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Sample GSM147667 Query DataSets for GSM147667
Status Public on May 30, 2007
Title NA_reactivation_1 time_rep2
Sample type genomic
 
Channel 1
Source name EBV-positive cell lines derived from nasopharyngeal carcinoma, without EBV reactivation, low-passage-number
Organism Homo sapiens
Characteristics Cell line: an EBV-positive NPC cell line
Gender: male
Tissue: Nasopharyngeal carcinoma
Treatment protocol without and treatment
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 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 from nasopharyngeal carcinoma, EBV reactivation, one time
Organism Homo sapiens
Characteristics Cell line: an EBV-positive NPC cell line
Gender: male
Tissue: Nasopharyngeal carcinoma
Treatment protocol 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 medium for 24 hours prior genomic DNA extraction.
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 -1.70E-02 5332.97 5128.204 65.294 46.7649
2 0.00E+00 14.3022 25.0302 65.2708 46.7501
3 -4.99E-02 1090.604 972.1402 65.2472 46.7434
4 -2.99E-02 1555.444 1451.951 65.2226 46.7283
5 -7.45E-02 821.7091 692.1475 65.1967 46.7113
6 -7.04E-02 1254.932 1067.113 65.1711 46.7005
7 8.17E-03 410.2419 418.0338 65.1462 46.6946
8 -1.08E-01 1308.145 1020.638 65.1181 46.678
9 -4.68E-02 424.6566 381.2337 65.0889 46.6611
10 -1.65E-02 605.569 583.0288 65.0585 46.6438
11 -1.63E-02 1017.008 979.48 65.0287 46.6301
12 -4.81E-02 1749.258 1565.791 64.9996 46.6191
13 -4.88E-02 1185.766 1059.828 64.9658 46.6
14 -9.14E-02 843.2648 683.2066 64.931 46.581
15 -2.94E-02 846.1268 790.7052 64.902 46.5732
16 -6.57E-02 1822.768 1566.837 64.866 46.5546
17 6.81E-03 803.046 815.7302 64.8318 46.5403
18 -4.42E-02 1363.116 1231.078 64.8031 46.5346
19 1.61E-02 1689.043 1752.975 64.7708 46.5241
20 4.61E-02 812.6423 903.5775 64.7327 46.5063

Total number of rows: 43890

Table truncated, full table size 2090 Kbytes.




Supplementary file Size Download File type/resource
GSM147667.tif.gz 27.1 Mb (ftp)(http) TIFF
GSM147667.txt.gz 11.3 Mb (ftp)(http) TXT

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