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Sample GSM966573 Query DataSets for GSM966573
Status Public on Oct 01, 2012
Title normal skin sample 2
Sample type RNA
 
Source name normal
Organism Mus musculus
Characteristics histology: normal
genotype/variation: K14-Cre;Zmiz1 double transgenic mouse
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from snap-frozen tissues using the PerfectPure RNA Tissue kit with on-column Dnase I treatment (5-PRIME). Extracted total RNA was then quality verified by Agilent Bioanalyzer
Label biotin
Label protocol Four ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer's recommended protocol.
 
Hybridization protocol Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Mouse Gene 1.0 ST Arrays [probe set (exon) version], and incubated at 45C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven. Following hybridization, the arrays will be washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.
Scan protocol Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the using the GeneChip operating software (GCOS) v1.4.
Description normal skin from a K14-Cre;Zmiz1 double transgenic mouse
Data processing Data were processed using Partek Genomics Suite software. Corrected intensities were RMA normalized.
probe group file: MoEx-1_0-st-v1.r2
meta-probeset file: MoEx-1_0-st-v1.na27.mm9.transcript
 
Submission date Jul 13, 2012
Last update date Oct 01, 2012
Contact name Adam Dupuy
E-mail(s) adam-dupuy@uiowa.edu
Phone 319-335-8090
Fax 319-335-7198
Organization name University of Iowa
Street address 51 Newton Road
City Iowa City
ZIP/Postal code 52242
Country USA
 
Platform ID GPL10740
Series (1)
GSE39360 Comparison of Zmiz1-induced keratoancanthoma and normal skin

Data table header descriptions
ID_REF
VALUE Data were processed using Partek Genomics Suite software. Corrected intensities were RMA normalized.

Data table
ID_REF VALUE
10338001 12.0803
10338002 5.92719
10338003 10.6786
10338004 9.8121
10338005 2.03942
10338006 2.54473
10338007 3.11578
10338008 4.01929
10338009 6.98495
10338010 2.13672
10338011 5.50543
10338012 2.40093
10338013 1.94849
10338014 2.04362
10338015 1.94923
10338016 6.59197
10338017 12.4943
10338018 6.22281
10338019 5.18117
10338020 7.11944

Total number of rows: 241576

Table truncated, full table size 3987 Kbytes.




Supplementary file Size Download File type/resource
GSM966573_K14-Cre_Zmiz1-2.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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