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Sample GSM216655 Query DataSets for GSM216655
Status Public on Aug 10, 2007
Title folatesufficientAs0ppm3
Sample type RNA
 
Source name ODC mouse skin samples from a mouse fed folatesufficientAs0ppm
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 476.3
1415671_at 1606
1415672_at 2001
1415673_at 1597
1415674_a_at 756.5
1415675_at 395.1
1415676_a_at 2711
1415677_at 572.7
1415678_at 1293
1415679_at 1644
1415680_at 358.9
1415681_at 708.3
1415682_at 243.2
1415683_at 1451
1415684_at 394.1
1415685_at 297.4
1415686_at 759.9
1415687_a_at 2324
1415688_at 989.5
1415689_s_at 265.8

Total number of rows: 45101

Table truncated, full table size 758 Kbytes.




Supplementary file Size Download File type/resource
GSM216655.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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