Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix 250K StyI SNP array data from PBMCs and cell lines of metastatic melanoma patients

ABSTRACT: Allele call files from on 250K StyI SNP array using DNA from 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells (CEL and CHP files provided). Analysis of the 250K StyI arrays was performed for 60 malignant melanoma cell lines derived from metastatic tumors of melanoma patients with GCOS and GTYPE (Affymetrix). In addition, DNA from peripheral blood mononuclear cells (PBMC) was available for 44 of the 60 samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Andreas Gast

PROVIDER: E-GEOD-17534 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

SNP array genomic profiling of PTCL NOS

Project description:DNA extracted from frozen tissue of 47 peripheral T-cell lymphomasânot otherwise specified [PTCL-NOS] was hybridized to 250k StyI SNP arrays 47 PTCL NOS compared to healthy reference DNA. DNA of PTCL NOS was extracted from frozen tissue blocks, DNA of healthy individual was extracted from peripheral blood mononuclear cells. Array hybridization was performed according to manufacturerÂ´s protocol.

2010-03-17 | E-GEOD-15842 | biostudies-arrayexpress

Affymetrix SNP array data for rhabdomyosarcoma samples

Project description:Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen tissues. To obtain a profile of copy number alterations in RMS, we studied 65 samples in 60 RMS cases. Other data of 38 samples are deposited in GSE41263: GSM1528059 GSM1528057 GSM1528061 GSM1528058 GSM1528054 GSM1528060 GSM1012723 GSM1012722 GSM1012746 GSM1528055 GSM1528056 GSM1530028 GSM1012751 GSM1012724 GSM1012726 GSM1012747 GSM1012725 GSM1012716 GSM1012735 GSM1012713 GSM1012736 GSM1012737 GSM1012738 GSM1012730 GSM1012739 GSM1012740 GSM1012750 GSM1012717 GSM1012718 GSM1012719 GSM1012741 GSM1012732 GSM1012715 GSM1012720 GSM1012742 GSM1012721 GSM1012743 GSM1012744 Copy number analysis of Affymetrix 250K or Cytoscan_HD SNP arrays was performed for 27 rhabdomyosarcoma samples.

2015-06-30 | E-GEOD-63891 | biostudies-arrayexpress

Virtual Karyotyping of Androgen Insensitive Prostate Cancer

Project description:We investigated chromosomal imbalances in samples from patients with androgen insensitive prostate cancer. 4 archival FFPE tumor samples were analyzed with Affymetrix 250K Nsp SNP microarrays and virtual-karyotype results for PTEN region were compared to PTEN deletion analysis by FISH.

2010-04-03 | E-GEOD-13439 | biostudies-arrayexpress

Affymetrix SNP array data for oral squamous cell carcinoma samples

Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. To identify genes responsible for OSCC development, we performed high-density single-nucleotide polymorphism array analysis and genome-wide gene expression profiling on OSCC tumors. These analyses identified "absent in melanoma (AIM2)" and "interferon-inducible gene 16 (IFI16)," mapped to the hematopoietic IFN-inducible nuclear proteins with 200-amino acid repeat (HIN-200) gene cluster in the amplified region of chromosome 1q23, with overexpression in OSCCs. AIM2 and IFI16 are cytoplasmic double-stranded DNA sensors for innate immunity and act as tumor suppressors in several human cancers. Knockdown of AIM2 or IFI16 in OSCC cells resulted in the suppression of cell growth and the induction of apoptosis, accompanied by the downregulation of NF-κB activation. Because all of the OSCC cell lines had impairment of p53 activity, wild-type p53 was introduced in p53-deficient OSCC cells, and as a result, the expression of wild-type p53 suppressed cell growth and induced apoptosis via suppression of NF-κB activity. Finally, the coexpression of AIM2 and IFI16 significantly enhanced cell growth in p53-deficient cells; in contrast, the expression of AIM2 and/or IFI16 in cells bearing wild-type p53 suppressed cell growth. Moreover, AIM2 and IFI16 synergistically enhanced NF-κB signaling in p53-deficient cells. Thus, expression of AIM2 and IFI16 may have oncogenic functions in OSCC cells inactivating p53 system. Copy number analysis of Affymetrix 250K SNP arrays was performed for 5 oral leukoplakia samples, 20 oral squamous cell carcinoma samples, and 8 oral squamous cell carcinoma cell lines.

2011-12-30 | E-GEOD-34507 | biostudies-arrayexpress

Affymetrix SNP array data for acute T-cell leukemia/lymphoma (ATL)

Project description:SNP array analysis was performed using 168 ATL specimens. To obtain genotypes and intensities for each SNP, Affymetrix 250K SNP arrays were performed for 168 ATL samples.

2012-02-23 | E-GEOD-33602 | biostudies-arrayexpress

Genotyping data from 54 patients with deficit schizophrenia

Project description:Schizophrenia is a severe psychiatric disease with complex etiology, affecting approximately one percent of the general population. Most genetic studies so far focused on disease association with common genetic variation such as single nucleotide polymorphisms, but recently it has become apparent that large-scale genomic copy number variants (CNVs) are involved in disease development as well. To assess the role of rare CNVs in schizophrenia, we screened 54 patients with deficit schizophrenia using Affymetrixâ GeneChip 250K SNP arrays. Keywords: genomic hybridisation We hybridized genomic DNA of 54 patients with deficit schizophrenia to Affymetrix' GeneChip 250K SNP (Nsp) arrays, and identified genome-wide CNV using the Copy Number Analyzer for Affymetrix GeneChip (CNAG v2.0) software, which uses a Hidden Markov Model (HMM) algorithm to calculate copy numbers.

2010-05-18 | E-GEOD-12714 | biostudies-arrayexpress

Detection of chromosomal aberrations in renal tumors by virtual karyotyping with SNP microarrays

Project description:Renal epithelial neoplasms have characteristic chromosomal imbalances that can be used for classification. We have previously shown that virtual karyotypes (v-karyotype) derived from SNP microarrays can be performed on formalin-fixed paraffin embedded (FFPE) tissue samples but a direct comparison with karyotypes obtained by conventional cytogenetics has not been done. 20 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays. 19 archival FFPE tumor samples were analyzed with Affymetrix 10K 2.0 or 250K Nsp SNP microarrays and virtual-karyotype results compared to those obtained by Cytogenetics.

2009-02-19 | E-GEOD-12808 | biostudies-arrayexpress

Affymetrix SNP array data for pulmonary adenocarcinomas with or without ALK fusion

Project description:ALK fusion positive tumor constitutes a unique entitiy in lung adenocarcionmas. We compared the allelokaryotypes of ALK fusion positive and negative tumors with SNP array to get insight into the difference of genomic background of them. Copy number analysis with Affymetrix 250K SNP arrays of 35 ALK fusion positive and 95 ALK fusion negative lung adenocarcinomas was performed with annonymous references.

2013-10-10 | E-GEOD-41536 | biostudies-arrayexpress

Affymetrix SNP array data for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS)

Project description:We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. In this study, we performed SNP array analysis to detect abnormal copy number of the cohesin genes. Copy number analysis by Affymetrix 50K or 250K SNP arrays was performed for 93 AML and 70 MDS tumor samples.

2013-07-16 | E-GEOD-47682 | biostudies-arrayexpress

Virtual-Karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms

Project description:Genetic lesions characteristic for RCC subtypes can be identified by virtual karyotyping with SNP microarrays. In this study, we examined whether virtual karyotypes could be used to better classify a cohort of morphologically challenging/unclassified RCC. Tumor resection specimens from 17 patients were profiled by virtual karyotyping with Affymetrix 10K 2.0 or 250K Nsp SNP Mapping arrays and were also evaluated independently by a panel of seven genito-urinary pathologists. Tumors were classified by the established pattern of genomic imbalances based on a reference cohort of 98 cases with classic morphology and compared to the morphologic diagnosis of the pathologist panel. In 3 cases, samples from areas with different morphologic appearance were also tested (n=5).

2009-03-13 | E-GEOD-14670 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data