|
| Status |
Public on Jan 01, 2008 |
| Title |
Ventricle Animal 291 zeitgeber time 12 Transgenic |
| Sample type |
RNA |
| |
|
| Source name |
Ventricles
|
| Organism |
Mus musculus |
| Characteristics |
Transgenic
zeitgeber time 12
|
| Treatment protocol |
Atrial and ventricular tissue samples were collected from wildtype and transgenic animals lacking a functional circadian clock within the cardiomyocytes every three hours for a period of 24 hours (n=4 samples per time point).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from all tissues using a standard protocol and Tri-reagent.
|
| Label |
Cy-3
|
| Label protocol |
Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.
|
| |
|
| Hybridization protocol |
A total of 1.5 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with strepavidini-Cy3 prior to visualization.
|
| Scan protocol |
BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.
|
| Description |
Approximately 46,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
|
| Data processing |
After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value). Both non-normalized and normalized (qspline) data were generated for each tissue type.
|
| |
|
| Submission date |
Dec 31, 2007 |
| Last update date |
Dec 31, 2007 |
| Contact name |
Molly Bray |
| E-mail(s) |
mbray@bcm.edu
|
| Phone |
713-798-9311
|
| Fax |
713-798-7187
|
| Organization name |
Baylor College of Medicine
|
| Department |
Pediatrics/USDA/ARS Children's Nutrition Research Ctr
|
| Street address |
1100 Bates, Suite 8070
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6333 |
| Series (1) |
| GSE10045 |
Disruption of the Circadian Clock within the Cardiomyocyte |
|
