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Sample GSM674307 Query DataSets for GSM674307
Status Public on Apr 01, 2011
Title smoker 342PL
Sample type RNA
 
Source name term placenta, smoker
Organism Homo sapiens
Characteristics tissue: term placenta
smoking status: smoker
age (years): 22
maternal bmi: 25
parity: 3
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 500
newborn weight (g): 3480
apgar score (5s): 10
maternal blood cotinine (ng/ml): 118.53
cord blood cotinine (ng/ml): 111.89
individual: 342
Extracted molecule total RNA
Extraction protocol 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 the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. 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 342PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.
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

Data table header descriptions
ID_REF
VALUE Normalized data

Data table
ID_REF VALUE
ILMN_1802380 7.370583575
ILMN_1792389 1.102353637
ILMN_2375156 3.390572986
ILMN_1697642 8.857170768
ILMN_1681845 8.41892771
ILMN_1690979 3.297804023
ILMN_1811114 1.878363148
ILMN_1660729 8.146206206
ILMN_2129572 5.485184287
ILMN_1705659 1.990619776
ILMN_1674774 2.05977107
ILMN_1702329 1.345320627
ILMN_1658806 2.794842898
ILMN_2310896 1.861659936
ILMN_1675927 6.480075629
ILMN_2109994 7.894660522
ILMN_1745256 9.384985066
ILMN_2191313 3.323605972
ILMN_1689123 8.474823031
ILMN_1674337 9.870911453

Total number of rows: 24526

Table truncated, full table size 595 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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