|
| Status |
Public on Nov 05, 2012 |
| Title |
gastric cancer tissue sample 19 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
HKG19T
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: gastric cancer tissue sample 19
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Genomic DNA purification Kit (Qiagen, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
For hybridization, 1 microgram of tumor DNA and 1 microgram of gender matched reference DNA was labeled by random priming using Cy3-dCTP and Cy5- dCTP, respectively, using Bioprime Kit (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Three mixed normal blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Three mixed normal blood sample
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Genomic DNA purification Kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
For hybridization, 1 microgram of tumor DNA and 1 microgram of gender matched reference DNA was labeled by random priming using Cy3-dCTP and Cy5- dCTP, respectively, using Bioprime Kit (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
The hybridization solution was denatured for 10 min at 72°C and then incubated for 1 h at 37°C. Hybridization was performed for 48-72 h in a moist chamber on a slow rocking table. Next, Arrays were washed for 10 min in 50% formamide and 2 × SSC at 45°C, and 10 min in phosphate buffer at room temperature. Slides were mounted in mounting solutions containing 0.3 microgram/ml DAPI.
|
| Scan protocol |
Three single-color intensity images (DAPI, Cy3 and Cy5) were collected for each array using a charge coupled device camera.
|
| Data processing |
The UCSF SPOT software [PMID: 11827952] was used to automatically segment the spots based on the DAPI images, perform local background correction and calculate various measurement parameters, including log2 ratios of the total integrated Cy3 and Cy5 intensities for each spot.
|
| |
|
| Submission date |
Nov 06, 2011 |
| Last update date |
Nov 05, 2012 |
| Contact name |
Xin Chen |
| E-mail(s) |
[email protected]
|
| Phone |
(415) 502-6526
|
| Fax |
(415) 502-4332
|
| Organization name |
UCSF
|
| Street address |
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0446 |
| Country |
USA |
| |
|
| Platform ID |
GPL14846 |
| Series (1) |
| GSE33501 |
Gastric cancer tumor tissue samples and cell lines vs normal sample |
|
