|
| Status |
Public on Mar 13, 2008 |
| Title |
A23 (transfected with Pcdh7, cy5) / A23 (tranfected with empty vector, cy3), biological replica 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from A23 tranfected with Pcdh7 labeled with cy5
|
| Organism |
Cricetulus griseus |
| Characteristics |
A23 lung fibroblast derived cell line
|
| Treatment protocol |
Cells were transfected with Pcdh7 subcloned into the pCMV-sport6 vector (Invitrogen) using Effectene (Qiagen) according to manufacturer's instructions. Parallel transfections of the empty vector alone were also performed. The cells were harvested 48 hours after transfection.
|
| Growth protocol |
A23 and HEK cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done with Qiagen RNeasy Mini Kit per protocol recommended by the manufacturer.
|
| Label |
cy5
|
| Label protocol |
RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to manufacturer's instructions. This kit generated labeled cRNA targets.
|
| |
|
| Channel 2 |
| Source name |
total RNA from A23 transfected with empty vector labeled with cy3
|
| Organism |
Cricetulus griseus |
| Characteristics |
A23 lung fibroblast derived cell line
|
| Treatment protocol |
Cells were transfected with Pcdh7 subcloned into the pCMV-sport6 vector (Invitrogen) using Effectene (Qiagen) according to manufacturer's instructions. Parallel transfections of the empty vector alone were also performed. The cells were harvested 48 hours after transfection.
|
| Growth protocol |
A23 and HEK cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done with Qiagen RNeasy Mini Kit per protocol recommended by the manufacturer.
|
| Label |
cy3
|
| Label protocol |
RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to manufacturer's instructions. This kit generated labeled cRNA targets.
|
| |
|
| |
| Hybridization protocol |
Standard Agilent Hybridization protocols for expression microarrays were followed, 17 hour hybridization time
|
| Scan protocol |
Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.
|
| Description |
biological replicate 2 of 2
|
| Data processing |
The expression data was normalized using GeneSpring (Agilent Technologies). Each value was divided by the control channel and each chip normalized to the 50th percentile for the measurements taken from that chip.
|
| |
|
| Submission date |
Sep 17, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Christopher Park |
| Phone |
310-948-7917
|
| Organization name |
UCLA
|
| Department |
Molecular and Medical Pharmacology
|
| Lab |
Desmond Smith
|
| Street address |
23-151 CHS, 650 Charles E. Young Drive
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL2872 |
| Series (2) |
| GSE9052 |
Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids |
| GSE9066 |
Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids II |
|
