|
| Status |
Public on Feb 09, 2007 |
| Title |
baseline sample at T0, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
10-week-old normal female liver sample
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: Female CD-1 mouse
Age: 10 week
|
| Treatment protocol |
After anesthesia with 100 mg/kg ketamine and 10 mg/kg Xylazine, the abdomen was prepped with alcohol and betadyne. Aftermidline laparotomy, the tip of the xiphoid was resected, and the liver exteriorized. A silk tie was placed around the three anterior lobes of the liver, including the gallbladder, and the 2/3 hepatectomy with cholecystectomy was completed. The liver was returned to the abdominal cavity and the abdomen closed in two layers. Postoperative analgesia consisted of Buprenorphine 0.05-0.1 mg/kg twice daily for 48 hours or until sacrifice. At harvest,mice were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation.
|
| Growth protocol |
All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from 10-week-old normal female liver sample.
|
| Data processing |
The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.
|
| |
|
| Submission date |
Feb 08, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Hasan Huseyin Otu |
| E-mail(s) |
hotu@bidmc.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Medicine
|
| Lab |
BIDMC Genomics Center
|
| Street address |
4 Blackfan Circle Rm. 238
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE6998 |
Expression profiling of developmental and regenerating liver in mice |
|
| Relations |
| Reanalyzed by |
GSE119085 |
