|
Status |
Public on Jun 30, 2009 |
Title |
lacZ siRNA transfected HCT116-3(6), replicate 1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Human HCT116-3(6) cells lacZ transfected, HU treated
|
Organism |
Homo sapiens |
Characteristics |
Human HCT116-3(6) cells lacZ transfected, HU treated
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo with treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
|
Label |
Cy3
|
Label protocol |
Total RNA were converted to cRNA, labeled with Cy3 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array
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|
|
Channel 2 |
Source name |
Human HCT116-3(6) cells lacZ transfected, untreated
|
Organism |
Homo sapiens |
Characteristics |
Human HCT116-3(6) cells lacZ transfected, untreated
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from HCT116-3(6) cells transiently transfected with lacZ siRNA oligo without treatment of HU was isolated using RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
|
Label |
Cy5
|
Label protocol |
Total RNA were converted to cRNA, labeled with Cy5 dUTP using Agilent Low Input Linear RNA Amplification, and hybridized to the Phalanx Human One array
|
|
|
|
Hybridization protocol |
standard hybridization procedure
|
Scan protocol |
After hybridization, the slides were scanned with Axon 4000B, and the raw data were generated by Genepix 6.0.
|
Description |
Four biological repeats were performed for each condition (-HU or +HU), with two technical repeats (dye swap) per biological sample.
|
Data processing |
The data was normalized with quantile normalization of DNAMR (http://www.rci.rutgers.edu/~cabrera/DNAMR), and fitted with the linear model from the R package Limma (Smyth, 2004).
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|
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Submission date |
Jul 24, 2008 |
Last update date |
Jun 30, 2009 |
Contact name |
Vera Huang |
E-mail(s) |
vera324@yahoo.com
|
Organization name |
UCSD-Moores Cancer Center
|
Department |
Medicine
|
Lab |
Jean Wang Lab
|
Street address |
3855 Health Science Drive, Room 4317
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093 |
Country |
USA |
|
|
Platform ID |
GPL6254 |
Series (1) |
GSE12242 |
Gene expression profiling in p53 and p73 double knockdown HCT116-3(6) cells |
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