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Sample GSM340086 Query DataSets for GSM340086
Status Public on Oct 31, 2009
Title UCB-MSC M02 Naïve state Rep2
Sample type RNA
 
Source name UCB-MSCs in naïve state
Organism Homo sapiens
Characteristics female, cord blood
Treatment protocol Proteins extracted from myocardium with AMI (MI proteins) were added to culture media with concentration of 25 ug/ml. Additionally, oscillating pressure was applied with specially designed oscillating pressure chamber to simulate intra-cardiac pressure change. Cells were harvested after three days of exposure to MI protein and one day in oscillating pressure chamber.
Growth protocol mononuclear cells were isolated by centrifugation (400G, 50 min) in a Ficoll hypaque gradient (density 1.077 g/cm3, Sigma). And these cells were cultured in α-minimum essential medium (α-MEM, Gibco BRL, Carlsbad), supplemented with 10% FBS (Gibco BRL, Carlsbad), 10,000 units/ml penicillin G sodium, 10,000 ug/ml streptomycin sulfate, and 25 ug/ml amphotericin B (Invitrogen Co.) at a concentration 5.0 x 106 cells/cm2. Cultures were maintained in a humidified 37℃ cell incubator with 5% CO2 with a change of culture medium twice a week. Three weeks later, monolayer of fibroblast-like adherent cells were trypsinized (0.25% trypsin, HyClone), washed, resuspended in culture medium and subcultured at a concentration of 1.0 x 106 cells/cm2
Extracted molecule total RNA
Extraction protocol Total RNAs from UCB-MSCs were isolated using TRIzol (Invitrogen, Carlsbad) and the RNeasy Mini kit (Qiagen, Valencia) as described previously
Label biotin
Label protocol cDNA was synthesized from total RNA using the One-Cycle cDNA Synthesis Kit. After clean up with a Sample Cleanup Module, double strand cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the GeneChip IVT Labeling Kit, in the presence of biotin-labeled CTP and UTP. After clean up with a Sample Cleanup Module, labeled cRNA was fragmented by fragmentation buffer.
 
Hybridization protocol Fragmented cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.
Scan protocol After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with wash buffer. After washing, the arrays were stained with a streptavidin-phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner 3000, controlled by GCOS Affymetrix software.
Description Gene expression data from UCB-MSC M02 naïve state
Data processing As a normalization process, RMA (Robust Multi-Array Average) normalization was applied to remove systematic variance. By applying RMA, the raw intensity values are background corrected, log2 transformed and then quantile normalized.
 
Submission date Nov 06, 2008
Last update date Nov 06, 2008
Contact name Hyo-Soo Kim
Organization name Seoul National University Hospital
Street address 28 Yongon-dong, Chongno-gu
City Seoul
ZIP/Postal code 110-744
Country South Korea
 
Platform ID GPL570
Series (1)
GSE13491 Therapeutic efficacy of human umbilical cord blood-derived mesenchymal stem cells in myocardial repair after infarction
Relations
Reanalyzed by GSE20125

Data table header descriptions
ID_REF
VALUE RMA normalized signal

Data table
ID_REF VALUE
1007_s_at 9.413389
1053_at 8.176585
117_at 4.964532
121_at 8.098197
1255_g_at 3.461932
1294_at 6.289884
1316_at 4.991876
1320_at 6.632568
1405_i_at 3.27136
1431_at 3.570054
1438_at 5.820868
1487_at 8.204588
1494_f_at 6.1822
1552256_a_at 7.082751
1552257_a_at 8.695135
1552258_at 4.482824
1552261_at 3.816348
1552263_at 6.82972
1552264_a_at 9.275869
1552266_at 3.188196

Total number of rows: 54675

Table truncated, full table size 1052 Kbytes.




Supplementary file Size Download File type/resource
GSM340086.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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