|
| Status |
Public on Apr 01, 2011 |
| Title |
non-smoker 398PL |
| Sample type |
RNA |
| |
|
| Source name |
term placenta, non-smoker
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: term placenta
smoking status: non-smoker
age (years): 33
maternal bmi: 20
parity: 3
gestational age (weeks): 41
mode of delivery: vaginal
placental weight (g): 600
newborn weight (g): 3400
apgar score (5s): 10
maternal blood cotinine (ng/ml): 0.25
cord blood cotinine (ng/ml): 0.25
individual: 398
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –20°C until RNA isolation. Placental total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 200 ng of total RNA using the 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 scanned using BeadArray Reader (Illumina), and bead level data were extracted by BeadStudio Software (Illumina).
|
| Description |
398PL
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 the R statistical environment (www.r-project.org) and normalized by the quantile method in the Lumi package. Only probes that reached detection P-value < 0.01 in all samples were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using the lmFit function. Using the Benjamini and Hochberg method, P-values were corrected for multiple testing. The M, PL, and D groups were normalized separately.
|
| |
|
| Submission date |
Feb 13, 2011 |
| Last update date |
Apr 01, 2011 |
| Contact name |
Hana Bruchova |
| E-mail(s) |
Hana.Bruchova@uhkt.cz
|
| 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 |
GPL6883 |
| Series (1) |
| GSE27272 |
Comprehensive Study of Tobacco Smoke-Related Transcriptome Alterations in Maternal and Fetal Cells |
|
