|
| Status |
Public on Nov 18, 2013 |
| Title |
Psoriasis-Patient-H |
| Sample type |
RNA |
| |
|
| Source name |
human skin biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Psoriasis
patient: PS-H
tissue: LS skin biopsy
kit: Affy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion
|
| Label |
biotin
|
| Label protocol |
GeneChip Affymetrix protocol
|
| |
|
| Hybridization protocol |
RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.
|
| Scan protocol |
Hewlett-Packard GeneArray Scanner
|
| Data processing |
Preprocessing was carried out using GCRMA (through gcrma package from R/Bioconductor). Since samples were processed using two different kits, Combat was used to eliminate the batch effect. However, the presence of genes with small variance precluded successful estimation of the parameters in the sophisticated model used by Combat in this dataset. To circumvent this issue, genes with SD<0.2 were eliminated prior to Combat adjustment of the batch effect.
|
| |
|
| Submission date |
Nov 18, 2013 |
| Last update date |
Nov 18, 2013 |
| Contact name |
Mayte Suarez-Farinas |
| E-mail(s) |
[email protected]
|
| Organization name |
Mount SinaiSchool of Medicine
|
| Street address |
1425 Madison Ave, L2-70C, Box 1077,
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10075 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE52471 |
Dominant Th1 and Minimal Th17 Skewing in Discoid Lupus Revealed by Transcriptomic Comparison with Psoriasis |
|
| Relations |
| Reanalysis of |
GSM300792 |
