|
| Status |
Public on Dec 31, 2013 |
| Title |
Colorectal mucosa #12 |
| Sample type |
RNA |
| |
|
| Source name |
Colorectal mucosa tissue, patient #12
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: colorectal cancer
duke's stage: II
tissue: matching normal colon mucosa
patient identifier: 12
|
| Growth protocol |
Human tissue samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from patient samples was purified by using the mirVana kit (Ambion, Life Technologies).
|
| Label |
Biotin
|
| Label protocol |
One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).
|
| |
|
| Hybridization protocol |
The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 2.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.
|
| Description |
exprs.12N
Colon mucosa tissue, patient #12
|
| Data processing |
Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.
|
| |
|
| Submission date |
May 17, 2013 |
| Last update date |
Dec 31, 2013 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (2) |
| GSE47074 |
Expression data for 4 colon tumor (Duke's stage II) /matching mucosa tissue pairs |
| GSE47076 |
Analysis of expression and epigenetic changes in human colorectal cancer and matching mucosa tissues |
|
