|
| Status |
Public on Apr 04, 2011 |
| Title |
HSF_rho0_4 h_control_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Skin fibroblast, depleted mitochondria, control, 4 hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line origin: DWFb1
cell type: human skin fibroblast immortalized with SV40 TAg
mitochondrial status: depleted
treatment: none
treatment time: 4 hours
|
| 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 |
Human skin fibroblasts (HSF) immortalized by SV40 T antigen were maintained in a 4.5 g/L glucose DMEM with 4 mM L-glutamine and 100 mg/L sodium pyruvate supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 microg/ml streptomycin. Mitochondrial (mt) DNA-depleted rho0 cells were established from the corresponding parent rho+cells using prolonged exposure to ethidium bromide (50 ng/ml) in growth medium supplemented with 50 microg/ml uridine.
|
| 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 300 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
1.5 ug of cRNA (>9 pmol Cy3 per ug 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 |
HSFrhozero_4HR_CX2
|
| 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 |
Oct 26, 2010 |
| Last update date |
Apr 04, 2011 |
| Contact name |
Shanaz Adi Ghandhi |
| E-mail(s) |
shanazg@gmail.com
|
| 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) |
| GSE24945 |
Human skin fibroblast mitochondrial depletion, 0.5 Gy alpha-particle |
|
