|
| Status |
Public on Apr 01, 2011 |
| Title |
non-smoker 316D |
| Sample type |
RNA |
| |
|
| Source name |
cord blood, non-smoker
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
smoking status: non-smoker
age (years): 29
maternal bmi: 18
parity: 2
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 440
newborn weight (g): 3450
apgar score (5s): 10
maternal blood cotinine (ng/ml): 0.28
cord blood cotinine (ng/ml): 0.35
individual: 316
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Umbilical cord blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. 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 |
316D
|
| 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 |
|
