|
| Status |
Public on Apr 24, 2014 |
| Title |
OB_Veh_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
MC3T3-E1 cells differentiated for 15 days
|
| Organism |
Mus musculus |
| Characteristics |
passage: 5-12
cell line: MC3T3-E1 cells differentiated for 15 days
treatment: ethanol vehicle
|
| Treatment protocol |
Cells were treated with 100nM 1,25(OH)2D3 or ethanol vehicle for 24 hours.
|
| Growth protocol |
MC3T3-E1 cells were cultured in alpha MEM with 10% heat-inactivated fetal bovine serum from Hyclone (Logan, UT) and 1% penicillin-streptomycin. Differentiated cells were cultured in complete media plus 10mM glycerol-2-phosphate and 50ug/mL ascorbic acid for 15 days, changing media every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the TRI-Reagent protocol (MRC, Cincinnati, OH) and amplification methods according Roche NimbleGen protocols.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed using the NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Oct 31, 2012 |
| Last update date |
Apr 24, 2014 |
| Contact name |
Mark B Meyer |
| E-mail(s) |
markmeyer@wisc.edu
|
| Phone |
608-890-0857
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Nutritional Sciences
|
| Lab |
Meyer Lab
|
| Street address |
1415 Linden Dr.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL13179 |
| Series (2) |
| GSE41954 |
The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression [gene expression] |
| GSE41955 |
The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression |
|
