|
| Status |
Public on Dec 22, 2005 |
| Title |
colon normal vs carcinoma 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
microdissected colon normal cell
|
| Organism |
Homo sapiens |
| Characteristics |
human normal colon byopsies
|
| Biomaterial provider |
Asan medical center, Seoul, Korea.
|
| Treatment protocol |
microdissected normal colonic mucosa cells from formalin-fixed, paraffin-embedded sections.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Deparaffinized sections are incubated at 70 ℃ for 1 hr, treated Proteinase K and extracted with TRIzol. The first strand are synthesized using T7dT primers and the second strand are treated RNaseH and are synthesized using T3N6 primers. Then the double stranded DNA was applied PCR with T3 and T7 promoter primer. Following the PCR amplification, aRNA synthesis (in vitro transcription) was performed using an T7 transcription kit.
|
| Label |
cy3
|
| Label protocol |
The probe labeling was done using the amine-modified random primer aminoallyl method
|
| |
|
| Channel 2 |
| Source name |
microdissedted colon carcinoma cell
|
| Organism |
Homo sapiens |
| Characteristics |
human carcinoma colon byopsies
|
| Biomaterial provider |
Asan medical center, Seoul, Korea.
|
| Treatment protocol |
microdissected carcinoma colonic mucosa cells from formalin-fixed, paraffin-embedded sections.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Deparaffinized sections are incubated at 70 ℃ for 1 hr, treated Proteinase K and extracted with TRIzol. The first strand are synthesized using T7dT primers and the second strand are treated RNaseH and are synthesized using T3N6 primers. Then the double stranded DNA was applied PCR with T3 and T7 promoter primer. Following the PCR amplification, aRNA synthesis (in vitro transcription) was performed using an T7 transcription kit.
|
| Label |
cy5
|
| Label protocol |
The probe labeling was done using the amine-modified random primer aminoallyl method
|
| |
|
| |
| Hybridization protocol |
Hybridization was done with formamide hybridization buffer overnight in a 42 ℃ .
|
| Scan protocol |
The arrays were scanned with a GenePix 4000B scanner
|
| Description |
colon cancer, adenoma, microdissected using LCM, amplification
|
| Data processing |
The resulting images were analyzed using the ImaGeneTM 4.0 software.
|
| |
|
| Submission date |
Dec 19, 2005 |
| Last update date |
Dec 21, 2005 |
| Contact name |
Inchul Lee |
| E-mail(s) |
iclee@amc.seoul.kr
|
| Phone |
82-2-3010-4167
|
| URL |
http://iclee.amc.seoul.kr
|
| Organization name |
University of Ulsan College of Medicine
|
| Department |
Pathology
|
| Lab |
Disease Genomic Research Lab.
|
| Street address |
388-1 Poongnap-Dong, Songpa-Gu
|
| City |
Seoul |
| ZIP/Postal code |
138-736 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL1818 |
| Series (1) |
| GSE3880 |
Gene expression profiling in colonic adenoma and carcinoma in situ |
|
