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Sample GSM118508 Query DataSets for GSM118508
Status Public on Jan 31, 2008
Title MRL liver control3 11wks
Sample type RNA
 
Source name Liver from 11-week-old female MRL +/+ control
Organism Mus musculus
Characteristics Strain: MRL +/+; Gender: female; Age: 11 weeks; Tissue: liver; Experiment: untreated
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the ToTALLY RNA kit from Ambion (Austin, TX) and processed through CHROMA SPIN-100 columns (BD Biosciences Clonetech, Mountain View, CA).
Label Phycoerythrin
Label protocol Reverse transcription was performed using 10-25 microg of total RNA and an oligo-dT primer that encodes a T7 RNA polymerase promoter sequence for first-strand cDNA synthesis. Second-strand synthesis converted the cDNA into double-stranded DNA templates for use in an in vitro transcription reaction. Bacteriophage T7 RNA polymerase and biotinylated nucleotides were used to produce biotinylated cRNA.
 
Hybridization protocol The biotin-labeled antisense cRNA was fragmented to a mean size of 200 bases, and the biotinylated cRNA-fragments served as targets for microarray hybridization. Standard protocols and a GeneChip Hybridization Oven 640 (Affymatrix) were used. Microarrays were washed in a GeneChip Fluidics Station 400 (Affymetrix) using standard and automated protocols. The washing protocol involves exposure to Phycoerythrin-labeled Streptavidin.
Scan protocol Arrays were scanned on a GeneChip Scanner 3000 (Affymetrix) with GeneChip Operating Software.
Description This sample served as a control in an experiment designed to measure the effects of exposure to dichloroacetyl chloride or dichloroacetic anhydride on liver gene expression in female MRL +/+ mice.
Data processing Data were analyzed using GCOS.
 
Submission date Jul 05, 2006
Last update date Jan 03, 2008
Contact name Rolf Konig
E-mail(s) rokonig@utmb.edu
Phone (409) 747-0395
Fax (409) 772-5065
Organization name UTMB
Department Microbiology & Immunology
Street address 301 University Blvd.
City Galveston
State/province TX
ZIP/Postal code 77555-1019
Country USA
 
Platform ID GPL1261
Series (1)
GSE5241 Liver toxicity of dichloroacetyl chloride and dichloroacetic anhydride in female MRL +/+ mice

Data table header descriptions
ID_REF
VALUE GCOS-calculated signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 532 P 0.002275
AFFX-BioB-M_at 941.8 P 0.00034
AFFX-BioB-3_at 437.7 P 0.003212
AFFX-BioC-5_at 1702.5 P 0.00006
AFFX-BioC-3_at 2002.8 P 0.00006
AFFX-BioDn-5_at 2430.4 P 0.000044
AFFX-BioDn-3_at 7938.3 P 0.000081
AFFX-CreX-5_at 20187.2 P 0.000052
AFFX-CreX-3_at 24574.8 P 0.000044
AFFX-DapX-5_at 87.7 A 0.089478
AFFX-DapX-M_at 106.2 A 0.368438
AFFX-DapX-3_at 90.5 A 0.39692
AFFX-LysX-5_at 2987.3 P 0.000052
AFFX-LysX-M_at 4780.9 P 0.000044
AFFX-LysX-3_at 9561.2 P 0.000044
AFFX-PheX-5_at 7604.6 P 0.000044
AFFX-PheX-M_at 10583 P 0.000044
AFFX-PheX-3_at 11474.2 P 0.000044
AFFX-ThrX-5_at 284.8 P 0.023929
AFFX-ThrX-M_at 169.8 P 0.036569

Total number of rows: 45101

Table truncated, full table size 1222 Kbytes.




Supplementary data files not provided

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