|
| Status |
Public on Oct 08, 2007 |
| Title |
1M-57_2_expression |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
1M-57_2
|
| Organism |
Homo sapiens |
| Characteristics |
HCT116+chr3, clone 1M-57
|
| Treatment protocol |
methotrexate resistant colony derived from clone 1M-57
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
Cy3
|
| Label protocol |
Total RNA (20 µg) was reverse transcribed in the presence of aminoallyl-dUTP followed by coupling with Cy3 dye.
|
| |
|
| Channel 2 |
| Source name |
HCT116+chr3, clone 1M-57
|
| Organism |
Homo sapiens |
| Characteristics |
HCT116+chr3, clone 1M-57
|
| Treatment protocol |
without methotrexate treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
Cy5
|
| Label protocol |
Total RNA (20 µg) was reverse transcribed in the presence of aminoallyl-dUTP followed by coupling with Cy5 dye.
|
| |
|
| |
| Hybridization protocol |
Labeled test and reference cDNAs together with 100 µg human Cot-1 DNA were hybridized overnight at 37º C using Genomic Solutions GeneTAC Hybridization Station. Hybridizations were carried out on arrays of printed long oligonucleotides (70mers) containing 21,000 elements (Operon V2.0, printed in the J. David Gladstone Institutes, Genomics Core Laboratory).
|
| Scan protocol |
Slides were scanned with an Axon scanner.
|
| Description |
Image analysis was performed using UCSF Spot (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332).
|
| Data processing |
Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. Expression data were filtered to exclude all spots with foreground intensity below 500 units in the Cy3 or Cy5 channel and were subsequently median normalized.
|
| |
|
| Submission date |
Nov 21, 2006 |
| Last update date |
Oct 08, 2007 |
| Contact name |
Donna G Albertson |
| E-mail(s) |
albertson@ucsf.edu
|
| Phone |
415-502-8463
|
| Organization name |
University of California San Francisco
|
| Department |
Comprihensive Cancer Center
|
| Street address |
Box 0808
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0808 |
| Country |
USA |
| |
|
| Platform ID |
GPL4419 |
| Series (1) |
| GSE6361 |
Genome position and gene amplification - expressional profiling of methotrexate resistant colonies |
|
