|
| Status |
Public on Jun 30, 2009 |
| Title |
lacZ siRNA transfected HCT116-3(6), replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| 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 |
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
|
| |
|
| Channel 2 |
| 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 |
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).
|
| |
|
| 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 |
|
