|
| Status |
Public on Apr 27, 2015 |
| Title |
Sample 2 siPGR |
| Sample type |
RNA |
| |
|
| Source name |
Human endometrial stromal cell sample 2 endogenous PGR knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endometrial stromal cell
treatment: PGR kd
|
| Treatment protocol |
treatment in 2% charcoal stripped serum sontaining DMEM:F12 medium, 48h siRNA transfection, 24h adenovirus transduction, 6h differentiation cocktail treatment composed of E, P and cAMP
|
| Growth protocol |
growth in 5%FBS containing DMEM:F12 medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was performed using TRIzol® according to the manufacturer's instructions. Total RNA was cleaned up using RNeasy Mini Kit (Qiagen) following manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
10 micrograms of labeled aRNA were hybridized to a Human Genome HG-U133 A2.0 Array . Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.
|
| Scan protocol |
Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.
|
| Description |
Human endometrial stromal cell, decidualization, PGR
PGR knock down, 6h differentiation
|
| Data processing |
To generate quality control metrics the Keck Center generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix Expression Console with default analysis settings.
|
| |
|
| Submission date |
Jul 14, 2013 |
| Last update date |
Apr 27, 2015 |
| Contact name |
Milan K Bagchi |
| Organization name |
UIUC
|
| Department |
MIP
|
| Lab |
Bagchi Lab 534 Burrill Hall
|
| Street address |
407 S. Goodwin Ave
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE48853 |
Expression data of PGR isoforms, PRA and PRB, regulated genes in differentiating human endometrial stromal cells |
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