|
| Status |
Public on Dec 20, 2011 |
| Title |
Human Rectal Adenoma Replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Human Rectal Adenoma Biopsy Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Adenoma
age: 52
Sex: Femaie
location: Rectal
|
| Treatment protocol |
Biopsy tissue was obtained by colonoscopy and stored at -80 ℃ until DNA extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
500 ng the reference commercial genomic DNA (promega) and the same amount of adenoma/carcinoma DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
|
| |
|
| Channel 2 |
| Source name |
Commercial Human Genomic DNA: Female
|
| Organism |
Homo sapiens |
| Characteristics |
company: Promega
catalog: G1521
|
| Treatment protocol |
Biopsy tissue was obtained by colonoscopy and stored at -80 ℃ until DNA extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen DNeasy Blood & Tissue Kit following manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
500 ng the reference commercial genomic DNA (promega) and the same amount of adenoma/carcinoma DNA were digested with Alu I (promega) and RSA I (promega) following Agilent's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol Version 6.1, August 2009)
The digested DNA fragments were labeled with cyanine-3 dUTP or cyanine-5 dUTP using Agilent Genomic DNA Enzymatic Labeling Kit (Agilent p/n 5190-0449). Then Microcon YM-30 (Millipore) was used to clear up the labeled probes.
|
| |
|
| |
| Hybridization protocol |
Reference DNA probes and adenoma/carcinoma DNA probes was combined and Human Cot-1 DNA (Invitrogen), 10 Blocking Agent and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, then samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.
|
| Scan protocol |
Scanned on an Agilent G2565BA Scanner
|
| Description |
Biological replicate 1 of 8.Human Rectal Adenoma Biopsy Tissue
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Agilent Genomic Workbench Lite Edition 6.5 was used to normalize and analyze the probe data.
|
| |
|
| Submission date |
Dec 15, 2011 |
| Last update date |
Dec 20, 2011 |
| Contact name |
Ming-Rong Wang |
| E-mail(s) |
wangmr2015@cicams.ac.cn
|
| Organization name |
Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
|
| Street address |
17 Panjiayuan Nanli, Chaoyang District, Beijing, China
|
| City |
Beijing |
| ZIP/Postal code |
100021 |
| Country |
China |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE34472 |
Human rectal adenoma (8 cases) vs. rectal carcinoma (8 cases) |
|
