|
| Status |
Public on May 25, 2010 |
| Title |
Parental Liver Pool (n=176) vs. 120017 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
reference: Parental Liver Pool (n=176)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy spin columns with DNAse treatment
|
| Label |
Cy3
|
| Label protocol |
custom automated version of the aminoallyl MessageAmp II kit from Ambion.
|
| |
|
| Channel 2 |
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6.129S7-Ldlrtm1Her/J
Sex: M
individual_id: 120017
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy spin columns with DNAse treatment
|
| Label |
Cy5
|
| Label protocol |
custom automated version of the aminoallyl MessageAmp II kit from Ambion.
|
| |
|
| |
| Hybridization protocol |
Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
|
| Scan protocol |
Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.
|
| Description |
Expression profiling of liver tissue from 22 different inbred strains representing both male and female mice. All mice were reared at Jackson Laboratories in Bar Harbor, ME and shipped to Jackson Laboratories in Sacramento, CA (JAX West) at 7 weeks of age. All mice were maintained on a 12h light-dark cycle and fed ad libitum. At 20 weeks of age all mice were euthanized and liver tissues were collected and flash frozen in liquid nitrogen and stored at -80 degrees C prior to RNA isolation. All procedures of housing and treatment of animals were performed in accordance with IACUC regulations.
|
| Data processing |
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002. INTENSITY1 and INTENSITY2 columns represents the raw data for each sample that we obtained from combining two hybridizations per sample.
|
| |
|
| Submission date |
Dec 08, 2008 |
| Last update date |
Sep 17, 2010 |
| Contact name |
Wan-Lin Su |
| Organization name |
Rosetta Inpharmatics (a wholly owned subsidiary of Merck & Co., Inc.)
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL3677 |
| Series (1) |
| GSE13870 |
Gene expression profiling of 22 inbred parental strains |
|
