|
| Status |
Public on Aug 10, 2009 |
| Title |
f2#276 versus pool Mouse Liver tissue |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
#276
|
| Organism |
Mus musculus |
| Characteristics |
Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Male
|
| 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 |
pool
|
| Organism |
Mus musculus |
| Characteristics |
Strain:C57BL/6J and C3H/HeJ Age:20 weeks (150 randomly selected F2)
|
| 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 |
Liver tissue from 302 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C. All sample were compared to a common pool created from equal portions of RNA from each of the samples.
|
| 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.
|
| |
|
| Submission date |
May 05, 2008 |
| Last update date |
Aug 10, 2009 |
| Contact name |
Leslie Ingram-drake |
| E-mail(s) |
lingram@mednet.ucla.edu
|
| Phone |
310-794-9036
|
| Fax |
310-794-7345
|
| URL |
http://www.mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Medicine/MIMG/Human Genetics
|
| Street address |
47-123 CHS
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1359 |
| Country |
USA |
| |
|
| Platform ID |
GPL2510 |
| Series (1) |
| GSE11338 |
Expression profiling of Liver tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J )F2 |
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