Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Copy number variation comparison between control and CC214-2 resistant GBM39 xenografts

ABSTRACT: Here we present genome-wide copy number variation data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts, showing the absence of significant differences between the two groups, demonstrating that resistance to CC214-2 is due to adaptation rather than gene mutations. The genomic DNA extracted from the 4 xenografts samples was analysed with genome-wide Affymetrix SNP6.0 array

ORGANISM(S): Homo sapiens

SUBMITTER: Paul Mischel

PROVIDER: E-GEOD-53042 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene Expression analysis comparison between control and CC214-2 resistant GBM39 xenografts

Project description:Here we present gene expression analysis data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts, showing that the expressioin profiles of 88 genes are significantly different between the two groups. GBM39 primary neurospheres were cultured in standard cancer stem cell medium conditions and then were injected in the mice flanks to generate xenograft tissues. Mice carrying CC214-2 resistant xenografts were treated with a solution of CC214-2 once every two days, by gavage, for 40 days. Total RNA was extracted from GBM39 control and CC214-2 resistant xenografts using the Qiagen RNA micro kit protocol and analysed by Affymetrix U133 plus 2.0 array

2014-11-19 | E-GEOD-63387 | biostudies-arrayexpress

95 Breast Cancer Exome Affymetrix SNP6 Array Data

Project description:A standard Affymetrix SNP6.0 assay was performed on the tumour samples of patients where we have exonic sequence data from both the tumour and normal DNA of the same patients. The resulting cellularity, copy number and ploidy information generated helped to inform bespoke algorithms in analysing the sequence data.

2013-06-01 | E-MTAB-1110 | biostudies-arrayexpress

Affymetrix SNP array data for Ovarian Cancer Samples

Project description:This study aimed to generate a new panel of comprehensively, genomically characterized high-grade serous ovarian carcinoma (HGSOC) cell line and xenograft models. Multidimensional genomic data were generated and compared between cell lines/xenografts and the tumours they were derived from, indicating the cell lines/xenografts are highly similar to their patient-matched tumours. Cell line/xenograft data were also compared to TCGA ovarian tumours to show the cell lines are good models of clinical HGSOC. Affymetrix SNP 6 arrays were performed according to the manufacturer's instructions on genomic DNA extracted from i) tumour cells purified from ovarian tumour ascites, ii) established cell lines, iii) patient derived xenografts, and iv) lymphoblast lines. Evaluation of the similarity in copy number/methylation/gene expression/mutational profiles of cell lines/tumours/xenografts was performed.

2016-08-11 | E-GEOD-71522 | biostudies-arrayexpress

Pfizer Molecular Profile Data for Cell Lines

Project description:Baseline gene expression for cell lines growing in culture were measured by Affymetrix U133Plus2 arrays. Copy Number Variation for selected cell lines was also measured. Baseline gene expression for cell lines growing in culture were measured by Affymetrix U133Plus2 arrays. Three different sources of arrays were combined. Arrays were from Pfizer, Wyeth Breast Panel, and Wyeth NCI50 subset of NCI60 cell lines. CNV was determined by Affymetrix SNP6.0 arrays.

2012-01-19 | E-GEOD-34211 | biostudies-arrayexpress

High-resolution genome-wide copy number analysis of low grade serous ovarian tumours

Project description:Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays) and oncogenic RAS/RAF mutation status with clinical features and tumour progression. This study found that loss of the 9p and the CDKN2A locus with the most significantly enriched copy number aberration distinguishing serous border tumors from low grade serous carcinomas, suggesting this is a key step to tumor progression. Epithelial tissue from 57 serous borderline tumors (SBTs), 19 low grade serous carcinomas (LGSC)(data for 4 of the carcinomas have previously been submitted to GEO - Series GSE19539) and 355 high grade serous carinomas (HGSC)(TCGA, 2011; GSE19539; and 8 new) were analysed for copy number aberrations using Affymetrix SNP6.0 arrays and normalised SNP6.0 data. Stromal tissue from 38 SBT and 1 HGSC were analysed for copy number aberrations using Affymetrix SNP6.0 arrays. Matching lymphocyte DNA was availabe for 54 SBT, 3 LGSC and 1 HGSC. Sanger sequencing of KRAS, BRAF, NRAS, HRAS, ERBB2 and TP53 mutational hotspots was performed on the epithelial and stromal DNA. This information was then correlated with clinical features of the tumors.

2015-03-01 | E-GEOD-58579 | biostudies-arrayexpress

Transcriptional profiling by array of pancreatic ductal adenocarcinoma xenograft models

Project description:We generated novel patient derived xenograft (PDX) and cell line -derived xenograft models for pancreatic ductal adenocarcinoma (PDAC) which reflect different molecular subtypes. Pancreatic ductal adenocarcinoma is currently the tumor with the fourth highest mortality rate. Recently, subtypes of PDAC have been reported by Collisson et al (Nat. Med. 17(4) 2011. DOI: 10.1038/nm.2344). However current fetal calf serum (FCS) cultured cell lines do not accurately model these subtypes. We thus generated novel serum-free cell lines derived from primary patient xenografts. We here analyse the gene-expression profiles of the xenografts and the derived cell lines. We show that indeed three different subtypes can be separated in our models based on gene-expression data. Further, we identify upregulation of a drug-detoxification pathway specifically in xenografts and cell lines of one of the subtypes. These models and data will help to better understand inter-patient heterogeneity in PDAC and identify novel drug targets and diagnostic markers.

2016-01-12 | E-MTAB-4029 | biostudies-arrayexpress

Identification and molecular characterization of distinct glioblastoma cancer stem cell populations

Project description:Malignant glioblastoma (GBM) is a highly aggressive brain tumor with a dismal prognosis and limited therapeutic options. Genomic profiling of GBM samples in the TCGA database has identified four molecular subtypes (Proneural, Neural, Classical and Mesenchymal), which may arise from different glioblastoma stem-like cell (GSC) populations. In the present study, we identify two GSC populations that produce GBM tumors by subcutaneous and intracranial injection with identical histological features. Gene expression analysis revealed that xenografts of GSCs grown as spheroid cultures had a Classical molecular subtype similar to that of bulk tumor cells. In contrast xenografts of GSCs grown as adherent cultures on laminin-coated plates expressed a Mesenchymal gene signature. Adherent GSC-derived xenografts had high STAT3 and ANGPTL4 expression as well as enrichment for stem cell markers, transcriptional networks and pro-angiogenic markers characteristic of the Mesenchymal subtype. Examination of clinical samples from GBM patients showed that STAT3 expression was directly correlated with ANGPTL4 expression, and that increased expression of these genes correlated with poor patient survival and performance. A pharmacological STAT3 inhibitor abrogated STAT3 binding to the ANGPTL4 promoter and exhibited anticancer activity in vivo. Taken together, we identified two distinct GSC populations that produce histologically identical tumors but with very different gene expression patterns, and a STAT3/ ANGPTL4 pathway in glioblastoma that may serve as a target for therapeutic intervention. 2 samples of each variable were analyzed. Cells were cultured under normal adherent conditon (Bulk tumor cells), non-adherent plates with stem cell medium (Sp-GSC) or laminin-coated plates with stem cell medium (Ad-GSC). Xenografts were generated in NSG mice by subcutaneous inoculation.

2015-07-01 | E-GEOD-65576 | biostudies-arrayexpress

Mcl-1 is a key determinant of breast cancer cell survival [copy number]

Project description:Copy number profile of cultured Breast Cancer cell line measured by Affymetrix SNPs microarrays Whole genome copy number profile of 2 breast cancer cell lines were analyzed using Affymetrix SNP6.0 arrays

2015-08-07 | E-GEOD-66070 | biostudies-arrayexpress

SNP/CNV analysis in a breast cancer metastasis model

Project description:The Affymetrix SNP/CNV (SNP 6.0) platform was used to analyze a cell line model of lymph node metastasis comprised of a poorly metastatic MDA-MB-468GFP human breast adenocarcinoma cell line and its highly metastatic variant (468LN). DNA derived from 2 biological replicates of a highly metastatic (via lymph nodes) breast cancer cell line (468GFP-LN) was compared to 2 biological replicates of DNA prepared from the parental cell line, 468GFP.

2010-05-20 | E-GEOD-14867 | biostudies-arrayexpress

Expression Profiling and Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines

Project description:This SuperSeries is composed of the following subset Series: GSE25273: Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines GSE26088: Expression Profiling of Pancreatic Xenografts and Cell Lines Refer to individual Series

2011-12-15 | E-GEOD-26089 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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