|
| Status |
Public on Oct 20, 2017 |
| Title |
GPA 1 |
| Sample type |
RNA |
| |
|
| Source name |
GPA, lacrimal gland
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
diagnosis: GPA
tissue: lacrimal gland
|
| Treatment protocol |
Specimens were formalin-fixed and paraffin embedded as soon as possible after surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After deparaffinization, total RNA was extracted from tissue sections with the miRNeasy FFPE kit (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
Approximately 20 to 50 ng of RNA were amplified and labeled with the SensationPlus FFPE Amplification and 3’ IVT Labeling kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Biotin-labeled cDNA targets were hybridized with a GeneChip Human Genome U133 Plus 2.0 array (Affymetrix, Santa Clara, CA) according to standard Affymetrix protocol. Following hybridization, arrays were washed and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
Arrays scanned using the GeneChip Scanner 3000 7G system (Affymetrix) and Affymetrix GeneChip Command Console (AGCC) v. 3.1.1
|
| Description |
Gene expression data from formalin-fixed, paraffin-embedded tissues
|
| Data processing |
Initial quality control analysis was performed using Affymetrix Expression Console v. 1.1 software. Affymetrix CEL files preprocessed by the Robust Multi-array Analysis algorithm for R for expression analysis
|
| |
|
| Submission date |
Oct 19, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
James Rosenbaum |
| E-mail(s) |
rosenbaj@ohsu.edu
|
| Phone |
503-494-5023
|
| Organization name |
Oregon Health & Science University
|
| Department |
Casey Eye Institute
|
| Street address |
3181 SW Sam Jackson Park Road
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE105149 |
Gene Expression in the Human Lacrimal Gland |
|
