Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A framework for identification of actionable cancer genome dependencies in small cell lung cancer

ABSTRACT: We analyzed copy numbers of 60 SCLC cell lines using 6.0 SNP-arrays. For a subgroup of 36 cell lines, previously published copy number data was utilized. CEL and SEG files are included for all cell lines, for which copy number data were not publicly available.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40142 | GEO | 2012/09/21

SECONDARY ACCESSION(S): PRJNA172918

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A framework for identification of actionable cancer genome dependencies in small cell lung cancer

Project description:We analyzed copy numbers of 60 SCLC cell lines using 6.0 SNP-arrays. For a subgroup of 36 cell lines, previously published copy number data was utilized. CEL and SEG files are included for all cell lines, for which copy number data were not publicly available. DNA was extracted from SCLC cell lines and copy number data was generated for all samples

2012-09-21 | E-GEOD-40142 | biostudies-arrayexpress

Affymetrix SNP6.0 data for human induced pluripotent stem cells (hiPSCs), human Fibroblasts, and human embryonic stem cells (hESCs)

Project description:In this study, copy number variations of hiPSCs were compared to their parental fibroblast lines and hESCs to assess the level of DNA damage incurred due to the process of reprogramming of somatic cells. Higher levels of copy number changes were observed in hiPSCs (especially in early passage hiPSCs) compared to the other cell types. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from in vitro cultured cells. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 35 hiPSC samples, 2 hESC samples, and 5 fibroblast samples. Other hESC and the reference Hapmap sample CEL files were obtained from Narva et al. 2010, Nat. Biotech., GEO accession code GSE15097 (see readme file below for details).

2011-01-31 | E-GEOD-26173 | biostudies-arrayexpress

A framework for identification of actionable cancer genome dependencies in small cell lung cancer.

Project description: Not available

| S-EPMC3479457 | biostudies-literature

Genotyping of human SCLC cell line profiling on 100K arrays

Project description:Twenty three small-cell lung carcinoma (SCLC) cell lines from ATCC profiled on 100K genotyping arrays Experiment Overall Design: The cell lines were run on 100K SNP genotyping arrays to obtain copy number information

2008-06-15 | E-GEOD-7068 | biostudies-arrayexpress

High-resolution mapping of copy-number alterations with massively parallel sequencing

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

2008-11-14 | GSE13372 | GEO

Affymetrix SNP 6.0 profiles of 10 Human B-NHL lines

Project description:B-cell Non Hodgkin Lymphoma are a heterogenous group chracterized by a variety of genetic changes, including translocations, deletions and amplifications. Here we analyzed 10 B-NHL lines by Affymetrix SNP 6.0 to detect copy number changes. Specifically, we aim to identify cell lines suitable for testing the consequences of acute reintroduction of candidate tumor suppressor genes as they harbor deletions which include the candidate gene(s). 10 BNHL cell lines were grown in standard cell culture conditions. Genomic DNA was exptracted from frozen pellets and analyzed for copy number variations with Affymetrix SNP 6.0 Arrays

2012-04-02 | E-GEOD-36967 | biostudies-arrayexpress

Affymetrix SNP 6.0 array data from neuroendocrine primary tumor and its metastasis

Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.

2012-07-16 | E-GEOD-39371 | biostudies-arrayexpress

Affymetrix SNP 6.0 profiles of 10 Human B-NHL lines

2012-04-03 | GSE36967 | GEO

Array CGH-based Characterization of Genetic Alterations in Pulmonary Neuroendocrine Tumors

Project description:The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on Array Comparative Genomic Hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestinal (GI) carcinoids. In contrast to the relatively stable karyotypes of carcinoid tumors, the karyotypes of SCLC tumors and cell lines were highly aberrant. High copy number (CN) gains were detected in SCLC tumors and cell lines in cytogenetic bands encoding JAK2, FGFR1, and MYC family members. In some of those samples, the CN of these genes exceeded 100, suggesting that they could represent driver alterations and potential drug targets in subgroups of SCLC patients. Recurrent CN alterations of a total of 203 genes, including the RB1 gene, and 59 microRNAs, most of which locate in the DLK1-DIO3 domain, were observed in SCLC tumors, bronchial carcinoids and carcinoids of GI origin; in contrast, CN alterations of the TP53 gene and the MYC family members were observed more frequently in SCLC. These findings suggest the existence of partially shared tumor-specific CN alterations in these tumors. Furthermore, we demonstrated that the aCGH profile of SCLC cell lines highly resemble that of clinical SCLC specimens. Finally, by analyzing potential drug targets, we provide a genomics based rationale for targeting the AKT-mTOR and apoptosis pathways in SCLC.

2010-04-22 | GSE21468 | GEO

Affymetrix SNP6.0 on Ollier disease-related tumors

Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.

2011-08-26 | GSE22984 | GEO

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