Affymetrix SNP array data for a melanoma lesion and a cellline derived thereof
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE35991 | GEO | 2012/06/18
SECONDARY ACCESSION(S): PRJNA151679
REPOSITORIES: GEO
Similar Datasets
Project description:Here we report on a bulk culture termed MCM1, which was derived from a 61 year old male diagnosed with a nodular melanoma stage T2a, N0. At passage three of culturing, DNA was isolated and Affymetrix SNP6.0 array hybridizations were performed. Cultured MCM1 cells revealed overall identical copy number gains and losses as compared with the primary patient-derived lesion and were therefore used in this study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA, which was extracted from a patient derived melanoma sample and from a cellline generated from the same melanoma sample at passage three.
2012-06-17 | E-GEOD-35991 | biostudies-arrayexpress
Project description:Here we report on the DNA profile of the isogenic melanoma cell lines MCM1, MCM1G, MCM1D and MCM1DLN. MCM1 cells are melanoma cells generated from a nodular melanoma stage T2a, N0 of a 61 year old male patient (see GSE35991). Two subclones were derived from MCM1 termed MCM1G and MCM1D. When transplanted into SCID mice, MCM1, MCM1G and MCM1D formed tumors at the injection site. However, only MCM1D metastasized to lymph nodes. Subsequently, MCM1D cells were isolated from the lymph nodes of SCID mice and termed MCM1DLN. Upon reimplantation into SCID mice, MCM1DLN cells showed a stable metastatic phenotype. Interestingly, MCM1D and MCM1DLN tumors showed reduced NLGN4X expression on the mRNA and protein level, suggesting a role in melanoma progression.
2020-03-16 | GSE96708 | GEO
Project description:Melanoma cell lines were genotyped to evaluate copy number differences between nodular melanoma (NM) and superficial spreading melanoma (SSM). Cell lines were also evaluated for copy number alterations in the SKP2/p27 axis. Affymetrix SNP arrays were performed according to manufacturer's instructions using DNA extracted from 18 melanoma cell lines and 4 melanocyte controls. Affymetrix SNP6.0 Array data for melanoma cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed on 18 melanoma cell lines including 2 primary superficial spreading melanoma, 2 primary nodular melanoma, 2 metastatic nodular melanoma, and 12 metastatic cell lines. Four melanocyte control lines were also evaluated including 2 immortalized melanocyte cell lines (Hermes 1 and 2B) and 2 normal melanocyte lines cultured from neonatal foreskin (HEM-N and HEM-LP) that were used to construct the baseline for copy number analysis.
2010-10-21 | E-GEOD-22305 | biostudies-arrayexpress
Project description:Cytogenetic profiles of 50 meningiomas using high-density GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in the tumor tissues and in the peripheral blood of the same patients. A total of two hundred 500k arrays (100 tumor samples and 100 blood samples) and 14 SNP6.0 arrays (7 tumour samples and 7 peripheral blood samples) were studied to explore the most common recurrent chromosomal abnormalities (gains and losses) in meningiomas. Our results confirm that del(22q) (52%) and del(1p) (16%) (common deleted regions: 22q11.21-22q13.3. and 1p31.2-p36.33) are the most frequent abnormalities. Additionally, recurrent monosomy 14 (8%), del(6p) (10%), del(7p) (10%) and del(19p) (6%) were also observed, while copy number variation (CNV) patterns consistent with recurrent chromosome gains, gene amplification was absent or rare. Based on their overall SNP profiles meningiomas could be classified into: i) diploid cases, ii) meningiomas with a single chromosome change (e.g. monosomy 22/del(22q) and iii) tumours with ≥2 altered chromosomes.
2012-11-30 | GSE42624 | GEO
Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the Cyto2.7M data. GEO submission, GSE37977 contains the SNP6.0 data.
2012-11-26 | GSE37978 | GEO
Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the SNP6.0 data. GEO submission, GSE37978 contains the Cyto2.7M data.
2012-11-26 | GSE37977 | GEO
Project description:Idiopathic nodular mesangial sclerosis, also called idiopathic nodular glomerulosclerosis (ING) is a rare clinical entity with unclear pathogenesis. The hallmark of this disease is the presence of nodular mesangial sclerosis on histology without clinical evidence of diabetes mellitus or other predisposing diagnoses. To achieve insights into its pathogenesis, we queried the clinical, histopathologic and transcriptomic features of ING and nodular diabetic nephropathy (DN)
2020-12-09 | GSE162830 | GEO
Project description:We have analyzed the genome-wide patterns of gene expression with DNA microarrays in skin biopsies from 34 subjects: 17 patients with SSc with diffuse scleroderma (dSSc), 7 patients with SSc with limited scleroderma (lSSc), 3 patients with morphea and 6 healthy controls. In total, 61 skin biopsies were analyzed. The addition of 14 technical replicates resulted in a total of 75 microarray hybridizations. The Intrinsic_scleroderma_genes.txt supplementary file lists the 995 genes with the most consistent expression between each forearm-back pair and technical replicates, but with the highest variance across all samples analyzed. An intrinsic gene identifier algorithm was used to select a set of intrinsic scleroderma genes. A total of 34 experimental groups were defined, each representing the 34 different subjects in our study. Replicate hybridizations for a given patient were assigned to the same experimental group. Each gene was analyzed and assigned a score that is inversely related to how intrinsic the gene's expression is across the samples analyzed. The analysis was repeated on randomized data in order to estimate a False Discovery Rate (FDR). An intrinsic score of 0.3 selected 995 genes with an FDR of 4% (39 ± 7 genes) while retaining reproducible clustering of technical replicates. Keywords: global gene expression profiling using Agilent Whole Human genome oligo arrays common reference design; we used Universal Human Reference RNA (Stratagene) as our reference for every array; For every hybridization sample RNA was always labeled with Cy3, and reference RNA was always labeled with Cy5; Microarray hybridizations were performed for 61 RNA samples from 34 subjects resulting 61 hybridizations. Fourteen replicate hybridizations were added, resulting in a total of 75 microarray hybridizations.
2010-05-26 | E-GEOD-9285 | biostudies-arrayexpress
Project description:In this study we have identified a new morphological pattern in IMPC defined by the presence of numerous bi-nucleated cells, related to abnormal expression of genes involved in regulation of mitosis. We also demonstrated that IMPC presented tight and adherens junctions proteins expression modifications that could participate to their clinical behavior. We showed that IMPC was associated with a specific genomic profile compared to ER+ grade-matched IDC consisting of gains of 17q, high rates of 17q23 and 17q12 ERBB2 amplifications, losses of heterozygosity of 6q. The putative role of the genes located in this 6q LOH should be further investigated in order to determine if they could play a role in the presence of numerous bi-nucleated cells and inverted polarity of IMPC cells. In addition, we identified two genomic IMPC subsets: the first characterized by numerous amplicons with frequently near-tetraploid cells and the second, associated with different complex gains and losses in addition to 8q gains and 16q losses, and predominantly composed of near-diploïd cells. The observation of two genomic subsets within the IMPC entity suggests the existence of two possible oncogenic mechanisms leading to the development of a single disease. Phenotypical analysis was combined with copy number, genotyping (SNP6.0 Affymetrix) and transcriptomic analyses in a series of 39 pure IMPC. The results were compared to those of 27 ER and grade-matched invasive ductal carcinomas (IDC).
2014-04-01 | E-GEOD-37035 | biostudies-arrayexpress