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Sample GSM674317 Query DataSets for GSM674317
Status Public on Apr 01, 2011
Title smoker 356PL
Sample type RNA
 
Source name term placenta, smoker
Organism Homo sapiens
Characteristics tissue: term placenta
smoking status: smoker
age (years): 22
maternal bmi: 19
parity: 1
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 520
newborn weight (g): 3200
apgar score (5s): 10
maternal blood cotinine (ng/ml): 68.44
cord blood cotinine (ng/ml): 80.11
individual: 356
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 356PL
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 8.398203474
ILMN_1792389 3.318728195
ILMN_2375156 2.867748204
ILMN_1697642 7.093936058
ILMN_1681845 7.256107571
ILMN_1690979 3.872964801
ILMN_1811114 2.120463174
ILMN_1660729 9.189072219
ILMN_2129572 5.435517989
ILMN_1705659 2.471791922
ILMN_1674774 1.250096767
ILMN_1702329 1.360069571
ILMN_1658806 1.399131329
ILMN_2310896 2.046771902
ILMN_1675927 5.672335948
ILMN_2109994 8.049543037
ILMN_1745256 9.603533367
ILMN_2191313 3.336738504
ILMN_1689123 8.758381905
ILMN_1674337 9.826605737

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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