|
| Status |
Public on Sep 11, 2013 |
| Title |
~17d gestation mouse_liver tissue_untreated_5d, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
SKH:QS mouse liver tissue from untreated pregnant mouse, day 5
|
| Organism |
Mus musculus |
| Characteristics |
strain: SKH:QS
tissue: ~17d gestation liver
|
| Treatment protocol |
Mice were fitted with Elizabethan collars to minimise oral ingestion of sunscreens. Mice were treated six times over four days with sunscreen containing 68ZnO microparticles, 68ZnO nanoparticles, or no ZnO particles at all (formulation-only), or were untreated. Mice were sacrificed on day five by intraperitoneal injection of Xylase (50mg/kg)/ketamine (50mg/kg) followed by cervical dislocation.
|
| Growth protocol |
Mice were individually housed in polycarbonate cages in an isolated temperature (~21˚C) and moisture (~55-65% relative humidity) controlled room with a 14-hr light/10-hr dark cycle, with ad libitum access to food and water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from liver tissue using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, ~600-700 ng of single-stranded DNA were hybridised on Affymetric 1.0 ST human gene arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix 7G GeneChip® Scanner.
|
| Description |
Gene expression data from liver tissue harvested from ~17d pregnant untreated SKH:QS mouse
|
| Data processing |
The data was processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.
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| |
|
| Submission date |
May 02, 2013 |
| Last update date |
Sep 11, 2013 |
| Contact name |
Megan Osmond-McLeod |
| E-mail(s) |
megan.osmond@csiro.au
|
| Organization name |
CSIRO
|
| Street address |
11 Julius Avenue
|
| City |
North Ryde |
| ZIP/Postal code |
1670 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE46568 |
Expression data from mouse liver tissue from SKH:QS mice treated with 68ZnO sunscreens |
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