|
| Status |
Public on Oct 30, 2017 |
| Title |
Wnt+ rectal tumor 1 [CGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Surgically removed rectum
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age: 50
tissue: Rectal adenocarcinoma
Stage: PT3N0
grade: 1
|
| Treatment protocol |
DNA was isolated using DNeasy tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol and labeled using BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using DNeasy blood & tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
Using Cy-5 and Cy-3 fluorescent dyes (GE Healthcare Lifesciences, NJ, USA) and BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA) as per manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Total DNA from matched gender normal
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using DNeasy blood & tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
Using Cy-5 and Cy-3 fluorescent dyes (GE Healthcare Lifesciences, NJ, USA) and BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA) as per manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized to HEEBO arrays and were incubated at 65 °C for 40 hours in rotating microarray hybridization oven. After hybridization, slides were washed sequential.
|
| Scan protocol |
Scanned on Genepix 4000B scanner.
Images were quantified using Spot Reader (Niles scientific, USA) software.
|
| Description |
T177
Gender matched control
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. snapCGH package in R was used.
|
| |
|
| Submission date |
Mar 17, 2016 |
| Last update date |
Oct 30, 2017 |
| Contact name |
Murali Dharan Bashyam |
| E-mail(s) |
bashyam@cdfd.org.in
|
| Organization name |
CDFD
|
| Street address |
MJ MARKET
|
| City |
HYDERABAD |
| State/province |
(Click to Select US State) |
| ZIP/Postal code |
500001 |
| Country |
India |
| |
|
| Platform ID |
GPL21604 |
| Series (2) |
| GSE79328 |
Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [CGH] |
| GSE79330 |
Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor |
|
