|
| Status |
Public on May 02, 2011 |
| Title |
Primary fibroblast_10Gy24hr_5 |
| Sample type |
RNA |
| |
|
| Source name |
Skin punch biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblast
individual: 32
control or radiosensitive: CL
dose: 10
hour: 24
|
| Treatment protocol |
Approximately 1x 108 lymphoblast cells or 1x107 primary fibroblasts were irradiated with 0 Gy, 2 Gy or 10 Gy IR at RT using a Cs137 source with a dose rate of 1.7min/Gy
|
| Growth protocol |
EBV-transformed lymphoblast cell lines were grown in RPMI medium and fibroblasts in DMEM medium, both supplemented with 10% FBS and gentamicin and incubated in a 5% CO2 humidified incubator at 37oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown to a density of 1 x 107, pelleted, resuspended in 3 ml PBS and an equal volume of Trizol (Invitrogen, Carlsbad, CA, USA) was added, mixed and the aqueous layer was mixed with and equal volume of 70 percent ethanol and added onto a RNeasy column (Qiagen, Venlo, The Netherlands). The RNA extraction was continued by using the RNeasy method as per manufactures recommendation except starting with the addition of the sample of Buffer RW1. RNA concentration and integrity was determined by analysing on a bioanalyzer (Agilent, Santa Clara, CA, USA). RNA was determined to be high enough quality if a minimum RIN of 8.5 was obtained.
|
| Label |
biotin
|
| Label protocol |
Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).
|
| |
|
| Hybridization protocol |
Followed the exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix).
|
| Scan protocol |
Chips were scanned with a Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Data were processed using aroma.affymetrix (R package). RMA background correction were applied to probe intensities, gene level expression were quantile normalized. Only the Core probesets have been used for analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Jan 24, 2011 |
| Last update date |
Feb 15, 2012 |
| Contact name |
Jason Li |
| E-mail(s) |
jason.li@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
St Andrews Pl
|
| City |
East Melbourne |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE26841 |
The response to ionizing radiation at the exon level |
|
