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Sample GSM674378 Query DataSets for GSM674378
Status Public on Apr 01, 2011
Title smoker 351D
Sample type RNA
Source name cord blood, smoker
Organism Homo sapiens
Characteristics tissue: cord blood
smoking status: smoker
age (years): 31
maternal bmi: 21
parity: 3
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 360
newborn weight (g): 3430
apgar score (5s): 10
maternal blood cotinine (ng/ml): 3.99
cord blood cotinine (ng/ml): 5.39
individual: 351
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 351D
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 9.257780377
ILMN_1792389 6.93645781
ILMN_2375156 3.520169071
ILMN_1697642 6.001694806
ILMN_1681845 9.003237192
ILMN_1690979 2.910807651
ILMN_1811114 1.784937466
ILMN_1660729 1.624227248
ILMN_2129572 1.687408848
ILMN_1705659 1.847911392
ILMN_1674774 1.13850647
ILMN_1702329 1.017206891
ILMN_1658806 2.32314944
ILMN_2310896 7.979898764
ILMN_1675927 1.13850647
ILMN_2109994 7.651631215
ILMN_1745256 9.755177787
ILMN_2191313 5.213772026
ILMN_1689123 8.866866122
ILMN_1674337 6.516815539

Total number of rows: 24526

Table truncated, full table size 595 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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