|
| Status |
Public on Oct 02, 2010 |
| Title |
chondrocytes_day28_donor2 |
| Sample type |
RNA |
| |
|
| Source name |
chondrocytes from articular cartilage, 28 days culture
|
| Organism |
Bos taurus |
| Characteristics |
tissue: articular cartilage
cell type: chondrocytes
age: 3-6 months
days in culture: 28
donor: 2
|
| Biomaterial provider |
cartilage was harvested from joints acquired from Research 87
|
| Treatment protocol |
chondrocyte-seeded agarose was cultured in chemically defined media containing 10 ng/mL TGF-beta3 for 28 days.
|
| 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 |
cartilage was dissected from juvenile (3-6 months) calves and encapsulated in agarose immediately after isolation.
|
| 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 |
|
