Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA139979 | ENA |
REPOSITORIES: ENA
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Project description:In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays. Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations. DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). DNA from patient-matched Lung cancer and Blood cell lines NCI-H1395 and NCI-BL1395 were mixed to simulate tumor tissue with 30,50,70,100% cancer cells. The DNA ratio was adjusted to compensate for NCI-H1395 being nearly triploid. DNA was analyzed on Affymetrix SNP6.0 microarrays according to the manufacturer's protocol.
2011-09-08 | E-GEOD-29172 | biostudies-arrayexpress
Project description:Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient.
2011-09-09 | GSE26302 | GEO
Project description:Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient. Copy number analysis is presented on 12 colorectal cancer tumor samples and on in silico dilutions of a lung cancer cell line and its patient-matched blood cell line.
2011-09-08 | E-GEOD-26302 | biostudies-arrayexpress
Project description:In cancer, proto-oncogenes are often altered by genomic amplification. Recent studies have highlighted a role for PDGFRA as an oncogene in non-small cell lung cancer. To characterize 4q12 copy number status in NSCLC, both previously published (Weir et al. PMID 17982442) and unpublished Affymetrix 250K SNP array data for 733 NSCLC samples (628 primary samples, 105 cell lines) were evaluated for copy number aberrations. 4q12 amplifications overlapping the PDGFRA/KIT locus were observed in 31 (4.2%) NSCLC samples. SNP array and FISH analysis indicate that 4q12 is amplified in 3-7% of lung adenocarcinomas and 8-10% of lung squamous cell carcinomas. In addition, the NSCLC cell line NCI-H1703 exhibits focal amplification of PDGFRA and is dependent on PDGFRα activity for cell growth. Treatment of NCI-H1703 cells with PDGFRA-specific shRNAs or with the PDGFRα/KIT small molecule inhibitors imatinib or sunitinib leads to cell growth inhibition. However, these observations do not extend to NSCLC cell lines with lower-amplitude and broader gains of chromosome 4q. Together these observations implicate PDGFRA and KIT as potential oncogenes in NSCLC, but further study is needed to define the specific characteristics of those tumors that could respond to PDGFRα/KIT inhibitors.
2009-09-15 | GSE17429 | GEO
Project description:Intratumor mutational heterogeneity has been documented in primary non-small cell lung cancer. Here, we elucidate mechanisms of tumor evolution and heterogeneity in metastatic thoracic tumors (lung adenocarcinoma and thymic carcinoma) using whole-exome and transcriptome sequencing, SNP array for copy number alterations (CNA) and mass spectrometry-based quantitative proteomics of metastases obtained by rapid autopsy. APOBEC-mutagenesis, promoted by increased expression of APOBEC3 region transcripts and associated with a high-risk germline APOBEC3 variant, strongly correlated with mutational tumor heterogeneity. TP53 mutation status was associated with APOBEC hypermutator status. Interferon pathways were enriched in tumors with high APOBEC mutagenesis and IFN- induced expression of APOBEC3B in lung adenocarcinoma cells in culture suggesting a role for the immune microenvironment in the generation of mutational heterogeneity. CNA occurring late in tumor evolution correlated with downstream transcriptomic and proteomic heterogeneity, although global proteomic heterogeneity was significantly greater than transcriptomic and CNA heterogeneity. These results illustrate key mechanisms underlying multi-dimensional heterogeneity in metastatic thoracic tumors.
2019-05-07 | PXD012845 | Pride
Project description:Array comparative genomic hybridization characterization and comparison of cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel.
2005-11-23 | E-TABM-65 | biostudies-arrayexpress
Project description:In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays. We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246 Keywords: disease state analysis 21 replicates of HCC1143 (breast ductal carcinoma), 21 replicates of HCC1143BL (matched normal), 13 replicates of HCC1954 (breast ductal carcinoma), 11 replicates of HCC1954BL (matched normal), 1 replicate of NCI-H2347 (lung adenocarcinoma), 1 replicate of NCI-H2347BL (matched normal)
2008-11-13 | E-GEOD-13372 | biostudies-arrayexpress
Project description:Affymetrix SNP array data for lung cancer samples
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Project description:Initial screening for potential metastases suppressors down regulated by methylation was performed using lung cancer cell line models specific for site-specific metastasation. Gene expression profiling and qRT-PCR validations were conducted on tumor tissues from primary lung cancer (LC) and brain metastasis. HERC5 was further characterized for the methylation pattern. Three human lung cancer cell lines H1993, H1395 and were compared to the (SV40)-transformed human bronchial epithelial cell line BEAS-2B in order to find genes, which might be specifically involved in brain metastasis formation. The cell lines were treated with 5-Aza-2'-deoxycytidine in order to find genes potentially down regulated by methylation. The non-tumorigenic cell line BEAS-2B was used to control for stress response after the treatment with 5-Aza-2'-deoxycytidine.
2014-11-18 | E-GEOD-57492 | biostudies-arrayexpress
Project description:To investigate the tumor suppressor roleof CYB5R3 in lung cancer, we infected with adenoviral empty vector (EV) or CYB5R3 in NCI-H1299 cells.
2024-04-20 | GSE229344 | GEO