|
| Status |
Public on Aug 31, 2012 |
| Title |
MUS_RT.2 |
| Sample type |
RNA |
| |
|
| Source name |
Muscle RT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: skeletal muscle (quadriceps)
treatment: room temperature (control)
replicate: 2
|
| Treatment protocol |
Animal studies were performed under approved UCLA animal research protocols and according to guidelines established in the Guide for Care and Use of Laboratory Animals. Mice were maintained in 12-h light/dark conditions and fed a laboratory chow diet that consisted of 4.5% fat, 50% carbohydrate by weight (Lab Diet, Purina 50010). Prior to cold exposure, C57BL/6J mice were provided with food and water ad libitum overnight. On the next morning, the mice were housed without food or bedding and then were placed at 4°C for 4 h. After euthanasia, tissues were collected and frozen until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse tissues by extraction with TRIzol (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Samples were then labeled using standard Illumina protocols (The Southern California Genotyping Consortium at UCLA). Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
|
| |
|
| Hybridization protocol |
Samples were hybridized to Illumina BeadChips using standard protocols (The Southern California Genotyping Consortium at UCLA). In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
|
| Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
|
| Description |
Muscle (quadriceps) control at room temperature replicate 2
|
| Data processing |
The data were normalized using quantile normalization through the beadarray R package.
|
| |
|
| Submission date |
Aug 30, 2012 |
| Last update date |
Aug 31, 2012 |
| Contact name |
Christopher L Plaisier |
| E-mail(s) |
[email protected]
|
| Phone |
2067322139
|
| Organization name |
Institute for Systems Biology
|
| Lab |
Nitin Baliga
|
| Street address |
401 Terry Avenue North
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL6103 |
| Series (1) |
| GSE40486 |
Zbtb16 Has a Role in Brown Adipocyte Bioenergetics |
|
