GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM674393 Query DataSets for GSM674393
Status Public on Apr 01, 2011
Title non-smoker 388D
Sample type RNA
Source name cord blood, non-smoker
Organism Homo sapiens
Characteristics tissue: cord blood
smoking status: non-smoker
age (years): 30
maternal bmi: 21
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): 0.30
cord blood cotinine (ng/ml): 0.24
individual: 388
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 388D
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 8.644857997
ILMN_1792389 5.971562523
ILMN_2375156 4.224025042
ILMN_1697642 6.714546215
ILMN_1681845 8.688724776
ILMN_1690979 3.218447825
ILMN_1811114 2.839910688
ILMN_1660729 1.812492008
ILMN_2129572 1.880241959
ILMN_1705659 1.910874544
ILMN_1674774 1.03898425
ILMN_1702329 1.155558159
ILMN_1658806 3.699084273
ILMN_2310896 7.737067777
ILMN_1675927 1.203105571
ILMN_2109994 7.455821054
ILMN_1745256 9.349521203
ILMN_2191313 4.589730117
ILMN_1689123 8.501368962
ILMN_1674337 7.259824193

Total number of rows: 24526

Table truncated, full table size 595 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap