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Sample GSM743236 Query DataSets for GSM743236
Status Public on Jul 20, 2011
Title passive smoker 232, placenta
Sample type RNA
 
Source name term placenta
Organism Homo sapiens
Characteristics smoking status: passive smoker
age (years): 34
maternal bmi: 37
parity: 2
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 650
placental volume (cm3): 1452
newborn weight (g): 3170
newborn length (cm): 49
apgar score (5s): 10
baby's sex: F
maternal blood cotinin (ng/ml): 0.49
cord blood cotinin (ng/ml): 0.36
Extracted molecule total RNA
Extraction protocol Umbilical cord bloods were sampled and processed using LeukoLOC 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. 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 RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. Integrity of the total RNAs was assayed by 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 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
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, which 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 lmFit function. Using Benjamini and Hochberg method P-values were corrected for multiple testing.
 
Submission date Jun 16, 2011
Last update date Jul 20, 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)
GSE30032 Deregulation of Gene Expression induced by Environmental Tobacco Smoke Exposure in Pregnancy

Data table header descriptions
ID_REF
VALUE lumi normalized signals with detection p-value p<0.01 in all samples

Data table
ID_REF VALUE
ILMN_1802380 7.875043577
ILMN_1792389 2.121854373
ILMN_2375156 3.349155859
ILMN_1697642 9.45844319
ILMN_1681845 8.514559702
ILMN_1690979 3.343205793
ILMN_1811114 1.989527269
ILMN_1660729 8.755201382
ILMN_2129572 4.496478965
ILMN_1705659 2.147913475
ILMN_1674774 1.239108508
ILMN_1702329 1.570969533
ILMN_1658806 2.275948604
ILMN_2310896 2.324310771
ILMN_1675927 6.935744283
ILMN_2109994 8.241283087
ILMN_1745256 9.468539193
ILMN_2191313 3.906829422
ILMN_1689123 9.026361995
ILMN_1674337 9.770800459

Total number of rows: 24526

Table truncated, full table size 596 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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