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| Status |
Public on Aug 02, 2023 |
| Title |
ACC63 (Agilent) |
| Sample type |
genomic |
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| Channel 1 |
| Source name |
adenoid cystic carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: adenoid cystic carcinoma
obtained from: Sahlgrenska University Hospital
tumor grade: 1
age: 74
gender: female
tumor material: FF
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| Treatment protocol |
Fresh frozen (FF) tumor material from 58 ACCs and formalin-fixed paraffin-embedded (FFPE) tumor material from 42 ACCs were obtained from Sahlgrenska university hospital, Gothenburg university, Sweden; MD Anderson Cancer Center, University of Texas, US; the University of Virginia Hospital, Virginia, US; Hamburg University Medical Centre, Hamburg, Deutschland, the Portuguese Institute of Oncology, Lisboa, Portugal; and Icahn School of Medicine at Mount Sinai, New York, US. Tumors were classified according to the WHO histological classification of salivary gland tumors and graded as tumors with no solid component (grade 1), <30% solid component (grade 2), and ≥30% solid component (grade 3).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FF and FFPE tumor specimens using the Qiagen DNeasy Blood & Tissue Kit and QIAamp DNA FFPE Tissue Kit respectively (Qiagen GmbH, Hilden, Germany).
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| Label |
Cy5
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| Label protocol |
Genomic tumor DNA and sex-matched reference normal DNA (pooled peripheral blood cells from 5 normal female and male genomes) were labeled with Cy5-dUTP and Cy3-dUTP (Agilent).
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| Channel 2 |
| Source name |
normal tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: normal tissue
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| Treatment protocol |
Fresh frozen (FF) tumor material from 58 ACCs and formalin-fixed paraffin-embedded (FFPE) tumor material from 42 ACCs were obtained from Sahlgrenska university hospital, Gothenburg university, Sweden; MD Anderson Cancer Center, University of Texas, US; the University of Virginia Hospital, Virginia, US; Hamburg University Medical Centre, Hamburg, Deutschland, the Portuguese Institute of Oncology, Lisboa, Portugal; and Icahn School of Medicine at Mount Sinai, New York, US. Tumors were classified according to the WHO histological classification of salivary gland tumors and graded as tumors with no solid component (grade 1), <30% solid component (grade 2), and ≥30% solid component (grade 3).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from FF and FFPE tumor specimens using the Qiagen DNeasy Blood & Tissue Kit and QIAamp DNA FFPE Tissue Kit respectively (Qiagen GmbH, Hilden, Germany).
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| Label |
Cy3
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| Label protocol |
Genomic tumor DNA and sex-matched reference normal DNA (pooled peripheral blood cells from 5 normal female and male genomes) were labeled with Cy5-dUTP and Cy3-dUTP (Agilent).
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| Hybridization protocol |
Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent SurePrint G3 Human CGH Microarray 4X180K and Human Genome CGH Microarray 244K) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.
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| Scan protocol |
The arrays were scanned on an Agilent Microarray Confocal Scanner (G2506B) and the images were quantified with Agilent Feature Extraction Software (v.12.0.1.1) using the intensity-dependent linear normalization method.
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| Description |
GPL4091_TMA.txt
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| Data processing |
Data analysis was carried out using Nexus Copy Number software v.8.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the FASST2 segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to P=1.0E-8 for FFPE and P=10E-6 for FF and the Log2 ratio thresholds for gain/loss were set to 0.25/−0.2 for FF and 0.3/-0.3 for FFPE; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.
*TMA.txt processed data files report normalized log10 ratio (Cy5/Cy3) representing tumor DNA/normal DNA
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| Submission date |
Jun 25, 2020 |
| Last update date |
Aug 02, 2023 |
| Contact name |
Mattias Andersson |
| Organization name |
University of Gothenburg
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| Department |
Sahlgrenska Cancer Center
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| Lab |
Stenman
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| Street address |
Medicinaregatan 1F
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| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
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| Platform ID |
GPL4091 |
| Series (2) |
| GSE153228 |
Integrated copy number and transcriptomic profiling reveal novel oncogenic drivers and clinically significant biomarkers in adenoid cystic carcinoma [Agilent] |
| GSE153230 |
Integrated copy number and transcriptomic profiling reveal novel oncogenic drivers and clinically significant biomarkers in adenoid cystic carcinoma |
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| Relations |
| Reanalysis of |
GSM855767 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4636289_C1096.txt.gz |
61.4 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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