|
Status |
Public on Mar 08, 2009 |
Title |
Liver, WT Chow Diet Control pool (n=6) vs. Liver, Tgfbr-/+ males Chow Diet -4 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Liver
|
Organism |
Mus musculus |
Characteristics |
Liver, WT Chow Diet Control pool (n=6)
|
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 |
Liver, Tgfbr-/+ males Chow Diet -4
|
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 gene expression profiling of 6 transforming growth factor receptor beta 2 (Tgfbr2) heterozygous knockout mice and 4 littermate control mice.
|
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.
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|
|
Submission date |
Jul 02, 2008 |
Last update date |
Mar 04, 2009 |
Contact name |
Xia Yang |
E-mail(s) |
xia.yang@sagebase.org
|
Phone |
206-667-2118
|
Organization name |
Sage Bionetworks
|
Street address |
1100 Fairview Ave N
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98109 |
Country |
USA |
|
|
Platform ID |
GPL3562 |
Series (2) |
GSE11994 |
Liver gene expression profiling of transforming growth factor beta receptor 2 heterozygous knockout (Tgfbr2+/-) mice |
GSE12000 |
Obesity study in transgenic and knockout animals |
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