|
| Status |
Public on Jun 27, 2012 |
| Title |
control colon tissue, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
control colon tissue, biological rep2
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type
strain: C57BL/6
gender: male
age: 8 weeks, 3 days
tissue: colon
|
| Treatment protocol |
The mice were exposed to 4% dextran sulfate sodium (DSS) in the drinking water for 6 days followed by 4 days of water or 1% L-arginine in the drinking water (10-day protocol). The mice were assigned to one of the following groups: Control (Ctrl), Ctrl + L-Arg, DSS, or DSS + L-Arg
|
| Growth protocol |
7-week-old male wild-type C57BL/6 mice were used in our experiment. Animals were maintained on a 12 h light/12 h dark cycle under biosafety level 2 conditions. The mice had ad libitum access to a standard diet and water until reaching the desired age for experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the time sacrifice (day 10 of protocol), a piece of the colon was obtained, cleaned, and placed in RNALater. The following day, the RNALater was removed and the RNA was isolated from the tissue using a Qiagen Rneasy kit per manufacturer's protocol. The samples were submitted to the Vanderbilt Genomic Sciences Resource for first strand cDNA synthesis, 2nd strand cDNA synthesis and IVT-cRNA synthesis. Reactions were performed with Ambion's WT-Expression target preparation kit .
|
| Label |
Biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the Whole Transcript Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials. A total of 2 μg of fragmented, labeled target was hybridized to the array. The cartridge array was washed and stained per standard Affymetrix Protocols using Affymetrix Hybridization Wash and Stain kit reagents on the Affymetrix Fluidics Station 450, using script FS450_0007
|
| Scan protocol |
Affymetrix 7G plus scanner using AGCC v. 1.1
|
| Description |
colon
|
| Data processing |
Data were processed using the Affymetrix Expression Console v. 1.1 using an RMA normalization algorithm producing log base 2 results
probe group file: MoEx-1_0-st-v1.r2.pgf
probe group file: MoEx-1_0-st-v1.r2.dt1.mm9.mps
|
| |
|
| Submission date |
Jan 05, 2012 |
| Last update date |
Jun 27, 2012 |
| Contact name |
Keith Wilson |
| E-mail(s) |
keith.wilson@vanderbilt.edu
|
| URL |
http://
|
| Organization name |
Vanderbilt University School of Medicine
|
| Street address |
2215B Garland Ave.
|
| City |
Nashville |
| ZIP/Postal code |
TN 37232-0252 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE34874 |
Expression data from murine colon tissue after exposure to 4% DSS for 6 days DSS followed by 4 days of water or 1% L-arginine |
|
