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Sample GSM124680 Query DataSets for GSM124680
Status Public on Sep 19, 2006
Title 50mg Acetaminophen 6h Rat 3126 vs. 50mg Acetaminophen 6h 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) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
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

Data table header descriptions
ID_REF probeset IDs from the Agilent G4130A Rat oligo array
VALUE Rosetta Resolver Error Model, Log10 transformed ratios

Data table
ID_REF VALUE
19150 0.06411
19152 0.38893
19153 0.09258
19155 0.08934
19156 -8.38E-03
19157 0.10553
19158 0.07655
19159 -0.1661
18500 2.61E-03
18501 0.11577
18502 0.01336
18503 4.34E-03
19160 0.09941
18504 0.03017
18505 0
18506 -0.1706
19162 -0.19085
19163 -0.27604
18507 0.13572
18508 0.08209

Total number of rows: 20500

Table truncated, full table size 276 Kbytes.




Supplementary data files not provided

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