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Sample GSM310326 Query DataSets for GSM310326
Status Public on Aug 08, 2008
Title Gene expression profiles of HL-60 cells exposed to toluene (IC50) [sample 3]
Sample type RNA
 
Channel 1
Source name HL-60 cells treated with DMSO for 3 h
Organism Homo sapiens
Characteristics cell line: HL-60
cell type: human promyelocytic leukemia cells
treatment: DMSO
treatment time: 3 h
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the HL-60 cells treated to DMSO for 3 h using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).
Label Cy3
Label protocol Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy3 dye for the controls (DMSO).
 
Channel 2
Source name HL-60 cells treated with toluene (IC50) for 3 h
Organism Homo sapiens
Characteristics cell line: HL-60
cell type: human promyelocytic leukemia cells
treament: toluene
treament dose: IC50
treament time: 3 hr
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the HL-60 cells treated to IC50 dose of toluene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).
Label Cy5
Label protocol Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy5 dye for the treated samples.
 
 
Hybridization protocol Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) or Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62℃ for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58℃, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT.
Scan protocol Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.
Description HL-60 cells were treated with 2.74 mM toluene for 3 h, and the RNA was subjected to microarray analysis.
Data processing The fluorescent intensity of each spot was calculated by local median background subtraction. The robust scatter-plot smoother LOWESS function was used to perform intensity dependent normalization for the gene expression. Scatter plot analysis was made by Microsoft Excel 2003. Significance Analysis of Microarray (SAM) was performed for the selection of the genes with significant gene expression changes (Tusher et al., 2001). Computing a p-value for each gene assessed the statistical significance of the differential expression of genes. To determine the p-value, a permutation procedure was used and for each permutation, two-sample t statistics were computed for each gene. Genes were considered differentially expressed when logarithmic gene expression ratios in three independent hybridizations were more than 1.5 or less than 0.66, i.e., 1.5-fold difference in expression level, and when the p-values were less than 5.
 
Submission date Aug 06, 2008
Last update date Feb 24, 2010
Contact name Sailendra Nath Sarma
E-mail(s) sarma@kist.re.kr
Phone +8229585080
Fax +8229585059
Organization name Korea Institute of Science and Technology
Lab Toxicology
Street address P.O. Box 131, Cheongryang
City Seoul
ZIP/Postal code 136-791
Country South Korea
 
Platform ID GPL7080
Series (2)
GSE12353 Gene expression profiles of human promyelocytic leukemia cell lines exposed to six volatile organic compounds
GSE24899 Differential gene expression profiles of human promyelocytic leukemia cell line exposed to benzene toluene, and o-xylene

Data table header descriptions
ID_REF
VALUE Lowess normalized log2 cy5/cy3 ratio representing treated/control
PRE_VALUE lowess cy3/cy5
INV_VALUE lowess normalized log2 cy3/cy5

Data table
ID_REF VALUE PRE_VALUE INV_VALUE
2
4
5 -0.21 1.156648641 0.2100
6 0.7142 0.609534246 -0.7142
7 -0.0191 1.013305311 0.0191
8 0.3035 0.81026732 -0.3035
9
10 0.3254 0.798100353 -0.3254
11 -0.1675 1.123085948 0.1675
12 -0.0903 1.064585715 0.0903
13
14 -0.0329 1.023092193 0.0329
15 0.5422 0.686701933 -0.5422
16
17 -0.4735 1.388462518 0.4735
18 0.0516 0.964896713 -0.0516
19 -0.018 1.012578628 0.0180
20 0.9617 0.513437909 -0.9617
21 0.4549 0.729576544 -0.4549
22

Total number of rows: 30996

Table truncated, full table size 702 Kbytes.




Supplementary file Size Download File type/resource
GSM310326.gpr.gz 4.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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