|
| Status |
Public on Sep 11, 2007 |
| Title |
CMix Self-Self 5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
CMix Test1
|
| Organism |
Rattus norvegicus |
| Characteristics |
Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used to generate the labeled probe.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
indirect labeling protocol
|
| |
|
| Channel 2 |
| Source name |
CMix Ref1
|
| Organism |
Rattus norvegicus |
| Characteristics |
Total RNA was isolated from each of three rat livers and brains, and equal mass amounts of each of these six samples were combined to create a mixed RNA population. One 20 microgram aliquot of the total RNA mixture was used to generate the labeled probe.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
indirect labeling protocol
|
| |
|
| |
| Hybridization protocol |
Cy3 and Cy5 labeled probes were combined and competitively hybridized to microarrays for 18 hours at 37C.
|
| Scan protocol |
Slides were scanned using ScanArray 5000 fluorescent scanner (GSI Lumonics, Billerica, MA). The resulting images were quantified using QuantArray v3.0 image analysis software with the Fixed Circle spot finding algorithm software (GSI Lumonics, Billerica, MA) with a spot diameter of 150µm, an inner background diameter of 234µm, and an outer background diameter of 313µm. Minimum and maximum intensity limits for signal classification were the 55th and 90th percentile, and those for background classification were the 5th and 20th percentile.
|
| Description |
This experiment was conducted to study dye-byes effects. Channel 1 and Channel 2 have identical biological sample labeled with two different dyes.
|
| Data processing |
Raw quantitated array data was normalized using subaray-based quadratic correction algorithm.
|
| |
|
| Submission date |
Sep 04, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Egle Juskeviciute |
| Organization name |
Thomas Jefferson University
|
| Department |
Pathology
|
| Street address |
1020 Locust st. JAH 527
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL5803 |
| Series (1) |
| GSE8950 |
Rat Brain-Heart-Liver Control Mix Self-Self Hybridization |
|
