|
| Status |
Public on Jun 08, 2007 |
| Title |
White adipose adult rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Epididymal White Adipose Tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: male
age: 10-12 week old
tissue: Epididymal White Adipose Tissue
|
| Biomaterial provider |
Taconic
|
| Treatment protocol |
Untreated, ambient temperature
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol (Invitrogen) extraction, followed by purification using Qiagen RNeasy column
|
| Label |
biotin
|
| Label protocol |
cDNA was prepared using a T7 promoter-tailed oligo-dT primer, followed by second strand synthesis. Double-stranded cDNA was used as the template for in vitro transcription (IVT) catalyzed by T7 polymerase and containing biotinylated CTP and UTP. Biotinylated complementary RNA (cRNA) is purified using the RNeasy system (Qiagen).
|
| |
|
| Hybridization protocol |
The purified cRNA was fragmented for hybridization and purified by phenol/chloroform extraction and ethanol precipitation. The fragmented cRNA and several biotinylated control oligonucleotides (for quality control) were hybridized to a mouse 430_2 chip overnight at 45°C. The chip was then transferred to a fluidics instrument for washes to remove unbound cRNA. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were added using biotinylated anti-streptavidin antibody and SAPE.
|
| Scan protocol |
Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
|
| Description |
no additional information
|
| Data processing |
Array normalization, expression value calculation and clustering analysis were performed using DNA-Chip Analyzer. The Invariant Set Normalization method was used to normalize arrays at probe cell level to make them comparable, and the model-based method was used for probe-selection and computing expression values
|
| |
|
| Submission date |
Jun 06, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Patrick Seale |
| E-mail(s) |
sealep@upenn.edu
|
| Phone |
6176324661
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Cancer Biology
|
| Lab |
Smith 946
|
| Street address |
1 Jimmy Fund Way
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE8044 |
Brown versus white tissue adipose selective genes |
|
| Relations |
| Reanalyzed by |
GSE119085 |
