|
| Status |
Public on Feb 14, 2013 |
| Title |
Normal colon tissue, NBRCCC036 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Normal colon tissue, recurrence-free group
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal colon adjacent to colon cancer
age: 57 yr
relapse status: recurrence-free
|
| Growth protocol |
Tissues were obtained and immediately snap-frozen in liquid nitrogen and stored.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was prepared using the phenol/chloroform/isoamyl alcohol method.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.
|
| |
|
| Channel 2 |
| Source name |
Commerical gDNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Control DNA: Promega #G1471 (male) and #G1521 (female).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed according to Agilent's recommended protocol. Briefly, 5 μg gDNA was digested with restriction enzymes Alu I (Promega) and Rsa I (Promega), and was labeled fluorescently using the Agilent DNA Labeling kit (Agilent). Patients' gDNAs were labeled with Cy5 and commercial gDNAs as a reference were labeled with Cy3 dUTP, respectively.
|
| |
|
| |
| Hybridization protocol |
The labeled DNA was denatured and pre-annealed with Cot-1 DNA and Agilent blocking reagent and hybridized for 40 hours at 20 rpm in an Agilent hybridization oven.
|
| Scan protocol |
The arrays were scanned at 5-㎛ resolution using an Agilent scanner (Agilent), and the image was analyzed with Feature Extraction Software 9.1.1.1.
Images were quantified using Agilent Feature Extraction Software.
|
| Description |
NBRCCC036
|
| Data processing |
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Feb 13, 2013 |
| Last update date |
Feb 14, 2013 |
| Contact name |
Park Chan Hee |
| E-mail(s) |
haema@yuhs.ac
|
| Phone |
80222277650
|
| Organization name |
Cancer Metastasis Research Center
|
| Street address |
Shinchondong 134
|
| City |
Seodaemun-gu |
| State/province |
Seoul |
| ZIP/Postal code |
120-752 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE44300 |
DNA profiling of human normal colon tissues |
|
