|
| Status |
Public on Dec 31, 2011 |
| Title |
Patient 3 microGIST |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
microGIST FFPE tumor genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Gastrointestinal stroml tumor cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp® DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) for manual microdissection samples and PicoPure® DNA Extraction Kit (Arcturus Bioscience, Mountain View, CA, USA) for laser microdissection samples, respectively, in accordance with the manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA ULS Labeling Kit (Agilent Technologies) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol; Version 3.1, August 2009; Manual Part Number G4410-90020
|
| |
|
| Channel 2 |
| Source name |
FFPE normal tissue DNA from the same patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: GI tract smooth muscle cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp® DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) for manual microdissection samples and PicoPure® DNA Extraction Kit (Arcturus Bioscience, Mountain View, CA, USA) for laser microdissection samples, respectively, in accordance with the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA ULS Labeling Kit (Agilent Technologies) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) Protocol; Version 3.1, August 2009; Manual Part Number G4410-90020
|
| |
|
| |
| Hybridization protocol |
Agilent Oligo aCGH Hybridization Kit (p/n 5188-5220) and Agilent Oligo aCGH Wash Buffers (p/n 5188-5226) were used according to manufacturer protocols.
|
| Scan protocol |
Agilent G2565BA Scanner was used according to manufacturer protocol. Data extraction has been performed with Agilent G2567AA Feature Extraction Software v10.5.1.1.
|
| Data processing |
Feature extraction data was obtained using Agilent G2567AA Feature Extraction Software (v10.5.1.1), normalized using LOcally-WEighted regression Scatterplot Smoother
|
| |
|
| Submission date |
Apr 07, 2011 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Cher-wei Liang |
| E-mail(s) |
[email protected]
|
| Organization name |
National Taiwan University Hospital
|
| Department |
Pathology
|
| Street address |
7 Chung-Shan S. Rd.
|
| City |
Taipei |
| ZIP/Postal code |
10002 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13346 |
| Series (1) |
| GSE28469 |
Array comparative genomic hybridization (aCGH) study of formalin-fixed paraffin-embedded (FFPE) small gastrointestinal stromal tumors (GISTs) less than 1 cm in greatest diameter (microGISTs) |
|
