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Series GSE157515 Query DataSets for GSE157515
Status Public on Dec 04, 2020
Title Array comparative genomic hybridization analysis of metastatic lung tumors
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary Comparative genomic hybridization analysis for detection of recurring gene copy number variation (CNV) among a set of lung cancer mestastatic brain tumors
DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled Agilent characterized normal human reference DNA
Overall design Twenty-seven de-identified, fresh-frozen surgically resected lung metastatic brain tumors were analyzed. The work was approved by the Wayne State University Institutional Review Board. Genomic DNA was isolated using the EZ1 Advanced workstation and DNA Tissue Kit (Qiagen, Germantown, MD). A Trinean DropSense96 Spectrophotometer (PerkinElmer, Waltham, MA) and TapeStation (Agilent, Santa Clara, CA) were used to measure DNA quantity and quality. aCGH analysis employed the Agilent SureScan platform and SurePrint G3 Cancer CGH+SNP (4x180K) microarrays following manufacturer’s recommendations. Agilent’s characterized normal human DNA (male or female, used according to patient gender) was the reference sample. Tumor sample DNA was labeled with Cy5 and normal reference DNA was labeled with Cy3. Probe fluorescence intensity data was extracted from scanned microarray images using Agilent Cytogenomics software. GC Correction, Diploid Peak Centralization (normalization) and Aberration Detection Method 2 (quality control) algorithms were also applied using this software. Aggregate data (all 27 samples) were analyzed using Nexus Copy Number software (Biodiscovery, El Segundo, CA).
Contributor(s) Bollig-Fischer A
Citation(s) 35006496
Submission date Sep 04, 2020
Last update date Feb 08, 2022
Contact name Aliccia Bollig-Fischer
Organization name Karmanos Cancer Institute & Wayne State University
Department Oncology
Street address 4100 John R
City Detroit
ZIP/Postal code 48201
Country USA
Platforms (1)
GPL16237 Agilent-030587 CCMC CGH plus SNP 180k Microarray
Samples (27)
GSM4769156 Fresh frozen metastatic tumor_1
GSM4769157 Fresh frozen metastatic tumor_2
GSM4769158 Fresh frozen metastatic tumor_3
BioProject PRJNA661554

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE157515_NEXUS_analysis_results.xlsx 21.4 Kb (ftp)(http) XLSX
GSE157515_RAW.tar 499.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
Processed data are available on Series record

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