|
Status |
Public on Nov 06, 2011 |
Title |
Jurkat Tat cells vs. Jurkat cells replicate 2 |
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 |
|