|
| Status |
Public on Jan 31, 2007 |
| Title |
SPI-4 |
| Sample type |
RNA |
| |
|
| Source name |
rat mammary epithelial cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
Female Sprague-Dawley rat, postnatal day 50, life-time ingestion of casein based diet SPI diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.
|
| Label |
biotin
|
| Label protocol |
Pooled RNA (equal amounts of RNA from #4 mammary gland of two animals; 8 ug total) was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.
|
| |
|
| Hybridization protocol |
10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.
|
| Scan protocol |
GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.
|
| Description |
Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.
|
| Data processing |
Value column are raw signal intensity generated from MAS 5.0.
|
| |
|
| Submission date |
Jan 26, 2007 |
| Last update date |
Jan 30, 2007 |
| Contact name |
Ying Su |
| E-mail(s) |
[email protected]
|
| Phone |
501-364-2033
|
| Fax |
501-364-3161
|
| Organization name |
UAMS
|
| Department |
physiology
|
| Street address |
1120 Marshall St. South Campus
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72202 |
| Country |
USA |
| |
|
| Platform ID |
GPL341 |
| Series (1) |
| GSE6879 |
Dietary effect of SPI or Genistein alters rat mammary epithelial global gene expression profiles |
|
