|
| Status |
Public on Feb 27, 2007 |
| Title |
6h PQ hepatotoxicity F |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mice Liver
|
| Organism |
Mus musculus |
| Characteristics |
Mus musculus, Male, 10-12 weeks, Liver
|
| Biomaterial provider |
Central Drug Research Institute, Lucknow
|
| Treatment protocol |
Vehicle Treated
|
| Growth protocol |
Mice were kept under control temparature and humidity conditions. Food and water was allowed ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRI Reagent Protocol
|
| Label |
Cy3
|
| Label protocol |
CyScribe First Strand cDNA Labelling Kit Protocol
|
| |
|
| Channel 2 |
| Source name |
Mice Liver
|
| Organism |
Mus musculus |
| Characteristics |
Mus musculus, Male, 10-12 weeks, Liver
|
| Biomaterial provider |
Central Drug Research Institute, Lucknow
|
| Treatment protocol |
Mice were sacrificed 6h after drug administration
|
| Growth protocol |
Mice were kept under control temparature and humidity conditions. Food and water was allowed ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRI Reagent Protocol
|
| Label |
Cy5
|
| Label protocol |
CyScribe First Strand cDNA Labelling Kit Protocol
|
| |
|
| |
| Hybridization protocol |
The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0 at default settings.
|
| Description |
Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent(Sigma).25 ug of total RNA was converted into labelled cDNA using CyScribe first strand cDNA labelling kit(Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically.
|
| Data processing |
Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Background corrected raw data was LOWESS normalized using Avadis V4. Normalized data was analysed to find differentially expressed genes.
|
| |
|
| Submission date |
Oct 04, 2006 |
| Last update date |
Oct 06, 2006 |
| Contact name |
Sanjeev Noel |
| E-mail(s) |
sanjeevnoel@gmail.com
|
| Phone |
91-9935392997
|
| Organization name |
Central Drug Research Institute
|
| Department |
Toxicology
|
| Lab |
Genotoxicity
|
| Street address |
M G Marg
|
| City |
Lucknow |
| State/province |
Uttar Pradesh |
| ZIP/Postal code |
226001 |
| Country |
India |
| |
|
| Platform ID |
GPL3493 |
| Series (1) |
| GSE5979 |
Differential gene expression in mice liver following primaquine administration |
|
