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Sample GSM674238 Query DataSets for GSM674238
Status Public on Apr 01, 2011
Title smoker 395M
Sample type RNA
 
Source name maternal peripheral blood, smoker
Organism Homo sapiens
Characteristics tissue: maternal peripheral blood
smoking status: smoker
age (years): 34.5653661875428
maternal bmi: 30.1162131519274
parity: 4
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 600
newborn weight (g): 3580
apgar score (5s): 10
maternal blood cotinine (ng/ml): 23.262199506782
cord blood cotinine (ng/ml): 31.609536528361
individual: 395
Extracted molecule total RNA
Extraction protocol Peripheral blood was sampled and processed using the LeukoLOCK™ 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. 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 395M
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 9.262182508
ILMN_1792389 3.996696886
ILMN_2375156 2.896301427
ILMN_1697642 5.781847611
ILMN_1681845 8.749841653
ILMN_1690979 2.661126483
ILMN_1811114 1.785302081
ILMN_1660729 1.596843108
ILMN_2129572 1.739791026
ILMN_1705659 2.174715453
ILMN_1674774 1.235760356
ILMN_1702329 1.147917945
ILMN_1658806 2.529859071
ILMN_2310896 8.029031166
ILMN_1675927 1.47181403
ILMN_2109994 6.849544749
ILMN_1745256 7.395882668
ILMN_2191313 4.845505184
ILMN_1689123 8.823236759
ILMN_1674337 6.683685948

Total number of rows: 24526

Table truncated, full table size 596 Kbytes.




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

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