|
| Status |
Public on Sep 15, 2009 |
| Title |
non-smoker 129 |
| Sample type |
RNA |
| |
|
| Source name |
term placenta
|
| Organism |
Homo sapiens |
| Characteristics |
age (years): 33
status: non-smoker
maternal bmi: 24.6
parity: 2
gestational age (weeks): 39
mode of delivery: vaginal
placental volume (cm3): 2500
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –80°C until RNA isolation. Total RNA was extracted from the tissue using Rneasy Mini Kit (Qiagen) according to the manufacture instructions. Quality control was performed with Agilent 2100 Bioanalyser (Agilent) and only samples with the RIN above 7.0 were processed.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.
|
| |
|
| Hybridization protocol |
750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to cy-3 fluorescent dye.
|
| Scan protocol |
Arrays were scaned using BeadArray Reader (Illumina) and bead level data were extracted by BeadStudio Software (Illumina).
|
| Description |
middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion
|
| Data processing |
Bead summary data were imported into R statistical environment (www.r-project.org) and normalized by quantile method in Lumi package. Only probes with detection p-value p<0.01 in more than 50% of arrays were included for further analyses (n=10,590). Differential gene expression between smokers and non-smokers was analysed in Limma package. Linear model was fitted for each gene given a series of arrays using lmFit fiction. Multiple testing correction was performed using Benjamini & Hochberg method.
|
| |
|
| Submission date |
Sep 09, 2009 |
| Last update date |
Nov 09, 2009 |
| Contact name |
Hana Bruchova |
| E-mail(s) |
[email protected]
|
| Phone |
+420221977306
|
| Fax |
+420221977371
|
| Organization name |
Institute of Hematology and Transfusion
|
| Department |
Molecular Genetics
|
| Lab |
Genomics
|
| Street address |
U nemocnice 1
|
| City |
Prague 2 |
| ZIP/Postal code |
128 20 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE18044 |
Effect of maternal tobacco smoke exposure on the placental transcriptome |
|
