|
| Status |
Public on Aug 31, 2012 |
| Title |
Human Colon Tumor Tissue 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human Colon Tumor Tissue 1
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age (y): 52
braf/kras mutation: Wild type
tumor location: left
tissue: colon tumor
pathology: TV-ad potion
cimp: CIMP-N
|
| Growth protocol |
A total of 84 colorectal tumor specimens were obtained from endoscopic biopsy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.
|
| Label |
Cy5
|
| Label protocol |
Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
Human Genomic DNA (Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Human Genomic DNA (Promega)
|
| Growth protocol |
A total of 84 colorectal tumor specimens were obtained from endoscopic biopsy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh frozen tissue specimens using the standard phenol-chloroform procedure.
|
| Label |
Cy3
|
| Label protocol |
Five hundred nanograms of genomic DNA was labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent technologies) according to manufacturer's instruction. Tumor DNA was labeled with Cy5 and gender-matched reference DNA (Promega) was labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using an aCGH/ChIP-on-chip Hybridization Kit (Agilent technologies) according to manufacturer's instruction.
|
| Scan protocol |
Array was scanned with an Agilent G2565BA Microarray Scanner.
|
| Data processing |
Agilent Feature Extraction Software (v 9.5) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Feb 01, 2012 |
| Last update date |
Aug 31, 2012 |
| Contact name |
Eiichiro Yamamoto |
| E-mail(s) |
eiichiro@xa3.so-net.ne.jp
|
| Phone |
+81-11-611-2111
|
| Organization name |
Sapporo medical university
|
| Street address |
South-1, West-16, Chuo-ku
|
| City |
Sapporo |
| ZIP/Postal code |
060-8543 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE35476 |
Array CGH analysis of human colorectal tumors |
| GSE35534 |
Genome-wide copy number aberrations and methylation profiles in human colorectal lesions |
|
