|
| Status |
Public on Nov 06, 2012 |
| Title |
PCOS, biological rep 5 |
| Sample type |
RNA |
| |
|
| Source name |
PCOS, biological rep 5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: granulosa cells
disease: Polycystic ovary Syndrome
|
| Treatment protocol |
Normal and PCOS women were treated with FSH after pituitary downregulation until E2 levels reached 300 pg/mL per dominant follicles. hCG was then administered followed by transvaginal oocyte retrieval.
|
| Growth protocol |
Ovarian aspirates were collected after oocyte retrieval from the consented normal and PCOS patients in the operating room and processed immediately for granulosa cell isolation and RNA extraction to minimize RNA degradation. RNA was stored at -80°C until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 C on the HG-133 Plus 2 Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using GeneChip® Scanner 7G by Affymetrix.
|
| Description |
Gene expression using RMA method
|
| Data processing |
The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.
|
| |
|
| Submission date |
Dec 19, 2011 |
| Last update date |
Nov 06, 2012 |
| Contact name |
Rita Singh |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Delhi
|
| Department |
Department of Zoology
|
| Lab |
Molecular Reproduction
|
| Street address |
Department of Zoology
|
| City |
Delhi |
| ZIP/Postal code |
110007 |
| Country |
India |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE34526 |
Differential Gene Expression in Granulosa Cells from Polycystic Ovary Syndrome Patients with and without Insulin Resistance: Identification of Susceptibility Gene Sets through Network Analysis |
|
