|
| Status |
Public on Sep 19, 2006 |
| Title |
2000mg Acetaminophen 24h Rat 3107 vs. 2000mg Acetaminophen 24h Rat Pool |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA prepared from left liver lobes
|
| Organism |
Rattus norvegicus |
| Characteristics |
control
|
| Biomaterial provider |
Male F344/N rats, 8-12 weeks old
|
| Treatment protocol |
Rats were exposed to vehicle alone by oral gavage
|
| Growth protocol |
Rats were housed in groups of 3 in polycarbonate cages (Lab Products, Inc., Maywood, NJ) with Sani-Chips® (P.J. Murphy Forest Products Corp., Montville, NJ) bedding. The animal rooms were maintained at 21-22° C and 48-53% relative humidity with a 12-hr dark-light cycle with lights coming on at 6 a.m. and room air changes of 10/hour. Cages were changed twice per week. NIH-07 diet and tap water was provided ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total hepatic RNA was isolated from individual rat livers using QIAGEN RNeasy Maxi Kits® (QIAGEN, Valencia, CA). Equal amounts of RNA from each of the control animals at every dose and time period were pooled for control gene expression and compared with individual rats at each dose and time period. The samples were hybridized in duplicate for each individual rat.
|
| Label |
Cy5
|
| Label protocol |
One ug of RNA per sample was converted to cDNA with reverse transcriptase and then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP. The labeled cRNA’s from treated individuals and control pools were hybridized together twice, with Cy3 and Cy5 dye swap.
|
| |
|
| Channel 2 |
| Source name |
RNA prepared from left liver lobes
|
| Organism |
Rattus norvegicus |
| Characteristics |
treated
|
| Biomaterial provider |
Male F344/N rats, 8-12 weeks old
|
| Treatment protocol |
Rats were exposed to acetaminophen in methyl cellulose by oral gavage
|
| Growth protocol |
Rats were housed in groups of 3 in polycarbonate cages (Lab Products, Inc., Maywood, NJ) with Sani-Chips® (P.J. Murphy Forest Products Corp., Montville, NJ) bedding. The animal rooms were maintained at 21-22° C and 48-53% relative humidity with a 12-hr dark-light cycle with lights coming on at 6 a.m. and room air changes of 10/hour. Cages were changed twice per week. NIH-07 diet and tap water was provided ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total hepatic RNA was isolated from individual rat livers using QIAGEN RNeasy Maxi Kits® (QIAGEN, Valencia, CA). Equal amounts of RNA from each of the control animals at every dose and time period were pooled for control gene expression and compared with individual rats at each dose and time period. The samples were hybridized in duplicate for each individual rat.
|
| Label |
Cy3
|
| Label protocol |
One ug of RNA per sample was converted to cDNA with reverse transcriptase and then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP. The labeled cRNA’s from treated individuals and control pools were hybridized together twice, with Cy3 and Cy5 dye swap.
|
| |
|
| |
| Hybridization protocol |
The labeled cRNA samples from individual treated animals and control pools were mixed and hybridized for 16 hr at 60?C to the oligonucleotide probes on the Agilent Rat Oligo Microarray (Agilent #G4130A)
|
| Scan protocol |
Chips were scanned with an Agilent G2565 AA Scanner and processed with the Agilent G2566AA Feature Extraction Software.
|
| Description |
Gene expression analysis was conducted using Rattus Norvegicus Agilent Arrays.Starting with 1ug of total RNA, Cy3 and Cy5 labeled cRNA was produced using the Agilent low input labeling and amplification kit according to manufacturer’s protocol. The labeled cRNA samples from individual treated animals and control pools were mixed and hybridized for 16 hr at 60?C to the oligonucleotide probes on the Agilent Rat Oligo Microarray (Agilent #G4130A).Chips were scanned with an Agilent G2565 AA Scanner and processed with the Agilent G2566AA Feature Extraction Software.
|
| Data processing |
Rosetta Resolver Error Model
|
| |
|
| Submission date |
Aug 02, 2006 |
| Last update date |
Mar 28, 2008 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL890 |
| Series (1) |
| GSE5860 |
Gene expression analysis of rat livers after exposure to acetaminophen |
|
