|
| Status |
Public on Sep 20, 2018 |
| Title |
16B_tumor vs reference |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
histology: large cell carcinoma
egfr_mutation: WT
kras_mutation: positive
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10x10mu FFPE sections were cut for DNA isolation according to protocol by HF van Essen et al. (2012)
|
| Label |
Cy3
|
| Label protocol |
ENZO labeling for Cy3 and Cy5 following manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
reference
|
| Organism |
Homo sapiens |
| Characteristics |
histology: normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10x10mu FFPE sections were cut for DNA isolation according to protocol by HF van Essen et al. (2012)
|
| Label |
Cy5
|
| Label protocol |
ENZO labeling for Cy3 and Cy5 following manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following manufacturer's instructions
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) according to the specifications of the used platforms: 4x44k, 4x105k, 4x180k. All data was processed with HG18.
|
| Description |
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_3.txt
|
| Data processing |
Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction. Sample processed data reflects normalized log2 ratio representing test/reference (ch1/ch2) according to sample information.
|
| |
|
| Submission date |
Sep 18, 2016 |
| Last update date |
Sep 20, 2018 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16694 |
| Series (1) |
| GSE87058 |
Genome-wide copy number analysis by Array CGH for the analysis of clonality of thoracic tumors |
|
