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Sample GSM743261 Query DataSets for GSM743261
Status Public on Jul 20, 2011
Title non-smoker 284, placenta
Sample type RNA
 
Source name term placenta
Organism Homo sapiens
Characteristics smoking status: non-smoker
age (years): 27
maternal bmi: 29
parity: 2
gestational age (weeks): 36
mode of delivery: vaginal
placental weight (g): unknown
placental volume (cm3): 1000
newborn weight (g): 2870
newborn length (cm): 48
apgar score (5s): 10
baby's sex: F
maternal blood cotinin (ng/ml): 0.11
cord blood cotinin (ng/ml): 0.23
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 8.047524438
ILMN_1792389 1.951339477
ILMN_2375156 3.752985551
ILMN_1697642 8.293669207
ILMN_1681845 7.870916418
ILMN_1690979 3.214635717
ILMN_1811114 3.16640585
ILMN_1660729 8.988321876
ILMN_2129572 3.783619267
ILMN_1705659 1.900711035
ILMN_1674774 1.510633211
ILMN_1702329 1.794834339
ILMN_1658806 2.617768903
ILMN_2310896 2.502627952
ILMN_1675927 6.308966852
ILMN_2109994 7.901905002
ILMN_1745256 9.359925726
ILMN_2191313 4.730547661
ILMN_1689123 8.43213892
ILMN_1674337 10.64583362

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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