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Sample GSM135470 Query DataSets for GSM135470
Status Public on Oct 01, 2006
Title IRF6 knockout, biological rep1
Sample type RNA
 
Source name Skin from Irf6 null
Organism Mus musculus
Characteristics Background: mixed genetic backgroud of C57Bl/6 and 129/SvJ
Genotype: IRF6 null
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 null
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 1836.4 P 0.000297
AFFX-BioB-M_at 2449.6 P 0.000044
AFFX-BioB-3_at 1807.7 P 0.00007
AFFX-BioC-5_at 4927.9 P 0.000081
AFFX-BioC-3_at 6097.8 P 0.000044
AFFX-BioDn-5_at 9679.7 P 0.000044
AFFX-BioDn-3_at 20675.2 P 0.00007
AFFX-CreX-5_at 56703.8 P 0.000052
AFFX-CreX-3_at 73310.6 P 0.000044
AFFX-DapX-5_at 1584 P 0.000127
AFFX-DapX-M_at 2767.2 P 0.000857
AFFX-DapX-3_at 3069.6 P 0.00011
AFFX-LysX-5_at 139.7 P 0.013811
AFFX-LysX-M_at 334.3 A 0.156732
AFFX-LysX-3_at 657.2 P 0.000127
AFFX-PheX-5_at 269.7 P 0.020022
AFFX-PheX-M_at 238 P 0.030976
AFFX-PheX-3_at 205.6 M 0.050229
AFFX-ThrX-5_at 508.2 P 0.01667
AFFX-ThrX-M_at 746.2 P 0.000297

Total number of rows: 45101

Table truncated, full table size 1241 Kbytes.




Supplementary data files not provided

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