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Sample GSM743223 Query DataSets for GSM743223
Status Public on Jul 20, 2011
Title passive smoker 209, placenta
Sample type RNA
 
Source name term placenta
Organism Homo sapiens
Characteristics smoking status: passive smoker
age (years): 30
maternal bmi: 26
parity: 2
gestational age (weeks): 39
mode of delivery: vaginal
placental weight (g): 580
placental volume (cm3): 880
newborn weight (g): 3830
newborn length (cm): 50
apgar score (5s): 10
baby's sex: F
maternal blood cotinin (ng/ml): 0.11
cord blood cotinin (ng/ml): 0.20
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 8.016429632
ILMN_1792389 1.674884635
ILMN_2375156 3.669429343
ILMN_1697642 8.459029191
ILMN_1681845 8.250305568
ILMN_1690979 3.603577555
ILMN_1811114 2.259501057
ILMN_1660729 9.401863856
ILMN_2129572 3.893183539
ILMN_1705659 1.69942103
ILMN_1674774 1.253049232
ILMN_1702329 1.089659316
ILMN_1658806 2.710894707
ILMN_2310896 2.431285432
ILMN_1675927 5.961779954
ILMN_2109994 8.16519699
ILMN_1745256 9.435959648
ILMN_2191313 1.780577265
ILMN_1689123 8.73789683
ILMN_1674337 10.24581093

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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