|
| Status |
Public on Apr 13, 2011 |
| Title |
placenta normal first trimester rep.1 |
| Sample type |
RNA |
| |
|
| Source name |
placenta
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
trimester: first
|
| Growth protocol |
patient material
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MagNa Pure Compact RNA isolation Kit (Roche Applied Science)
|
| Label |
DIG
|
| Label protocol |
Chemiluminescent Fluorescence (Digoxigenin); 0.5 mikrograms of total RNA was processed into digoxigenein (DIG)-labeled cRNA using the Applied Biosystems NanoAMP RT-IVT Labeling Kit.
|
| |
|
| Hybridization protocol |
The labeled DIG-cRNA (10 micrograms per microarray) was then injected into each microarray hybridization chamber. Following hybridization at 55oC for 16 hours, the unbound material was washed from the microarrays. Features that retained bound DIG- labeled cRNA were visualized using the Applied Biosystems Chemiluminescenct detection Kit. Anti-DIG alkaline phophatase (Roche Applied science) was used to hydrolyze a chemiluminescence substrate to generate light at 458 nm
|
| Scan protocol |
Images were quantified using the integrated ABI1700 software
|
| Description |
normal placenta
|
| Data processing |
The pre-normalized intensity values were extracted per spot from the data files. Probes with signal to noise ratio <3.0, or signal means under 9.5, or variability less than 0.1 were removed from dataset. Control spots were filtered out. Arrays were quantile normalized (R preprocessCore library). Missing expression levels were inferred by imputed by KNN (R impute library). Rscript available from authour.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Apr 13, 2011 |
| Contact name |
Chris Fenton |
| E-mail(s) |
chrisf@fagmed.uit.no
|
| Phone |
776 481 96479
|
| Organization name |
UITO
|
| Department |
Microarray
|
| Lab |
Microarray
|
| Street address |
Thor Knutsen vg 6
|
| City |
Tromsø |
| ZIP/Postal code |
9007 |
| Country |
Norway |
| |
|
| Platform ID |
GPL2986 |
| Series (1) |
| GSE28551 |
Global placental gene expression profiling in the first and third trimesters of normal human pregnancy |
|
