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Sample GSM1132563 Query DataSets for GSM1132563
Status Public on Sep 11, 2013
Title Virgin mouse_liver tissue_untreated_5d, biological rep3
Sample type RNA
 
Source name SKH:QS mouse liver tissue from untreated virgin mouse, day 5
Organism Mus musculus
Characteristics strain: SKH:QS
tissue: Virgin 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 virgin 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.
 
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 12.070663
10338003 10.336503
10338004 9.4396687
10338017 12.84979
10338025 8.8965149
10338026 13.374903
10338029 9.3898668
10338035 8.9885769
10338036 9.352519
10338037 3.7831006
10338041 11.123287
10338042 10.145462
10338044 12.302938
10338047 6.5591311
10338056 2.5477583
10338059 13.339907
10338060 3.9101787
10338063 3.3474977
10338064 5.5177422
10338065 6.500278

Total number of rows: 35512

Table truncated, full table size 655 Kbytes.




Supplementary file Size Download File type/resource
GSM1132563_Not_Pregnant__No_Treatment-3.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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