|
| Status |
Public on Nov 01, 2017 |
| Title |
high grade MEC 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 43
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
6 sections of 10 μm were deparaffinized, macro-dissected and incubated with 1M sodium thiocyanate at 38°C, for 16 h, followed by a proteinase K treatment at 55°C for another 16 h. DNA was isolated using the QIAmp DNA micro-kit (Qiagen, Hilden, Germany). Purity and quantity of the DNA samples was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham, USA).
|
| Label |
Cy5
|
| Label protocol |
Equal amounts (500 ng) of DNA from MEC samples and from matching normal salivary gland tissue were labeled with cyanine 3’-dUTP (Cy3) and cyanine 5’-dUTP (Cy5) nucleotides (Enzo Life Sciences, Farmingdale, NY, USA). Free nucleotides were removed using the MinElute PCR Purification Kit (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
normal salivary gland tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 43
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
6 sections of 10 μm were deparaffinized, macro-dissected and incubated with 1M sodium thiocyanate at 38°C, for 16 h, followed by a proteinase K treatment at 55°C for another 16 h. DNA was isolated using the QIAmp DNA micro-kit (Qiagen, Hilden, Germany). Purity and quantity of the DNA samples was measured using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham, USA).
|
| Label |
Cy3
|
| Label protocol |
Equal amounts (500 ng) of DNA from MEC samples and from matching normal salivary gland tissue were labeled with cyanine 3’-dUTP (Cy3) and cyanine 5’-dUTP (Cy5) nucleotides (Enzo Life Sciences, Farmingdale, NY, USA). Free nucleotides were removed using the MinElute PCR Purification Kit (Qiagen).
|
| |
|
| |
| Hybridization protocol |
Oligonucleotide arrayCGH was performed using the SurePrint G3 Human CGH Microarray Kit, containing 180880 in situ synthesized 60-mer oligonucleotides representing 169793 unique chromosomal locations evenly distributed over the genome (space ~17kb) and 4548 additional unique oligonucleotides, located at 238 of the Cancer Census genes (4x180K array, Agilent Technologies, Palo Alto, CA, USA). The exact array design can be found online in the Gene Expression Omnibus (GEO) GPL8687
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) according to the specifications of the used platform 4x180k. All data was processed with HG18.
|
| Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction.
|
| |
|
| Submission date |
Sep 26, 2016 |
| Last update date |
Nov 01, 2017 |
| Contact name |
Johannes Hendrikus Muatse |
| E-mail(s) |
[email protected]
|
| Organization name |
VU University medical center
|
| Department |
Department of Oral and Maxillofacial Surgery and Oral Pathology
|
| Street address |
Gustav Mahlerlaan 81
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 LA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8687 |
| Series (1) |
| GSE87353 |
High number of chromosomal copy number aberrations inversely relates to t(11;19)(q21;p13) translocation status in Mucoepidermoid Carcinoma of the Salivary Glands |
|
