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Sample GSM458783 Query DataSets for GSM458783
Status Public on Oct 02, 2010
Title MSC_day0_donor2
Sample type RNA
 
Source name mesenchymal stem cells from bone marrow, undifferentiated, 0 days culture
Organism Bos taurus
Characteristics tissue: bone marrow
cell type: undifferentiated mesenchymal stem cells
age: 3-6 months
days in culture: 0
donor: 2
Biomaterial provider bone marrow was harvested from joints acquired from Research 87
Treatment protocol undifferentiated MSC-seeded agarose was harvested immediately after encapsulation.
Extracted molecule total RNA
Extraction protocol total RNA was extracted using two sequential isolations of trizol-chloroform.total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence. Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript
Label biotin
Label protocol the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated.
 
Hybridization protocol cDNA yields ranged from 5-10 μg, and 5 μg were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to 9 Bovine GeneChips (Affymetrix Inc., Santa Clara, CA).
Scan protocol Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. Fluorescence signals were collected after excitation at 570 nm by the Affymetrix Gene Chip Scanner 3000 (Affymetrix Inc.)
Description mesenchymal stem cells derived from bone marrow of juvenile calves (3-6 months), matched to chondrocytes.
Data processing data normalization was performed with the RMA algorithm.
 
Submission date Oct 02, 2009
Last update date Oct 08, 2009
Contact name Alice H Huang
E-mail(s) halice@seas.upenn.edu
Phone 2157460400
Organization name University of Pennsylvania
Department Bioengineering
Lab McKay Orthopaedics Laboratory
Street address 424 Stemmler Hall, 3450 Hamilton Walk
City Philadelphia
State/province PA
ZIP/Postal code 19103
Country USA
 
Platform ID GPL2112
Series (1)
GSE18394 Comparison of bovine undifferentiated MSCs, chondrogenic MSCs and chondrocytes in 3D culture

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensity

Data table
ID_REF VALUE
Bt.1087.1.S1_at 9.07784
Bt.982.1.S1_a_at 3.20422
Bt.3034.1.S1_at 4.5574
Bt.10442.2.S1_a_at 9.76152
Bt.7032.1.S1_at 7.28571
Bt.4646.1.S1_at 8.47879
Bt.28344.1.S1_at 2.45737
Bt.6775.1.S1_at 7.56315
Bt.19380.1.A1_at 3.59397
Bt.26718.1.S1_a_at 8.3679
Bt.20566.1.A1_at 3.91246
Bt.833.1.A1_at 7.79322
Bt.28405.1.S1_at 2.19689
Bt.926.1.S1_at 10.5091
Bt.20272.1.S1_at 3.87054
Bt.18225.1.A1_at 3.19171
Bt.16786.1.A1_at 8.45798
Bt.4235.1.S1_at 2.89413
Bt.982.1.S1_at 2.12984
Bt.30.1.S1_at 7.51501

Total number of rows: 24128

Table truncated, full table size 582 Kbytes.




Supplementary file Size Download File type/resource
GSM458783.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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