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Sample GSM135474 Query DataSets for GSM135474
Status Public on Oct 01, 2006
Title IRF6 wt, biological rep2
Sample type RNA
 
Source name Skin from Irf6 wt
Organism Mus musculus
Characteristics Background: mixed genetic backgroud of C57Bl/6 and 129/SvJ
Genotype: IRF6 wt
Age: Embryonic day 17.5
Treatment protocol Skin from E17.5 mice was removed and flash frozen.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated as recommended (RNeasy, Qiagen, Valencia, CA), except that tissue was treated with proteinase K (20 mg/ml) for 20 minutes at 55°C.
Label biotin
Label protocol Five micrograms of total RNA was processed for use on the microarray by using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix, Inc., Santa Clara, CA) according to the manufacturer’s recommended protocols
 
Hybridization protocol The resultant biotinylated cRNA was fragmented then hybridized to the GeneChip Mouse Genome 430 2.0 Array (45,000 probe sets used to analyze over 39,000 mouse transcripts and variants from over 34,000 well-characterized mouse genes; Affymetrix, Inc.). The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station
Scan protocol GeneChips were scanned using the Affymetrix Model 3000 scanner
Description Gene expression data from E17.5 mouse skin, IRF6 wt
Data processing Expression values were generated using the microarray suite (MAS) v5.0 software (Affymetrix, Inc)
 
Submission date Sep 08, 2006
Last update date Sep 08, 2006
Contact name David Michael Alvarado
E-mail(s) dmalvara@genetics.wustl.edu
Phone 314-747-1063
Organization name Washington University in St. Louis
Department Genetics
Lab Michael Lovett
Street address 4565 Scott Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL1261
Series (1)
GSE5800 Expression data from mouse IRF6 null and wt skin

Data table header descriptions
ID_REF
VALUE (MAS) v5.0 -calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE '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 2076.8 P 0.000296
AFFX-BioB-M_at 3604.1 P 0.000044
AFFX-BioB-3_at 2497.7 P 0.00006
AFFX-BioC-5_at 6272.9 P 0.00006
AFFX-BioC-3_at 7704.3 P 0.000044
AFFX-BioDn-5_at 12674.1 P 0.000044
AFFX-BioDn-3_at 28173.1 P 0.000052
AFFX-CreX-5_at 71060.3 P 0.000052
AFFX-CreX-3_at 86809.8 P 0.000044
AFFX-DapX-5_at 1501.9 P 0.00011
AFFX-DapX-M_at 3018.6 P 0.000857
AFFX-DapX-3_at 3898.9 P 0.000081
AFFX-LysX-5_at 123.5 A 0.216524
AFFX-LysX-M_at 489.5 M 0.062929
AFFX-LysX-3_at 979.7 P 0.000147
AFFX-PheX-5_at 290.4 P 0.000297
AFFX-PheX-M_at 224.3 P 0.042962
AFFX-PheX-3_at 766.5 P 0.000389
AFFX-ThrX-5_at 501.6 P 0.021902
AFFX-ThrX-M_at 768.8 P 0.000169

Total number of rows: 45101

Table truncated, full table size 1240 Kbytes.




Supplementary data files not provided

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