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Sample GSM147668 Query DataSets for GSM147668
Status Public on May 30, 2007
Title NA_reactivation_15 time_rep1
Sample type genomic
 
Channel 1
Source name EBV-positive cell lines derived from nasopharyngeal carcinoma, recurrent EBV reactivation, 15 times
Organism Homo sapiens
Characteristics Cell line: an EBV-positive NPC cell line
Gender: male
Tissue: Nasopharyngeal carcinoma
Treatment protocol Induction of EBV reactivation was performed 15 times, once per passage.
Induction of EBV reactivation was established by combinational use of 12-O-tetradecanoylphorbol -13-acetate (TPA) and sodium n-butyrate (SB). Briefly, NA cells seeded in cultured medium and allow adhering overnight before treatment. TPA and SB were dissolved in medium at final concentration of 20 ng/ml and 3 mM, respectively. Twenty four hours post incubation, medium containing TPA and SB was removed following by incubation in normal culture medium for 24 hours prior next passage or genomic DNA extraction.
Growth protocol NA cells were all maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 400 microgram/ml of G418
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from NPC cells harboring 15 times of EBV-reactivation with DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions.
Label Cy5
Label protocol Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer's instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy5-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.
 
Channel 2
Source name EBV-positive cell lines derived fromnasopharyngeal carcinoma, without EBV reactivation, low-number-passage
Organism Homo sapiens
Characteristics Cell line: an EBV-positive NPC cell line
Gender: male
Tissue: Nasopharyngeal carcinoma
Treatment protocol without any treatment.
Growth protocol NA cells were all maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% FBS and 400 microgran/ml of G418.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated with DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions
Label Cy3
Label protocol Genomic DNA labeling was performed according to the standard array-CGH protocol provided by Agilent Technologies. After 3 μg of genomic DNA was completely fragmented and purified, all of the digested DNAs were subjected to labeling reactions with a Bioprime labeling kit (Invitrogen) according to the manufacturer's instructions. Labeling reactions were performed in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60μM dTTP; and 60μM Cy3-dUTP (PerkinElmer). After incubation for 2 h at 37 ℃, the reactions were inactivated.
 
 
Hybridization protocol To prepare the hybridization mixture, the experimental and reference samples were subsequently pooled, purified and concentrated with a Centricon YM-30 column (Millipore), resuspended to a final volume of 150 μl, and then mixed with 50 μg of human Cot-1 DNA (Invitrogen), 50 μl of 10× blocking buffer (Agilent), and 250 μl of 2× aCGH hybrixization buffer (Agilent). Before hybridization, the 500 μl hybridization mixtures were denatured at 95℃ for 3 min and incubated at 37℃ for 30 min. Array hybridizations were carried out for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).
Scan protocol Hardware: Agilent G2565BA DNA microarray scanner (Agilent Technologies)
Software: ScanControl Software (Agilent Technologies)
The scanning and image acquisition protocols: the arrays were imaged at a resolution of 10 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each arrays was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.
Description NA is an EBV-positive NPC cell line previously generated by in vitro infection of NPC-TW01 cells with recombinant Akata EBV.
Data processing The data in VALUE column were generated by using Linear Normalization Method with rank consistent probes. The data was transformed into Log10-based scale.
 
Submission date Nov 30, 2006
Last update date Mar 23, 2007
Contact name Chia Huei Lee
E-mail(s) chlee124@nhri.edu.tw
Organization name Taiwan National Health Research Institute
Department National Institute of Cancer Research
Street address 35, Keyan Rd.
City Zhunan Miaoli County
ZIP/Postal code 114
Country Taiwan
 
Platform ID GPL2879
Series (1)
GSE6472 The influence of highly recurrent EBV reactivation on genetic copy number alterations

Data table header descriptions
ID_REF
VALUE log10(Cy5/Cy3)
g_Sig_Mean Green normalized signal
r_Sig_Mean Red normalized signal
g_Bkd_Mean Green background signal
r_Bkd_Mean Red background signal

Data table
ID_REF VALUE g_Sig_Mean r_Sig_Mean g_Bkd_Mean r_Bkd_Mean
1 2.94E-02 4660.83 4987.637 110.693 46.945
2 -9.37E-01 119.9571 13.8663 110.647 46.9696
3 -1.47E-02 956.2588 924.4415 110.614 46.9814
4 -2.92E-02 1561.587 1460.132 110.569 46.9885
5 -2.86E-02 595.1888 557.309 110.524 47.0008
6 -4.69E-02 1082.618 971.6862 110.487 47.0118
7 1.62E-01 295.2112 429.148 110.458 47.0161
8 -2.06E-02 1084.982 1034.699 110.416 47.0337
9 2.20E-02 340.6418 358.3561 110.375 47.0523
10 8.64E-02 499.6158 609.6017 110.334 47.058
11 -5.25E-02 926.7727 821.2027 110.299 47.0641
12 -9.94E-02 1723.959 1371.221 110.268 47.0676
13 -2.89E-02 1189.447 1112.841 110.229 47.0717
14 -5.58E-02 717.0063 630.5235 110.192 47.0865
15 -6.39E-02 693.6863 598.76 110.166 47.0889
16 -8.90E-02 1912.589 1558.21 110.131 47.0911
17 1.89E-01 471.9316 728.6756 110.101 47.1089
18 -1.10E-01 1326.047 1029.642 110.078 47.1251
19 5.82E-03 1496.563 1516.746 110.052 47.1341
20 8.53E-02 747.4442 909.5798 110.022 47.1432

Total number of rows: 43890

Table truncated, full table size 2091 Kbytes.




Supplementary file Size Download File type/resource
GSM147668.tif.gz 27.5 Mb (ftp)(http) TIFF
GSM147668.txt.gz 11.2 Mb (ftp)(http) TXT

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