|
| Status |
Public on Jan 01, 2014 |
| Title |
RU109_1142_mammary |
| Sample type |
RNA |
| |
|
| Source name |
Mammary fat pad
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammay fat pads
genetic background: [FVB/N x Spret/Ei] x FVB/N Backcross
mouse.id: 1142
lymph.cluster: 3
array.plate: 1
Sex: female
age: 8 wk
|
| Treatment protocol |
Mice were not treated
|
| Growth protocol |
Mice were housed in standard conditions with chow and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol followed by Qiagen RNEasy clean-up
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA
|
| |
|
| Hybridization protocol |
90uL of hybridization sample were incubated in the Affymetrix GeneTitan Oven instrument for 17 hours at 48C. Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the 550039 fluidics script and the GeneTitan Hybridization Module for WT Array Plates.
|
| Scan protocol |
An Affymetrix GeneTitan instrument was used to acquire the microarray image data
|
| Data processing |
CEL files were background corrected and normalized with RMA using the oligo package. Batch effects for array plate and lymph node cluster were corrected using ComBat, using covariates described in sample metadata
|
| |
|
| Submission date |
Apr 15, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
David Quigley |
| Organization name |
UCSF
|
| Department |
Helen Diller Comprehensive Cancer Center
|
| Lab |
Ashworth Lab
|
| Street address |
1450 Third St. Room 207
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL11533 |
| Series (1) |
| GSE46077 |
Identification of Hipk2 as an essential regulator of white fat development |
|
