|
| Status |
Public on Dec 12, 2006 |
| Title |
Pt_1 non-acne Normal Skin |
| Sample type |
RNA |
| |
|
| Source name |
patient skin sample-non-acne Normal Skin
|
| Organism |
Homo sapiens |
| Characteristics |
non-acne patient normal skin sample
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from skin samples and DNase treated using the RNeasy Fibrous Tissue Kit (Qiagen Inc., Valencia, CA). RNA was ethanol precipitated and quantified using a spectrophotometer. Approximately 2 mug of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA, produced through in vitro transcription.
|
| |
|
| Hybridization protocol |
Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray.
|
| Scan protocol |
The arrays were processed on a GeneChip Fluidics Station 450 and scanned on an Affymetrix GeneChip Scanner (Santa Clara, CA).
|
| Description |
Check paper for details. "Gene Array Expression Profiling in Acne Lesions Reveals Marked Upregulation of Genes Involved in Inflammation and Matrix Remodeling". Journal of Investigative Dermatology (JID 126:1071-1079, 2006).
|
| Data processing |
The expression signals were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biological variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et al., 2003). To remove outlier probes and summarize probe intensities within one probe set into a single expression value, the "Tukey Biweight" method was applied to the background adjusted, normalized PM intensities. Expression values were obtained based on PM intensities and not PM-MM intensities, because PM and MM intensities were found to be highly correlated, which suggested that MM intensities were composed of background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software Significance Analysis of Microarrays (Tusher et al., 2001).
|
| |
|
| Submission date |
Dec 07, 2006 |
| Last update date |
Dec 11, 2006 |
| Contact name |
Wei Zhao |
| E-mail(s) |
[email protected]
|
| Phone |
717 531 1262
|
| Organization name |
Penn State University
|
| Street address |
600 Centerview Drive, A210
|
| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE6475 |
Acne lesion vs. normal skin. Also includes non-acne patients' normal skin samples. |
|
