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Sample GSM674220 Query DataSets for GSM674220
Status Public on Apr 01, 2011
Title non-smoker 354M
Sample type RNA
Source name maternal peripheral blood, non-smoker
Organism Homo sapiens
Characteristics tissue: maternal peripheral blood
smoking status: non-smoker
age (years): 31.4524298425736
maternal bmi: 22.4913494809689
parity: 2
gestational age (weeks): 40
mode of delivery: vaginal
placental weight (g): 500
newborn weight (g): 3120
apgar score (5s): 10
maternal blood cotinine (ng/ml): 0.249861091064754
cord blood cotinine (ng/ml): 0.288087974049162
individual: 354
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 354M
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 10.06497495
ILMN_1792389 6.036412884
ILMN_2375156 4.234680687
ILMN_1697642 5.007125199
ILMN_1681845 8.472632626
ILMN_1690979 3.543109343
ILMN_1811114 2.420873398
ILMN_1660729 1.712592361
ILMN_2129572 1.788218729
ILMN_1705659 2.270151245
ILMN_1674774 1.19955894
ILMN_1702329 0.892365292
ILMN_1658806 3.070097799
ILMN_2310896 7.84566851
ILMN_1675927 1.488192852
ILMN_2109994 7.54595692
ILMN_1745256 8.57134594
ILMN_2191313 4.092241542
ILMN_1689123 8.966339799
ILMN_1674337 7.119582575

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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