|
Status |
Public on Sep 20, 2018 |
Title |
58A_tumor vs reference |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
tumor
|
Organism |
Homo sapiens |
Characteristics |
histology: squalors cell carcinoma egfr_mutation: NA kras_mutation: NA
|
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_252252210581_S01_CGH_105_Dec08_1_4.txt raw data file: US22502676_252252210581_S01_CGH_105_Dec08_1_4.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 |
|