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Sample GSM674234 Query DataSets for GSM674234
Status Public on Apr 01, 2011
Title non-smoker 388M
Sample type RNA
 
Source name maternal peripheral blood, non-smoker
Organism Homo sapiens
Characteristics tissue: maternal peripheral blood
smoking status: non-smoker
age (years): 30.217659137577
maternal bmi: 20.5693296602388
parity: 1
gestational age (weeks): 39
mode of delivery: vaginal
placental weight (g): 560
newborn weight (g): 2970
apgar score (5s): 10
maternal blood cotinine (ng/ml): 0.295885493523567
cord blood cotinine (ng/ml): 0.235097580379795
individual: 388
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 388M
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 9.240310593
ILMN_1792389 4.656848584
ILMN_2375156 3.019684569
ILMN_1697642 5.733100925
ILMN_1681845 8.916112692
ILMN_1690979 3.405993117
ILMN_1811114 1.770604466
ILMN_1660729 1.679320365
ILMN_2129572 2.153497229
ILMN_1705659 1.898743505
ILMN_1674774 0.7874799
ILMN_1702329 1.579626197
ILMN_1658806 2.308195013
ILMN_2310896 8.089465198
ILMN_1675927 1.653055136
ILMN_2109994 7.372442019
ILMN_1745256 6.931678458
ILMN_2191313 4.430722709
ILMN_1689123 8.896196797
ILMN_1674337 6.549448914

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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