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Sample GSM560520 Query DataSets for GSM560520
Status Public on Oct 01, 2010
Title Uncomplemented cells, replicate 3
Sample type RNA
 
Channel 1
Source name S1-1 cells
Organism Homo sapiens
Characteristics sample type: Experimental cells. They were transduced with empty retrovectors, induced for dnEBNA1 expression with doxycycline, and cultured 20 days to evict the virus.
cell line: S1-1
condition: EBV evicted with dnEBNA1
Growth protocol Cells were diluted to 3-5x104 cells/mL in culture medium and treated with either 10 ng/mL doxycycline or the vehicle, ethanol. Live cell concentrations were measured every two or four days with a hemocytometer. Cells stained with trypan blue (with a 1:10 dilution of 0.3% trypan blue dissolved in 1x PBS) or exhibiting an aberrant morphology were considered non-viable. After counting, in necessary cells were diluted in fresh medium back to approximately the starting concentration (3-5x104 cells/mL) and doxycycline or ethanol was added.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen), following the manufacturer’s protocols, except RNA precipitation was conducted in the presence of approximately 5 µg/mL linear acrylamide (Ambion) to enhance efficiency of precipitation as previously described (Gaillard and Strauss, 1990). The isolated RNA was then treated with Turbo DNAse (Ambion) following the manufacturer’s instructions and re-purified with TRIzol.
Label cy3
Label protocol Labelled cRNA was generated using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. This procedure uses T7 RNA polymerase, which both amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.
 
Channel 2
Source name S1-1 cells
Organism Homo sapiens
Characteristics sample type: Control cells. They were transduced with empty retrovectors, mock induced (dnEBNA1 kept off), and cultured 20 days.
cell line: S1-1
Growth protocol Cells were diluted to 3-5x104 cells/mL in culture medium and treated with either 10 ng/mL doxycycline or the vehicle, ethanol. Live cell concentrations were measured every two or four days with a hemocytometer. Cells stained with trypan blue (with a 1:10 dilution of 0.3% trypan blue dissolved in 1x PBS) or exhibiting an aberrant morphology were considered non-viable. After counting, in necessary cells were diluted in fresh medium back to approximately the starting concentration (3-5x104 cells/mL) and doxycycline or ethanol was added.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen), following the manufacturer’s protocols, except RNA precipitation was conducted in the presence of approximately 5 µg/mL linear acrylamide (Ambion) to enhance efficiency of precipitation as previously described (Gaillard and Strauss, 1990). The isolated RNA was then treated with Turbo DNAse (Ambion) following the manufacturer’s instructions and re-purified with TRIzol.
Label cy5
Label protocol Labelled cRNA was generated using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. This procedure uses T7 RNA polymerase, which both amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.
 
 
Hybridization protocol Scanned on an Agilent G2565BA scanner.
Scan protocol Images were recorded and quantified using Agilent’s Scan Control software, version A. 7.0.1 (includes XDR functionality) and Agilent Feature Extraction software (v. 9.5.3).
Description Uncomplemented loss of EBV, replicate 3 of 3
Data processing Agilent Feature Extraction software (v. 9.5.3) was used with the manufacturer's default settings.
 
Submission date Jun 26, 2010
Last update date Jun 29, 2010
Contact name Bill Sugden
E-mail(s) sugden@oncology.wisc.edu
Phone 608-262-6697
Organization name University of Wisconsin-Madison
Department Oncology
Street address 1400 University Avenue
City Madison
State/province WI
ZIP/Postal code 53706-1599
Country USA
 
Platform ID GPL4133
Series (1)
GSE22586 The forced loss of Epstein Barr virus from Burkitt's lymphoma cells: uncomplemented cells vs BART miRNA complemented cells.

Data table header descriptions
ID_REF
VALUE normalized log10 Cy3/Cy5

Data table
ID_REF VALUE
1 -0.241144
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.178941
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.162618
12 0.200003
13 0.110236
14 -0.115673
15 -0.038602
16 -0.105851
17 -0.208941
18 0.156433
19 -0.185056
20 -0.0654263

Total number of rows: 45015

Table truncated, full table size 762 Kbytes.




Supplementary file Size Download File type/resource
GSM560520_US22502567_251485017698_S01_GE2-v5_95_Feb07_2-local-background_1_3.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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