|
| Status |
Public on Jan 01, 2008 |
| Title |
LoxIVMI |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
control
|
| Organism |
Homo sapiens |
| Characteristics |
melanoma
|
| Treatment protocol |
All cultures were fed with fresh medium the day before treatment and treated in exponential growth. Duplicate cultures were treated with 0 Gy (mock-irradiated) or with 8 Gy gamma-radiation delivered at 2.9 Gy/minute with a Mark I-68 137Cs source (J.L. Shepherd and Associates, Inc.)
|
| Growth protocol |
All cell lines were maintained in exponential growth in RPMI1640 medium supplemented with 10% FBS in a humidified 5%CO2 incubator at 37-degrees C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After irradiation, cultures were incubated at 37ºC for 4 hours, and RNA was extracted using a modified guanidine thiocyanate method (Chomczynski and Sacchi, 1987, PMID: 2440339) followed by purification with RNeasy columns (Qiagen, Valencia, CA)
|
| Label |
Cy5
|
| Label protocol |
single round of reverse transcription (Superscript II, Invitrogen) in the presence of fluorescent dUTP (Cy3 dUTP or Cy5 dUTP, NEN) as described in Amundson et al., 1999 (PMID: 10380890)
|
| |
|
| Channel 2 |
| Source name |
8 Gy plus 4 hours
|
| Organism |
Homo sapiens |
| Characteristics |
melanoma
|
| Treatment protocol |
All cultures were fed with fresh medium the day before treatment and treated in exponential growth. Duplicate cultures were treated with 0 Gy (mock-irradiated) or with 8 Gy gamma-radiation delivered at 2.9 Gy/minute with a Mark I-68 137Cs source (J.L. Shepherd and Associates, Inc.)
|
| Growth protocol |
All cell lines were maintained in exponential growth in RPMI1640 medium supplemented with 10% FBS in a humidified 5%CO2 incubator at 37-degrees C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After irradiation, cultures were incubated at 37ºC for 4 hours, and RNA was extracted using a modified guanidine thiocyanate method (Chomczynski and Sacchi, 1987, PMID: 2440339) followed by purification with RNeasy columns (Qiagen, Valencia, CA)
|
| Label |
Cy3
|
| Label protocol |
single round of reverse transcription (Superscript II, Invitrogen) in the presence of fluorescent dUTP (Cy3 dUTP or Cy5 dUTP, NEN) as described in Amundson et al., 1999 (PMID: 10380890)
|
| |
|
| |
| Hybridization protocol |
Probes and targets were hybridized together for 16-18 hours in 3x SSC at 65oC in the presence of blocking agents human CoT1 DNA, yeast tRNA and polydeoxyadenine. Hybridized slides were washed at room temperature twice in 0.5X SSC, 0.01% SDS for 5 minutes and once in 0.06X SSC for 5 minutes.
|
| Scan protocol |
Agilent Microarray Scanner, 100% PMT voltage, 10 uM resolution scans
|
| Description |
no additional information
|
| Data processing |
ArraySuite 2.1 extensions in the IPLab program (Scanalytics Inc., Fairfax, VA) as described in Chen et al., 2002 (PMID: 12217912)
|
| |
|
| Submission date |
Apr 12, 2007 |
| Last update date |
Nov 28, 2007 |
| Contact name |
Sally Amundson |
| E-mail(s) |
saa2108@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Center for Radiological Research
|
| Street address |
630 W. 168th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL5080 |
| Series (1) |
| GSE7505 |
Microarray profiles of radiation response in the NCI60 cell lines |
|
