GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM135475 Query DataSets for GSM135475
Status Public on Oct 01, 2006
Title IRF6 wt, biological rep3
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
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
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
AFFX-BioB-5_at 1785.7 P 0.00034
AFFX-BioB-M_at 2999.8 P 0.000044
AFFX-BioB-3_at 1845.5 P 0.000044
AFFX-BioC-5_at 5453.9 P 0.000052
AFFX-BioC-3_at 7210.6 P 0.000044
AFFX-BioDn-5_at 12529.6 P 0.000044
AFFX-BioDn-3_at 24074.1 P 0.00006
AFFX-CreX-5_at 65948.1 P 0.000052
AFFX-CreX-3_at 85379.2 P 0.000044
AFFX-DapX-5_at 1409.6 P 0.00007
AFFX-DapX-M_at 2781 P 0.000754
AFFX-DapX-3_at 3159 P 0.00007
AFFX-LysX-5_at 138.8 P 0.005565
AFFX-LysX-M_at 277.5 A 0.083592
AFFX-LysX-3_at 703.7 P 0.000127
AFFX-PheX-5_at 257.8 P 0.002867
AFFX-PheX-M_at 316.2 P 0.018281
AFFX-PheX-3_at 494.1 P 0.00034
AFFX-ThrX-5_at 486.6 P 0.01667
AFFX-ThrX-M_at 524.9 P 0.000081

Total number of rows: 45101

Table truncated, full table size 1241 Kbytes.

Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap