|
| Status |
Public on Nov 25, 2016 |
| Title |
ZAM_replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
Choriodecidua, zone overlying the cervix
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: choriodecidua
zone: overlying the cervix
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissues, firstly crushed in Trizol (Life Technologies, Carlsbad, CA), using a Qiagen RNeasy Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug of Total RNA using the Low Input Quick Amp Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Human GE 8*60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using GE1_107_Sep09 scanning protocol (Scan resolution 2um)
|
| Description |
Gene expression in zone of altered morphology
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Sep 16, 2013 |
| Last update date |
Nov 26, 2016 |
| Contact name |
Céline Méhats |
| E-mail(s) |
celine.mehats@inserm.fr
|
| Organization name |
Inserm
|
| Department |
U1016
|
| Street address |
24 rue du Faubourg St jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE50900 |
Gene profiling of the zone of altered morphology of choriodecidua overlying the cervix before labor |
|
