|
| Status |
Public on Apr 29, 2019 |
| Title |
33FF1 - 252741410842 |
| 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) |
matthew.meier@hc-sc.gc.ca, lauren.bradford@hc-sc.gc.ca
|
| 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. |
|
