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Sample GSM762821 Query DataSets for GSM762821
Status Public on Nov 06, 2011
Title Jurkat Tat cells vs. Jurkat cells replicate 1
Sample type RNA
 
Channel 1
Source name Jurkat-Tat
Organism Homo sapiens
Characteristics expression: HIV Tat protein
cell line: Jurkat
Growth protocol Jurkat-Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum, 1%penicillin and streptomycin and 800 microg/ml of G418. Jurkat T cells were obtained from ATCC and cultured under standard tissue culture conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Jurkat and Jurkat-Tat cells using the RNeasy Mini kit (Qiagen). according to manufacturer's instructions. Labeled cRNAs were hybridized to the Agilent Human whole-genome array according to Agilent protocol.
Label Cy5
Label protocol cRNAs were generated from 250ng of total RNA and labeled with Cy3 (Jurkat) or Cy5 (Jurkat-Tat) using the Low Input Quick Amp Labeling Kit (Agilent)
 
Channel 2
Source name Jurkat
Organism Homo sapiens
Characteristics expression: control
cell line: Jurkat
Growth protocol Jurkat-Tat cells were maintained in RPMI supplemented with 10% fetal bovine serum, 1%penicillin and streptomycin and 800 microg/ml of G418. Jurkat T cells were obtained from ATCC and cultured under standard tissue culture conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Jurkat and Jurkat-Tat cells using the RNeasy Mini kit (Qiagen). according to manufacturer's instructions. Labeled cRNAs were hybridized to the Agilent Human whole-genome array according to Agilent protocol.
Label Cy3
Label protocol cRNAs were generated from 250ng of total RNA and labeled with Cy3 (Jurkat) or Cy5 (Jurkat-Tat) using the Low Input Quick Amp Labeling Kit (Agilent)
 
 
Hybridization protocol Hybridization onto the Whole Human Genome 4 x 44K Microarray (G4112F), washing, and scanning were carried out according to the manufacturer's instructions
Scan protocol Agilent DNA Microarray Scanner
Data processing Raw intensity data from resulting gene expression data were normalized by medium background-subtracted intensities between Cy5 and Cy3 channels followed by LOWESS normalization using Matlab. Normalized log2 ratios of Jurkat-Tat cRNAs (Cy5) over Jurkat cRNAs (Cy3) were calculated and results from replicates were averaged.
 
Submission date Jul 18, 2011
Last update date Nov 06, 2011
Contact name Siavash K Kurdistani
E-mail(s) Skurdistani@mednet.ucla.edu
Phone 310-794-5194
Fax 310 206-5272
Organization name University of California Los Angeles
Department Biological Chemistry
Street address 615 Charles E. Young Dr. South, 337
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL7031
Series (2)
GSE30734 Genome-wide binding map of the HIV Tat protein to the human genome (gene expression)
GSE30739 Genome-wide binding map of the HIV Tat protein to the human genome

Data table header descriptions
ID_REF
VALUE normalized log2 test/reference

Data table
ID_REF VALUE
1 -0.206692176
2 0.298530136
3 -0.442985988
4 0.138087815
5 -0.357487439
6 0.140897344
7 -0.249653432
8 0.052396578
9 0.676829623
10 0.389786523
11 1.391947308
12 0.272589669
13 0.279195929
14 0.042667263
15 0.086503353
16 -0.162464671
17 0.320655463
18 0.332696931
19 0.035616935
20 -0.217549815

Total number of rows: 13792

Table truncated, full table size 230 Kbytes.




Supplementary file Size Download File type/resource
GSM762821_US82903519_251485037872_S01_GE2_105_Dec08_1_1.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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