|
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 |
|