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Sample GSM1132567 Query DataSets for GSM1132567
Status Public on Sep 11, 2013
Title ~17d gestation mouse_liver tissue_formulation-only_5d, biological rep 1
Sample type RNA
 
Source name SKH:QS mouse liver tissue from formulation-only-treated 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).
 
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 SKH:QS mouse topically treated with a sunscreen formulation-only six times over four days
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.
 
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

Data table header descriptions
ID_REF
VALUE log2 gene expression levels

Data table
ID_REF VALUE
10338001 12.06960773
10338003 10.29440975
10338004 9.634249687
10338017 12.96697235
10338025 8.786546707
10338026 13.24569035
10338029 9.790344238
10338035 8.997415543
10338036 9.491380692
10338037 3.877251625
10338041 11.39340591
10338042 10.21988297
10338044 12.29039097
10338047 7.173692703
10338056 2.133624792
10338059 13.21139526
10338060 4.432834148
10338063 3.092067242
10338064 6.729990482
10338065 7.285026073

Total number of rows: 35512

Table truncated, full table size 724 Kbytes.




Supplementary file Size Download File type/resource
GSM1132567_Pregnant_Formulation_only-1_MoGene-1_0-st-v1_.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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