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Sample GSM42168 Query DataSets for GSM42168
Status Public on Dec 31, 2005
Title TRH+arg9
Sample type RNA
 
Source name GP7TB transformed rat hepatic cells cultured in high levels of arginine for 18 hours
Organism Rattus norvegicus
Extracted molecule total RNA
 
Description Biosource strain/age/gender/disease state:
neoplastically transformed cells derived from clonal subpopulations of derivation cell lines that were produced by 11 brief repeated exposures of normal diploid hepatic epithelial line WB-F344 cells to 5 ug/ml of N-methyl-N-Nitro-N-nitrosoguanidine

Growth protocol:
Cells were routinely cultured in modified Eagle's medium (Life Technologies, Inc.) containing 10% FBS.

Treatment protocol:
After growing to approximately 80% confluence, MEM culture medium was removed and replaced with a custom formulation of Chee's Essential Medium (CEM) containing 5% Fetal Bovine Serum with L-Arginine HCl at 0.168 gm/liter for an additional 18 hours.

Extraction protocol:
Total RNA was isolated from cells after 18 hours of treatment using TRI reagent -- RNA isolation Reagent Method (TRI Reagent, RNA/DNA/Protein Isolation Reagent, Molecular Research Center Inc. Cincinnati, Ohio)

Labeling/Scanning/Hybrization/Quantification protocol:
Target cRNA was prepared and hybridized (45 °C, 16 h) to GeneChip rat 230A arrays according to the manufacturer's directions (Affymetrix). Hybridized arrays were washed and stained using the GeneChip fluidics station 400 and scanned using the Agilent GeneArray scanner. Signals were analyzed using Microarray Suite 5.0 software (Affymetrix). Data obtained was analyzed with GeneSpring 6.0.

Keywords = arginine, hepatocyte, cancer, rat, amino acid, gene regulation, microarray
 
Submission date Feb 15, 2005
Last update date Oct 28, 2005
Contact name Xianne Leong
E-mail(s) xianne@brown.edu
Phone 401-444-8860
Organization name Rhode Island Hospital; Brown University
Department Medical Oncology
Street address
City Providence
State/province RI
ZIP/Postal code 02912
Country USA
 
Platform ID GPL1355
Series (1)
GSE2275 A Bioinformatic Analysis of Arginine-Sensitive Regulation of rat Hepatic Gene Expression

Data table header descriptions
ID_REF
VALUE MAS5
ABS_CALL Detection
DETECTION P-VALUE Significance

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1398835_at 22302 P 0.000244
1367557_s_at 20511.9 P 0.000244
AFFX_Rat_beta-actin_M_at 20467.9 P 0.000044
1367661_at 20074.1 P 0.000244
1398836_s_at 19931.1 P 0.000244
1388110_at 19697.3 P 0.000244
1367565_a_at 19301.4 P 0.000244
AFFX_Rat_beta-actin_3_at 19125.1 P 0.000044
AFFX_Rat_GAPDH_3_at 18342.7 P 0.000754
1367567_at 17901.9 P 0.000244
1375219_a_at 17533.8 P 0.000244
1370242_at 17409 P 0.000244
1375170_at 17408.1 P 0.000244
1371344_at 17355.7 P 0.000244
1367597_at 17139.4 P 0.000244
1371297_at 17004.5 P 0.000244
1367579_a_at 16910.7 P 0.000244
AFFX_Rat_GAPDH_5_at 16838.6 P 0.000052
AFFX_Rat_GAPDH_M_at 16781.8 P 0.000044
1371307_at 16570.9 P 0.000244

Total number of rows: 15923

Table truncated, full table size 428 Kbytes.




Supplementary file Size Download File type/resource
GSM42168.CEL.gz 2.4 Mb (ftp)(http) CEL
GSM42168.EXP.gz 588 b (ftp)(http) EXP
GSM42168.TIFF.tif.gz 804.1 Kb (ftp)(http) TIFF

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