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Sample GSM45491 Query DataSets for GSM45491
Status Public on Sep 21, 2005
Title Transcriptional profiling of EBV in SNT-16 cells
Sample type RNA
 
Channel 1
Source name SNT16 (T cell cell line established from chronic active EBV infection)
Organism human gammaherpesvirus 4
Extracted molecule total RNA
 
Channel 2
Source name Peer (EBV negative T cell line): reference
Organism human gammaherpesvirus 4
Extracted molecule total RNA
 
 
Description Comparison of Cy5-labeled SNT-16 cells and Cy3-labeled reference. 40 microgram of total RNA was used.The quality of extracted RNA was checked using a 2100 Bioanalyzer. The Label star array kit (Qiagen) was used for cDNA labeling with modification.EBV specific primers and control gene specific primers were used instead of oligo-dT. Prehybridization was done in buffer containing 5XSSC, 0.1% SDS, and 1% BSA for 1hr. Hybridization was done using Hybridization buffer (Sigma-Aldrich co) containing 1/100 vol. of Salmon testis, at 42oC for 16 hrs. Washing was done with washing buffer containing 2 x SSC, 0.1% SDS for 5 min with buffer containing 0.5 x SSC, 0.1 % SDS for 3 min,followed by buffer containing 0.5% SSC for 3 min, at room temp. Scanning of array data: GenePix 4000B. Data analysis was done using a Genomic Profiler (http://bio.mki.co.jp/en/product/index.html). Normalization: by signals obtained from 4 human house keeping genes. This DNA chip aimed to investigate the viral gene expression in EBV positive cell lines which is not be expressed in the reference cells. Therefore, we scanned the hybridization signals by GenePix 4000B as raw data, and then converted data into Genomic Profiler software to normalize the ratio of Cy5-labeled sample and Cy3-labeled reference properly. All the signals from viral genes were normalized by signals obtained from 4 housekeeping genes whose expression should be equal in both samples and the reference. In general, the signal of Cy-3 labeled cDNA from reference cells are stronger than that of Cy5-labeld cDNA from infected cells, therefore, this procedure was extremely important to normalize the amount of applied cDNA for each microarray. Detailed protocol of microarray analysis of virus gene: Ohyashiki JH et al. Biochem Biophys Res Commun. 2005 329(1):11-17
Keywords = EBV
 
Submission date Mar 17, 2005
Last update date May 29, 2005
Contact name Junko H Ohyashiki
E-mail(s) junko@hh.iij4u.or.jp
Phone +81-3-3342-6111(ext.5999)
Fax +81-3-5381-6651
Organization name Tokyo Medical University
Department Intractable Immune System Diseases Research Center
Street address 6-7-1, Nishishinjuku, Shinjuku-ku
City Tokyo
ZIP/Postal code 160-0023
Country Japan
 
Platform ID GPL1917
Series (1)
GSE2414 Transcriptional profiling of EBV gene in nasal NK/T lymphoma and chronic active EBV infection

Data table header descriptions
ID_REF
VALUE log ratio (log2 of PRE_VALUE)
PRE_VALUE Normalized ratio

Data table
ID_REF VALUE PRE_VALUE
1 0.3210043 1.2491993
2 0.4498183 1.3658683
3 0.3925583 1.3127187
4 0.3418983 1.267423
5 0.5940153 1.5094413
6 0.2481733 1.1877017
7 0.3058253 1.2361253
8 0.3912303 1.3115113
9 0.3503323 1.2748538
10 0.7475283 1.678914
11 0.7882253 1.7269485
12 0.6783763 1.6003373
13 0.3693263 1.2917488
14 0.1283323 1.0930289
15 0.1041423 1.0748553
16 0.2368123 1.1783862
17 0.3871093 1.3077705
18 0.2033233 1.1513469
19 0.5520843 1.4662019
20 0.6944493 1.6182663

Total number of rows: 336

Table truncated, full table size 7 Kbytes.




Supplementary data files not provided

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