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Sample GSM489414 Query DataSets for GSM489414
Status Public on Dec 25, 2009
Title RatL24DNT48h_99.5_3
Sample type RNA
 
Source name RatL24DNT48h_99.5_3
Organism Rattus norvegicus
Characteristics compounds/dose (mg/kg): 24DNT_99.5mg/kg
time: 48h
tissue: Liver
gender: Female
age: 2 months after weaning
weight: 175 to 225 g
Treatment protocol Female Sprague-Dawley rats received a single oral gavage of five doses for each 5 compound in 5% DMSO in corn oil emulsion. Animals were monitored for seizure activity after dosing and were euthanized using CO2, tissues were collected at 24 or 48 hours
Growth protocol Female Sprague-Dawley rats used were from the in-house breeding colony (college of pharmacy, ULM) and treated in accordance with the guide for use and care of animals. Housing consisted of a 12 h light/dark cycle with tap water and rodent chow available ad libitum. Temperature (21 C) and humidity( 50 +/-10%) were held constant. Rats were housed individually in polycarbonate cages on hardwood bedding one week prior to dose. Food was removed the night before dosing, which occurred the next morning between 8 and 11AM.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from about 30mg of liver tissue. Tissue were homogenized in the lysis buffer with FAST Prep-24 from MP at speed 6.0/s twice, each last 30s before using RNeasy kits (Qiagen). Total RNA concentrations were measured using NanoDrop® ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity and quality of total RNA was checked on an Agilent 2100 Bioanalyzer (Palo Alto, CA). The gel-like images generated by the Bioanalyzer show that total RNAs have two bands, represent 18S and 26S RNA of mammalian RNA . Nuclease-free water (Ambion) was used to elute total RNA.
Label CY3
Label protocol Rat whole genome oligo arrays in the format of 4X44K were purchased from Agilent. Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 1.0). 1ug of total RNA was used. The Agilent One-Color Spike-Mix (part number 5188-5282) was diluted 5000-fold and 5 μL of the diluted spike-in mix was added to 1000 ng of each of the total RNA samples prior to labeling reactions. The labeling reactions were performed using the Agilent Low RNA Input Linear Amplification Kit in the presence of cyanine 3-CTP.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol After washing, the arrays were scanned at PMT levels 350 using GenePix 4200AL scanner (Molecular Device Inc.),
Description Gene Expression after 48hexposed to24DNT_99.5mg/kgin rat liver
Data processing The Feature extraction software (V. 9.5.1) from Agilent was used to automatically find and place microarray grids, reject outlier pixels, accurately determine feature intensities and ratios, flag outlier pixels, and calculate statistical confidences. First normalize be median perchip, then by median per gene, which means normalization by median value across all samples, then transformed to log2 based value.
 
Submission date Dec 23, 2009
Last update date Jan 05, 2010
Contact name Xin Guan
E-mail(s) xin.guan@usace.army.mil
Phone 601-6343022
Organization name USACE-ERDC
Department EPP
Lab EGG
Street address 3909 Halls Ferry Rd
City Vicksburg
ZIP/Postal code 39180
Country USA
 
Platform ID GPL4135
Series (1)
GSE19628 Liver toxicity induced by munitions compounds TNT, 2,6-DNT, 2,4-DNT, 4A-DNT, and 2A-DNT

Data table header descriptions
ID_REF
VALUE If the scanned intensity was less than 5.0 for a probe, it was transformed to 5. A perchip (within) array normalization was performed using 50 percentile values of all the probe values in the array. Data were subsequently log (base 2) transformed for statistical analyses.

Data table
ID_REF VALUE
1 -0.3684039
2 1.6511288
3 1.6511288
4 1.6511288
5 1.6511288
6 1.6511288
7 1.6511288
8 1.6511288
9 1.6511288
10 1.6511288
11 1.6511288
12 0.5046365
13 2.03782
14 -0.0784359
15 1.2353599
16 -1.0973263
17 -1.1251879
18 -0.7292042
19 -0.69865704
20 -3.1475334

Total number of rows: 45220

Table truncated, full table size 714 Kbytes.




Supplementary file Size Download File type/resource
GSM489414_251487914483_RatL48hrs24DNT_PMT350_0001_GE1-v5_95_Feb07_1_2.txt.gz 8.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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