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Sample GSM340081 Query DataSets for GSM340081
Status Public on Oct 31, 2009
Title UCB-MSC M01 Naïve state Rep3
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 M01 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 9.488588
1053_at 8.925933
117_at 4.910024
121_at 7.514195
1255_g_at 4.127995
1294_at 5.287049
1316_at 4.78329
1320_at 6.267463
1405_i_at 3.026296
1431_at 3.776136
1438_at 5.444427
1487_at 8.090026
1494_f_at 5.806805
1552256_a_at 6.879259
1552257_a_at 8.619763
1552258_at 4.221497
1552261_at 3.804229
1552263_at 6.795816
1552264_a_at 9.415342
1552266_at 2.98241

Total number of rows: 54675

Table truncated, full table size 1051 Kbytes.




Supplementary file Size Download File type/resource
GSM340081.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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