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Sample GSM567862 Query DataSets for GSM567862
Status Public on Jul 24, 2010
Title Gene expression profiles of HL-60 cells exposed to benzoquinone (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 44 K whole human genome microarray (Agilent Technologies. Inc). 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 benzoquinone (IC50) for 3 h
Organism Homo sapiens
Characteristics cell line: HL-60
cell type: human promyelocytic leukemia cells
treament: benzoquinone
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 benzene 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 44 K whole human genome microarray (Agilent Technologies. Inc). 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 11.87 µM benzoquinone 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 Jul 20, 2010
Last update date Jul 23, 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 GPL10703
Series (1)
GSE23018 Differential gene expression profiles of human promyelocytic leukemia cell lines exposed to benzene and its metabolites

Data table header descriptions
ID_REF
VALUE LOWESS log2 ratio (Cy5/Cy3)
PRE_VALUE LOWESS ratio (Cy5/Cy3)

Data table
ID_REF VALUE PRE_VALUE
20 -0.3262 0.797630807
22 0.3512 1.275607173
23
24 0.2681 1.204255986
25 -0.1169 0.92214755
26 0.5146 1.428586
27 -0.7047 0.61358064
28 -0.4517 0.731159994
30 0.5814 1.49626267
31 0.6567 1.576516328
33 0.2819 1.215818245
50 -0.6916 0.619178604
51
53 -0.4144 0.750351004
54 -0.2646 0.832424972
55 0.5844 1.499409106
57 0.7643 1.698529947
59 0.4579 1.373570009
60 -0.6833 0.622743125
62 -0.2242 0.856096488

Total number of rows: 27507

Table truncated, full table size 499 Kbytes.




Supplementary file Size Download File type/resource
GSM567862_Agilent_Human_4x44K_251485038785_A1_BQ_IC50_3_.gpr 14.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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