|
| Status |
Public on Jul 06, 2018 |
| Title |
UT-SCC-87 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
head and neck cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UT-SCC-87
cancer type: Head and neck squamous cell carcinoma
gender: female
site-of-origin: tongue
|
| Treatment protocol |
No treatment was carried out for the cells
|
| Growth protocol |
The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine, 10% fetal bovine serum, non-essential amino acids solution, penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in an atmosphere of 5% CO2 (all reagents were purchased from Lonza BioWhittaker, Allendale, NJ, USA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the cell lines using a DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
An arrayCGH was carried out using an Agilent Human Genome CGH 244A Oligo Microarray. The samples were preprocessed according to an Agilent protocol (version 6.0, November 2008; Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis).
|
| |
|
| Channel 2 |
| Source name |
control female DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Treatment protocol |
No treatment was carried out for the cells
|
| Growth protocol |
The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine, 10% fetal bovine serum, non-essential amino acids solution, penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in an atmosphere of 5% CO2 (all reagents were purchased from Lonza BioWhittaker, Allendale, NJ, USA)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the cell lines using a DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
An arrayCGH was carried out using an Agilent Human Genome CGH 244A Oligo Microarray. The samples were preprocessed according to an Agilent protocol (version 6.0, November 2008; Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis).
|
| |
|
| |
| Hybridization protocol |
An arrayCGH was carried out using an Agilent Human Genome CGH 244A Oligo Microarray. The samples were preprocessed according to an Agilent protocol (version 6.0, November 2008; Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis).
|
| Scan protocol |
Scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Data processing |
Data were LOESS normalized, segmented with circular binary segmentation using an R package DNAcopy (1), and the regions with segment means more than two standard deviations from the mean (±0.67) of three self-versus-self control cell lines were called altered. The control cell lines are available under an ArrayExpress accession number E-MEXP-3415. The significance of frequent alterations was assessed with the GISTIC v.2.0.21 software (the parameters used were q < 0.25, tamp = 20.67, tdel = 2-0.67, cap = 2, join segment size = 20). Copy number polymorphic loci were excluded before data segmentation. The data were analyzed with the Anduril software framework (20). As due to the stringent criteria in arrayCGH analysis some previously reported alterations might be missed, the data were checked manually for consistency for selected regions with reported alterations.
The significance of frequent alterations was assessed with the GISTIC v.2.0.21 software (the parameters used were q < 0.25, tamp = 20.67, tdel = 2-0.67, cap = 2, join segment size = 20). Copy number polymorphic loci were excluded before data segmentation. The data were analyzed with the Anduril software framework (2).
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
Jul 06, 2018 |
| Contact name |
Outi Monni |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Helsinki
|
| Department |
Research Programs Unit
|
| Street address |
Haartmaninkatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL9128 |
| Series (2) |
| GSE107918 |
Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy [CGH] |
| GSE108062 |
Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy |
|
