|
| Status |
Public on Oct 30, 2013 |
| Title |
W19 MUSCLE |
| Sample type |
RNA |
| |
|
| Source name |
Male wild type (WT) mice, Biological replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal Muscle
genotype: Wild Type
age: 10 weeks
genetic background: FVB/N
|
| Treatment protocol |
Death of the mice was caused by subjecting them to CO2. Liver, Skeletal muscle, and adipose tissues were flash frozen in liquid nitrogen, stored at -80 oC, shipped on dry ice overnight, and kept at -80 oC prior to processing
|
| Growth protocol |
Mice were kept on a 12-h light/dark cycle, they were allowed free access to diet (Picolab rodent diet #5053) and fresh water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.
|
| Label |
biotin
|
| Label protocol |
100 ng of RNA from each sample was amplified to generate cDNA using NUGEN Applause WT – Amp ST system (NuGEN Technologies, CA), according to the manufacturer’s instructions. 2.5 µg of cDNA was fragmented and biotinylated using Encore Biotin module (NUGEN Technologies, CA).
|
| |
|
| Hybridization protocol |
Following labeling, samples were mixed with hybridization reagents (Affymetrix Inc. CA) and injected into affymetrix Mouse Gene 1.0 ST arrays and incubated for 18 + 2hours in hybridization oven rotating at 60 rpm at 45oC (Affymetrix Inc, CA) .
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip scanner 3000 operated by Gene Chip Operating Software, version 1. 4 (GCOS 1.4)
|
| Description |
Gene expression data from male wild type mice's skeletal muscle - Biological replicate 2
|
| Data processing |
The microarray raw data was analyzed using Partek software, version 6.3 Copyright 2008 Partek Inc., St. Louis, MO, USA. Raw data were subjected to Robust Multichip Average (RMA) quantile normalization to remove biases introduced by technical and experimental effects. All expression data were log base 2 -transformed to get near normal distribution for accurate statistical inference.
|
| |
|
| Submission date |
Oct 29, 2013 |
| Last update date |
Oct 30, 2013 |
| Contact name |
Amit Kumar |
| E-mail(s) |
amit.kumar3@nih.gov
|
| Phone |
443-850-6787
|
| Organization name |
National Institutes of Health
|
| Department |
NIDDK
|
| Lab |
NIDDK Biotechnology Core Lab
|
| Street address |
14A Service Rd West., Room 176
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL10740 |
| Series (1) |
| GSE51866 |
Gene expression data for liver, adipose, and skeletal muscle tissues of MKR and Healthy mice. |
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