NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM177486 Query DataSets for GSM177486
Status Public on Apr 12, 2007
Title Backskin_Get1_e18_WT1
Sample type RNA
 
Source name Backskin_Get1_e18
Organism Mus musculus
Characteristics Strain C57BL/6
Tissue: Backskin
Age: e18
Extracted molecule total RNA
Extraction protocol Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY). 15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
 
Hybridization protocol Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Genome 430 2.0 array.
Scan protocol The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).
Description Get1, grainyhead epithelial transactivator 1. Also known as grainyhead-like 3 (Grhl3)
Data processing MAS5.0
 
Submission date Mar 27, 2007
Last update date Apr 11, 2007
Contact name Kevin K Lin
E-mail(s) kklin@alumni.uci.edu
Organization name University of California, Irvine
Department Biological Chemistry & Medicine
Lab Bogi Andersen
Street address 250 Sprague Hall
City Irvine
State/province CA
ZIP/Postal code 92697-4030
Country USA
 
Platform ID GPL1261
Series (1)
GSE7381 Expression profiling of back skin of Get1 and control mice at e18.5

Data table header descriptions
ID_REF
VALUE VALUE
ABS_CALL ABS_CALL
DETECTION P-VALUE DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 368.103 P 0.000340305
AFFX-BioB-M_at 562.768 P 4.42873e-05
AFFX-BioB-3_at 405.099 P 7.00668e-05
AFFX-BioC-5_at 1221.23 P 5.16732e-05
AFFX-BioC-3_at 1632.83 P 4.42873e-05
AFFX-BioDn-5_at 2783.7 P 4.42873e-05
AFFX-BioDn-3_at 5828.47 P 7.00668e-05
AFFX-CreX-5_at 16589.6 P 4.42873e-05
AFFX-CreX-3_at 20039.3 P 4.42873e-05
AFFX-DapX-5_at 547.689 P 8.14279e-05
AFFX-DapX-M_at 1249.22 P 0.000146581
AFFX-DapX-3_at 1763 P 5.16732e-05
AFFX-LysX-5_at 86.8034 P 0.000224668
AFFX-LysX-M_at 132.951 P 0.00762003
AFFX-LysX-3_at 313.102 P 4.42873e-05
AFFX-PheX-5_at 110.98 P 0.000389797
AFFX-PheX-M_at 142.342 P 0.00010954
AFFX-PheX-3_at 245.327 P 0.000169227
AFFX-ThrX-5_at 159.227 P 0.0020226
AFFX-ThrX-M_at 235.872 P 5.16732e-05

Total number of rows: 45101

Table truncated, full table size 1390 Kbytes.




Supplementary file Size Download File type/resource
GSM177486.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM177486.CHP.gz 240.6 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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