|
| Status |
Public on Jun 30, 2012 |
| Title |
MUH7 8#3 Liver |
| Sample type |
RNA |
| |
|
| Source name |
Liver, male 44-45d
|
| Organism |
Mus musculus |
| Characteristics |
phenotype: high body weight
genetic background: mixed
weight: 77-42g
tissue: Liver
age: 44-45d
gender: male
line: MUHi
|
| Growth protocol |
Mice from each line were fed ad libitum with standard laboratory conditions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse tissue samples (muscle and liver) were collected from 44 and 45 days old males from each of the nine out of thirteen lines (5 High lines: BEHi, DUHi, EDHi, MUHi, ROHi and 4 Control lines: BELi, EDLi, MULi and ROLi; n=23 total) at the University of Edinburgh. Frozen tissue samples were stored at -80ºC until use. Tissues were dissociated using TissueLyser II with steel beads (both Qiagen) following manufacturers’ instructions. mRNA was extracted and purified using TRIzol Reagent and the PureLink RNA Mini Kit (Life Technologies GmbH, Darmstadt, Germany). cDNA was synthesized using Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, St. Leon-Rot, Germany).
|
| Label |
Cy3
|
| Label protocol |
Muscle and liver cDNA samples were hybridized on a Mouse GE 4x44k Microarray (Agilent Technologies, Inc., Waldbronn, Germany) according to manufacturer’s recommendations. Three technical replicate each was done on pooled cDNA samples from each mouse line.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression at age 44-45d in liver
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 12, 2012 |
| Last update date |
Jun 30, 2012 |
| Contact name |
Yingguang Frank Chan |
| E-mail(s) |
frank.chan@tue.mpg.de
|
| Phone |
07071601888
|
| Organization name |
Friedrich Miescher Laboratory
|
| Street address |
Max-Planck-Ring 9
|
| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4134 |
| Series (2) |
| GSE36443 |
Parallel selection mapping using artificially selected mice reveals body weight control loci (gene expression) |
| GSE36452 |
Parallel selection mapping using artificially selected mice reveals body weight control loci |
|
