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Sample GSM674208 Query DataSets for GSM674208
Status Public on Apr 01, 2011
Title non-smoker 338M
Sample type RNA
 
Source name maternal peripheral blood, non-smoker
Organism Homo sapiens
Characteristics tissue: maternal peripheral blood
smoking status: non-smoker
age (years): 38.9596167008898
maternal bmi: 22.7583067819754
parity: 2
gestational age (weeks): 38
mode of delivery: vaginal
placental weight (g): 500
newborn weight (g): 3170
apgar score (5s): 10
maternal blood cotinine (ng/ml): 0.144868788997287
cord blood cotinine (ng/ml): 0.0759723467482291
individual: 338
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 338M
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 9.613571041
ILMN_1792389 4.776785625
ILMN_2375156 3.452495819
ILMN_1697642 4.106980154
ILMN_1681845 8.876951465
ILMN_1690979 3.477134008
ILMN_1811114 1.606927283
ILMN_1660729 1.513364853
ILMN_2129572 1.825796985
ILMN_1705659 1.781621937
ILMN_1674774 1.58874259
ILMN_1702329 1.255976683
ILMN_1658806 2.208197529
ILMN_2310896 8.148869822
ILMN_1675927 1.708408126
ILMN_2109994 7.11441561
ILMN_1745256 7.093335562
ILMN_2191313 3.648004816
ILMN_1689123 9.469092181
ILMN_1674337 6.137024078

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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