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Sample GSM216662 Query DataSets for GSM216662
Status Public on Aug 10, 2007
Title folatesufficientAs1ppm1
Sample type RNA
 
Source name ODC mouse skin samples from a mouse fed folatesufficientAs1ppm
Organism Mus musculus
Characteristics samples were obtained from 6 treatment groups with 4 samples each ( 3 arsenic doses x 2 folate conditions)
Treatment protocol Mice were fed either a folate deficient purified diet (AIN-76A) with vitamin free casein, corn oil and 1% succinyl sulfathiazole, or the same diet supplemented with 5 mg/kg folic acid (Dyets, Bethlehem, PA; product nos. 117757 and 117758).Mice on both diets were treated with 0, 1, or 10 ppm sodium arsenite in the drinking water for 30 days prior to euthanasia. Skin samples were harvested from the mid-back, flash frozen in liquid nitrogen, and stored at -80C.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)
Label biotin-streptavidin-R-phycoerythrin
Label protocol Samples were labeled according to the 2004 Affymetrix One-Cycle IVT Target Labeling protocol
 
Hybridization protocol Samples were hybridized according to the 2004 Affymetrix Standard Format Protocol
Scan protocol Mouse 430 2.0 GeneChips were scanned according to 2004 Affymetrix protocol using a Affymetrix High Density GeneChip Scanner 3000
Description gene expression data from ODC mouse skin samples
Data processing Affymetrix GeneChip Operating System (GCOS) software was used for washing, staining, and scanning GeneChips. GCOS files were generated including quality control metric summaries. GCOS generated .cel files were used to calculate expression summaries in GeneSpring GX 7.3 using RMA normalization.
 
Submission date Aug 09, 2007
Last update date Aug 28, 2018
Contact name Gail M Nelson
E-mail(s) nelson.gail@epa.gov
Phone 919-541-3095
Organization name U.S. Environmental Protection Agency
Street address 109 TW Alexander Dr.
City Research Triangle Park
State/province NC
ZIP/Postal code 27711
Country USA
 
Platform ID GPL1261
Series (1)
GSE8733 Folate deficiency enhances arsenic effects on ODC mouse skin gene expression
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF Affymetrix Mouse Genome 430 2.0 probeset ID
VALUE expression summary

Data table
ID_REF VALUE
1415670_at 492.2
1415671_at 2109
1415672_at 1931
1415673_at 1710
1415674_a_at 804.1
1415675_at 400.9
1415676_a_at 2899
1415677_at 768.4
1415678_at 1658
1415679_at 2071
1415680_at 398.7
1415681_at 777.7
1415682_at 290.7
1415683_at 1666
1415684_at 480.2
1415685_at 316.5
1415686_at 898.5
1415687_a_at 5741
1415688_at 934.5
1415689_s_at 275.8

Total number of rows: 45101

Table truncated, full table size 758 Kbytes.




Supplementary file Size Download File type/resource
GSM216662.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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