformed fold change
CH1_SIG_MEAN Reference RNA sample mean signal
CH1_BKD-MEAN Reference RNA sample mean background
CH2_SIG_MEAN DMSO RNA replicate #1 mean signal
CH2_BKD_MEAN DMSO RNA replicate #1 mean background

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKD-MEAN CH2_SIG_MEAN CH2_BKD_MEAN
1 NULL 4208.016 51.28929 117.5405 69.14643
2 NULL 67.25772 51.68727 83.84203 69.06909
3 0.2796816 272.6476 51.26882 340.8442 69.08244
4 0.70432204 82.16888 52.34532 83.65458 69.44604
5 -0.17497869 1248.302 51.44599 1293.786 68.82927
6 NULL 103.6198 51.64729 143.6133 69.46899
7 NULL 2741.336 52.09343 101.2046 70.04152
8 0.24719952 1350.923 51.52479 1739.4 69.35124
9 1.173272 35.88653 51.42803 82.61074 69.38258
10 0.13631064 942.6666 51.22064 1173.765 69.27046
11 -0.020761877 1795.801 51.01901 1650.365 69.52471
12 -0.1311049 8589.241 50.87732 7640.695 69.27138
13 0.07891786 3410.298 50.97338 3806.081 69.4943
14 NULL 4184.771 51.42387 96.263 69.9177
15 -0.93038815 134.2616 50.85965 84.82285 69.70175
16 -0.6515462 263.0827 50.57639 228.5395 69.625
17 -0.1237503 2727.337 50.59779 2452.088 68.62362
18 -0.61408293 295.6158 50.65108 226.4077 68.89928
19 -0.04874018 2190.389 50.52574 1871.939 69.71691
20 -0.2210884 180.1312 50.94035 136.8687 70.36842

Total number of rows: 22575

Table truncated, full table size 1146 Kbytes.




Supplementary file Size Download File type/resource
GSM256781.txt.gz 6.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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