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Sample GSM674345 Query DataSets for GSM674345
Status Public on Apr 01, 2011
Title smoker 303D
Sample type RNA
Source name cord blood, smoker
Organism Homo sapiens
Characteristics tissue: cord blood
smoking status: smoker
age (years): 30
maternal bmi: 26
parity: 1
gestational age (weeks): 41
mode of delivery: vaginal
placental weight (g): 480
newborn weight (g): 3690
apgar score (5s): 10
maternal blood cotinine (ng/ml): 2.78
cord blood cotinine (ng/ml): 6.27
individual: 303
Extracted molecule total RNA
Extraction protocol Umbilical cord 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 303D
Data processing Bead summary data were imported into the R statistical environment ( 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
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
VALUE Normalized data

Data table
ILMN_1802380 9.262891368
ILMN_1792389 3.635771058
ILMN_2375156 3.617473078
ILMN_1697642 6.102340787
ILMN_1681845 9.027525194
ILMN_1690979 2.53493183
ILMN_1811114 1.951149465
ILMN_1660729 1.536353025
ILMN_2129572 1.811772253
ILMN_1705659 1.997605179
ILMN_1674774 0.938876247
ILMN_1702329 0.901237968
ILMN_1658806 1.984493685
ILMN_2310896 7.704458615
ILMN_1675927 1.416079488
ILMN_2109994 6.839452624
ILMN_1745256 8.3353046
ILMN_2191313 5.102938977
ILMN_1689123 8.54120734
ILMN_1674337 6.290887472

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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