|
| Status |
Public on Nov 02, 2012 |
| Title |
COLO320 CDX2 siRNA #6 24hr |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
COLO320 CDX2 siRNA #6 24hr
|
| Organism |
Homo sapiens |
| Characteristics |
knockdown: CDX2
cell line: COLO-320
|
| Treatment protocol |
Cells were transfected with 100 nM of either of two CDX2-targeting siRNA constructs or a non-targeting control siRNA construct. Cell culture media was changed the following morning, and cells were then harvested for RNA 24 hrs later (coinciding with the time of maximal CDX2 protein knockdown)
|
| Growth protocol |
COLO320 cells were grown in RPMI-1640 media + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's protocol
|
| Label |
Cy5
|
| Label protocol |
Time-matched RNA from cells transfected with siCDX2 and non-targeting control constructs were reverse-transcribed, fluorescently-labeled, and co-hybridized to Agilent Whole Human Genome 44K gene expression arrays according to manufacturer protocols.
|
| |
|
| Channel 2 |
| Source name |
COLO320 Non-targeting control siRNA 24hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: COLO-320
knockdown: Non-targeting control siRNA
|
| Treatment protocol |
Cells were transfected with 100 nM of either of two CDX2-targeting siRNA constructs or a non-targeting control siRNA construct. Cell culture media was changed the following morning, and cells were then harvested for RNA 24 hrs later (coinciding with the time of maximal CDX2 protein knockdown)
|
| Growth protocol |
COLO320 cells were grown in RPMI-1640 media + 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
Time-matched RNA from cells transfected with siCDX2 and non-targeting control constructs were reverse-transcribed, fluorescently-labeled, and co-hybridized to Agilent Whole Human Genome 44K gene expression arrays according to manufacturer protocols.
|
| |
|
| |
| Hybridization protocol |
Oligoarray hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slide was washed following manufacturer's instructions.
|
| Scan protocol |
Scanned on an Agilent G2505C Microarray Scanner System
Images were quantified using Agilent Feature Extraction Software (version 9.5.3).
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Jun 23, 2011 |
| Last update date |
Nov 02, 2012 |
| Contact name |
Keyan Salari |
| E-mail(s) |
ksalari@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Street address |
Gray/Bigelow Rm 1102, 55 Fruit Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE30181 |
COLO320 cells: siCDX2 vs. non-targeting control |
| GSE30475 |
Colorectal Cancer Cells |
|
