|
| Status |
Public on Oct 01, 2011 |
| Title |
Untreated-2 |
| Sample type |
RNA |
| |
|
| Source name |
Chondrocytes in micromass, untreated
|
| Organism |
Bos taurus |
| Characteristics |
cell type: articular chondrocyte micromass
treatment group: Untreated
|
| Treatment protocol |
After overnight culture, cells were treated with vehicle or with 5ng/ml of TGFß1 (R&D Systems) for 8 hours.
|
| Growth protocol |
Bovine articular chondrocyte micromass cultures were set up according to the methods of Chen et al., BBRC 1993; Luyten et al., ECR 1994.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the cells in culture using the standard Trizol method. RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.
|
| Label |
biotin
|
| Label protocol |
Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix). Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions. After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed. Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.
|
| |
|
| Hybridization protocol |
The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
|
| Scan protocol |
Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).
|
| Data processing |
The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used.
|
| |
|
| Submission date |
May 11, 2011 |
| Last update date |
Oct 01, 2011 |
| Contact name |
Rosa Serra |
| E-mail(s) |
rserra@uab.edu
|
| Phone |
205-934-0842
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Cell Biology
|
| Lab |
Serra
|
| Street address |
1918 University Blvd. 660 MCLM
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294-0005 |
| Country |
USA |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE29233 |
Genes regulated by TGF-beta in bovine articular chondrocytes |
|
