|
| Status |
Public on Nov 22, 2011 |
| Title |
400937_LS180_0hr_dscDNA_Veh1_532 |
| Sample type |
RNA |
| |
|
| Source name |
LS180 colorectal cancer cells treated for 0hrs with 1,25(OH)2D3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LS180 cells
treatment: 1,25(OH)2D3
time: 0 h
|
| Treatment protocol |
Cells were treated with 10-7M 1,25(OH)2D3 for 0 and 24 hours
|
| Growth protocol |
Human LS180 CRC cells were obtained from ATCC (Manassas, VA). LS180 cells were cultured in minimum Eagle’s medium supplemented with 10% non-heat-inactivated fetal bovine serum from Hyclone (Logan, UT), 1% non-essential amino acids, 1% sodium pyruvate, and 1% penicillin-streptomycin
|
| 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 by NimbleGen Systems Inc., Madison, WI USA, following their 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.
|
| Description |
This sample was treated for 0 hrs with 1,25(OH)2D3. It is the first in the series of biological replicate experiments.
|
| 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 26, 2011 |
| Last update date |
Nov 22, 2011 |
| Contact name |
Mark B Meyer |
| E-mail(s) |
[email protected]
|
| 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 |
GPL11219 |
| Series (1) |
| GSE31939 |
VDR/RXR and TCF4/beta-Catenin Cistromes in Colonic Cells of Colorectal Tumor Origin: Impact on c-FOS and c-MYC Gene Expression |
|
