|
| Status |
Public on Nov 01, 2010 |
| Title |
MSC_d42_noTGF |
| Sample type |
RNA |
| |
|
| Source name |
mesenchymal stem cells from bone marrow, undifferentiated, 42 days
|
| Organism |
Bos taurus |
| Characteristics |
sample type: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 42 days in defined media without TGF-beta3
cell type: mesenchymal stem cell
|
| Biomaterial provider |
cells were harvested from joints acquired from Research 87
|
| Treatment protocol |
MSCs were encapsulated in agarose and cultured for 42 days in defined media without TGF-beta3
|
| Growth protocol |
MSCs were encapsulated in agarose and cultured for 42 days in defined media without TGF-beta3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by two sequential isolations in TRIZOL-chloroform and quantified (ND-1000, Nanodrop Technologies, Wilmington, DE). Quality assessment of total RNA and synthesized cDNA was performed by Agilent Bioanalyzer. All protocols were conducted as described in the NuGEN Ovation manual and the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| Label |
biotin
|
| Label protocol |
Following second-strand cDNA synthesis, ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) was carried out for linear amplification of each transcript and the resulting cDNA was fragmented and biotinylated.
|
| |
|
| Hybridization protocol |
5 ug of cDNA was added to hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to 5 Bovine GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
To amplify fluorescence, biotinylated anti-streptavidin and streptavidin-phycoerythrin stain were added, and fluorescent signals were recorded after excitation at 570 nm by the Affymetrix Gene Chip Scanner 3000 (Affymetrix Inc., Santa Clara, CA).
|
| Description |
NA
|
| Data processing |
Data was normalized with MAS5.0
|
| |
|
| Submission date |
Nov 03, 2009 |
| Last update date |
Nov 04, 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) |
| GSE18879 |
Effects of dynamic compressive loading on MSC chondrogenesis |
|
