|
| Status |
Public on Dec 29, 2008 |
| Title |
IMR90_control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Lung fibroblast_control
|
| Organism |
Homo sapiens |
| Characteristics |
primary lung fibroblastTotal RNA
|
| Treatment protocol |
Cells were exposed to 0 (sham irradiated) or 50 cGy 4He ions (125 keV per micron) using the track segment mode of the 5.5-MV Singletron accelerator
|
| Growth protocol |
Early passage human lung fibroblast cell strain IMR-90 (Coriell repository, NJ) was sub-cultured in Dulbecco’s modified Eagle’s medium (Gibco) and Ham’s F10 medium in a 1:1 mixture plus 15% fetal bovine serum. Young fibroblasts at population doubling <35 were used in all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Ribopure (Ambion, Applied Biosytems), according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 g RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions
|
| |
|
| Hybridization protocol |
1.5 mg of cRNA (>9 pmol Cy3 per mg cRNA) was fragmented and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) using the Gene Expression Hybridization Kit as recommended by Agilent
|
| Scan protocol |
Slides were scanned immediately using the Agilent DNA Microarray Scanner (G2505B) and default parameters of Feature Extraction Software 9.1 (Agilent)
|
| Description |
Gene expression after 4hr in un-irradiated human lung fibroblasts
|
| Data processing |
Background corrected intensities were log2 transformed and median-normalized in BRB-ArrayTools, Version 3.7.0. Non-uniform outliers or features not significantly above background intensity in 20% or more of the hybridizations were filtered out.
|
| |
|
| Submission date |
Aug 13, 2008 |
| Last update date |
Jul 02, 2009 |
| Contact name |
Shanaz Adi Ghandhi |
| E-mail(s) |
[email protected]
|
| Phone |
212-3053911
|
| Organization name |
Columbia University Medical Center
|
| Department |
Center for Radiological Research
|
| Lab |
VC11-237
|
| Street address |
630, W 168th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE12435 |
IMR90 4hr bystander experiment 0.5Gy alpha particle strip dish format |
|
| Relations |
| Reanalysis of |
GSM526650 |
