|
| Status |
Public on Jul 14, 2009 |
| Title |
Wild Type Keratinocyte vs CHUK-LoxP Mutant Keratinocyte_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Wild Type Keratinocytes
|
| Organism |
Mus musculus |
| Characteristics |
Wild Type Keratinocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from wild type mouse keratinocytes using RNAeasy RNA purification kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
|
| |
|
| Channel 2 |
| Source name |
CHUK-LoxP Mutant Keratinocytes
|
| Organism |
Mus musculus |
| Characteristics |
CHUK gene deleted mouse keratinocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from wild type mouse keratinocytes using RNAeasy RNA purification kit (Qiagen, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
Labeling was done according to manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
|
| |
|
| |
| Hybridization protocol |
Manufacturer's protocol available at http://www.chem.agilent.com/temp/rad71A57/00001389.PDF
|
| Scan protocol |
Scanning and data acquisitions were performed using Agilent scanner and feature extraction protocol GE2-v5-95 (available at www.agilent.com)
|
| Description |
The current analysis was carried out to study the changes in the gene expression profiles of CHUK gene deleted mouse keratinocytes compared to wild type mouse keratinocytes
|
| Data processing |
The data was acquired using Agilent's feature extraction protocol GE2-v5_95 with inbuilt Lowess normalization feature and Log10ratio algorithms, for details visit www.agilent.com
|
| |
|
| Submission date |
Jul 14, 2008 |
| Last update date |
Jul 16, 2008 |
| Contact name |
Yinling Hu |
| E-mail(s) |
yhu@mdanderson.org
|
| Phone |
512-237 9338
|
| Fax |
512-237 2475
|
| Organization name |
UT M.D.Andreson Cancer Center
|
| Department |
Carcinogenesis
|
| Lab |
3
|
| Street address |
1808 Park Road 1C
|
| City |
Smithville |
| State/province |
TX |
| ZIP/Postal code |
78957 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE12111 |
IKKα Is Required to Maintain Skin Homeostasis and Prevent Skin Cancer |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Log10 ratio (ie, Log(Redsignal/Greensignal)per feature) |
| PValueLogRatio |
Significance level of the Log Ratio computed for feature |
| gProcessedSignal |
Cy3 Dye-normalized signal after surrogate algorithm, per channel, used for computation of Log Ratio |
| rProcessedSignal |
Cy5 Dye-normalized signal after surrogate algorithm, per channel, used for computation of Log Ratio |
| gProcessedSigError |
Cy3 processed signal error |
| rProcessedSigError |
Cy5 processed signal error |
| gMeanSignal |
Raw mean signal of feature in green (Cy3) channel |
| rMeanSignal |
Raw mean signal of feature in red (Cy5) channel |
| gBGMeanSignal |
Mean local (local to corresponding feature) back ground signal for Cy3 |
| rBGMeanSignal |
Mean local (local to corresponding feature) back ground signal for Cy5 |
| gDyeNormSignal |
Cy3 dye normalized signal |
| rDyeNormSignal |
Cy5 dye normalized signal |
| gDyeNormError |
The standard error associated with Cy3 dye normalized signal |
| rDyeNormError |
The standard error associated with Cy5 dye normalized signal |
