|
| Status |
Public on Feb 09, 2007 |
| Title |
developmental sample at T105, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver sample from mouse embryo liver at 10.5 days post conception (dpc)
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: CD-1 mouse embryo
Age: 10.5 dpc
|
| Treatment protocol |
Pregnant CD-1 females were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation. The abdomen was opened and the uterus removed. After removal of the uterine musculature, embryos were removed from the yolk sacs and livers microdissected, taking care to remove all extraneous tissue including the retrohepatic vena cava.
|
| 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. A maximum of five minutes was allowed to elapse between sacrifice and liver harvest to prevent RNA degradation and transcriptional changes.
|
| 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) |
[email protected]
|
| 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 |
