|
| Status |
Public on Oct 30, 2017 |
| Title |
Wnt+ rectal tumor 15 [GE] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Surgically removed rectum
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
age: 26
tissue: Rectal adenocarcinoma
Stage: PTXN0
grade: 1
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
pooled 11 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Universal reference RNA
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505B scanner
Images were quantified using Agilent Feature Extraction Software (version v10.7)
|
| Description |
2229
Microsatellite stable Wnt+ rectal adenocarcinoma
|
| Data processing |
Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization
|
| |
|
| Submission date |
Feb 24, 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 |
GPL4133 |
| Series (2) |
| GSE78250 |
Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor [GE] |
| GSE79330 |
Early-onset sporadic rectal cancer : Wnt- vs. Wnt+ rectal tumor |
|
