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Sample GSM3687634 Query DataSets for GSM3687634
Status Public on Apr 29, 2019
Title 37EF5 - 252741411856
Sample type genomic
 
Channel 1
Source name Mouse tissue
Organism Mus musculus
Characteristics treatment: BaP Exposure
Sex: Female
tissue: Liver
Treatment protocol Twelve MutaMouse males (BALB/C × DBA/2) approximately 15 weeks of age, were exposed daily to BaP (Sigma-Aldrich, Oakville, Ontario, Canada) dissolved in olive oil (Sigma-Aldrich; highly refined, low acidity) via oral gavage (approximately 150 µL) for 28 days (100 mg/kg body weight/day). Twelve concurrent males received olive oil and served as negative controls. Three days after the last treatment all males were mated with four C57Bl/6J females each over a two-week period to produce offspring
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from the liver of each animal using the DNeasy Blood & Tissue Kit as per the manufacturer’s instructions.
Label Cy5
Label protocol One µg of offspring DNA was labelled with Cy5 dye (5190-3400 SureTag DNA Labeling Kit). Five hundred ng of DNA from each respective parent were mixed together and labelled with Cy3 dye. As positive controls, and to identify existing strain differences, two additional arrays were used to compare MutaMouse with C57BL/6J DNA. DNA labelled with Cy3 and Cy5 were mixed together for hybridization onto the CGH array.
 
Channel 2
Source name Mouse tissue
Organism Mus musculus
Characteristics Sex: pooled male and female
tissue: Liver
Treatment protocol Twelve MutaMouse males (BALB/C × DBA/2) approximately 15 weeks of age, were exposed daily to BaP (Sigma-Aldrich, Oakville, Ontario, Canada) dissolved in olive oil (Sigma-Aldrich; highly refined, low acidity) via oral gavage (approximately 150 µL) for 28 days (100 mg/kg body weight/day). Twelve concurrent males received olive oil and served as negative controls. Three days after the last treatment all males were mated with four C57Bl/6J females each over a two-week period to produce offspring
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from the liver of each animal using the DNeasy Blood & Tissue Kit as per the manufacturer’s instructions.
Label Cy3
Label protocol One µg of offspring DNA was labelled with Cy5 dye (5190-3400 SureTag DNA Labeling Kit). Five hundred ng of DNA from each respective parent were mixed together and labelled with Cy3 dye. As positive controls, and to identify existing strain differences, two additional arrays were used to compare MutaMouse with C57BL/6J DNA. DNA labelled with Cy3 and Cy5 were mixed together for hybridization onto the CGH array.
 
 
Hybridization protocol Hybridization was performed using the protocol recommended by the manufacturer.
Scan protocol The hybridized slides were scanned using an Agilent C scanner and Feature Extraction v10.5 was used to extract the data.
Description BaP Exposure
Data processing Non-uniform features (outlier probes with signals influenced by array position) were removed from analysis. The algorithms previously used by Adewoye et al. were applied to detect autosomal CNVs as genomic segments with parent vs. offspring fluorescent signal log2 ratios above or below threshold values as described previously.
Following Feature Extraction, signal intensities (Cy3 and Cy5) were background subtracted and then normalized (Lowess normalization using Rank invariant probes). Log2 ratios of the Cy5/Cy3 were used for the analysis.
 
Submission date Mar 26, 2019
Last update date May 01, 2019
Contact name Matthew Meier
E-mail(s) [email protected], [email protected], [email protected]
Phone 613-447-6705
Organization name Government of Canada
Department Health Canada
Lab Mechanistic Studies Division Genomics Laboratory
Street address 251 Sir Frederick Banting Driveway
City Ottawa
State/province Ontario
ZIP/Postal code K1A 0K9
Country Canada
 
Platform ID GPL10448
Series (1)
GSE128869 CGH array used to identify de novo copy number variations in offspring of BaP exposed parents.

Supplementary file Size Download File type/resource
GSM3687634_37EF5_CGH_1100_Jul11.txt.gz 99.9 Mb (ftp)(http) TXT
Processed data are available on Series record

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