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Sample GSM743270 Query DataSets for GSM743270
Status Public on Jul 20, 2011
Title non-smoker 298, placenta
Sample type RNA
 
Source name term placenta
Organism Homo sapiens
Characteristics smoking status: non-smoker
age (years): 30
maternal bmi: 22
parity: 1
gestational age (weeks): 37
mode of delivery: caesarean
placental weight (g): unknown
placental volume (cm3): 864
newborn weight (g): 3250
newborn length (cm): 49
apgar score (5s): 10
baby's sex: F
maternal blood cotinin (ng/ml): 0.18
cord blood cotinin (ng/ml): 0.28
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 8.096888113
ILMN_1792389 2.586900631
ILMN_2375156 3.754960755
ILMN_1697642 8.649084856
ILMN_1681845 8.461207471
ILMN_1690979 2.807935959
ILMN_1811114 1.847508211
ILMN_1660729 9.215108751
ILMN_2129572 4.149008757
ILMN_1705659 2.316100852
ILMN_1674774 1.441678509
ILMN_1702329 1.382667569
ILMN_1658806 2.148855527
ILMN_2310896 2.270149048
ILMN_1675927 7.26733662
ILMN_2109994 8.84511658
ILMN_1745256 10.02156999
ILMN_2191313 4.000424961
ILMN_1689123 8.337381444
ILMN_1674337 10.08536029

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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