|
| Status |
Public on May 01, 2014 |
| Title |
Wild-type liver DSS colitis 7 days rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
Wild-type liver DSS colitis 7 days
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
gender: female
age: 6 weeks
genotype/variation: wild-type
treated with: 3% dextran sulfate sodium (DSS) in the drinking water for 7 days
tissue: liver
|
| Treatment protocol |
The mice were given 3% DSS in their drinking water for 7 days to induce colitis.
|
| Growth protocol |
Mice were maintained under specific pathogen-free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized on completion of 7 days of DSS treatment. At necropsy, segments of liver were excised and homogenized in Trizol reagent. Total RNA was prepared according to the manufacturer's guidelines.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 0.1 micrograms of total RNA using amplification kit (Ambion WT Expression Kit, Lot #1210014), followed by labeling 5.5 micrograms of cDNA using Affymetrix WT Terminal Labelin Kit (Lot #4182035).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 micrograms of cDNA were hybridized for 16 hours at 45 degrees C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.
|
| Description |
WT DSS a
|
| Data processing |
The data was normalized by robust multichip analysis (RMA) using the Bioconductor package (v.2.12) in R (v.3.0.1).
|
| |
|
| Submission date |
Nov 07, 2013 |
| Last update date |
May 01, 2014 |
| Contact name |
Bobby Cherayil |
| E-mail(s) |
bcherayil@partners.org
|
| Phone |
617-726-4170
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pediatrics
|
| Lab |
Mucosal Immunology and Biology Research Center
|
| Street address |
Building 114, 16th Street
|
| City |
Charlestown |
| State/province |
Massachusetts |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE52168 |
Liver transcriptional profile of wild-type and IL-10 knockout mice with colitis |
|
