Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive genomic profiling of matched glioblastoma tumors, cell-lines and xenografts reveals genomic stability and adaptation to disparate growth environments

ABSTRACT: Comprehensive genomic profiling of matched glioblastoma tumors, cell-lines and xenografts reveals genomic stability and adaptation to disparate growth environments

PROVIDER: PRJNA528418 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Comprehensive genomic profiling of matched glioblastoma tumors, cell-lines and xenografts reveals genomic stability and adaptation to disparate growth environments

Project description:Glioblastoma Multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole‐genome sequencing of 201 samples and RNA sequencing of 118 samples, we showed that typical GBM genomic driver alterations found in the tumors were retained in BTICs and xenografts. In contrast, gene expression and methylation profiles indicated higher levels of divergence, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from drug‐screens, and can help control for biases introduced by cell culture conditions and the microenvironment in mouse models.

2019-03-22 | GSE128654 | GEO

Comprehensive genomic profiling of matched glioblastoma tumours, cell-lines, and xenografts reveals genomic stability and adaptation to disparate growth environments

Project description:The mandate of this project was to use drug screening to deliver new drugs for glioblastoma (GBM) to clinical trials, and perform genomic assessment of GBM to discover new therapeutic targets and predictors of response. The sequencing data in this set was derived from GBM patient tumor samples, matched brain tumor initiating cells lines (BTICs), and tumor tissue derived from orthotopic implants.

| EGAS00001002709 | EGA

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair

Project description:Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair

| PRJNA1140114 | ENA

Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines

Project description:Array Comparative Genomic Hybridization (aCGH) of 70 pancreatic ductal adenocarcinoma (PDAC) samples was performed on Agilent 244K CGH arrays in order to find common genomic aberrations for cancer gene discovery. Additionally, matched expression profiling on Agilent 44K arrays was performed. Common copy number aberrations were identified in order to identify a list of putative cancer genes. Expression profiling data was used to further enrich this list of putative cancer genes for more likely candidates. Last, the most promising candidates were functionally interrogated using RNA interference-mediated knockdown to mimic loss. Well-known PDAC cancer genes were observed as amplified (KRAS and MYC) and deleted (CDKN2A, TGFBR2, SMAD4, and MAP2K4). 70 tumor samples (48 xenografts, 22 cell lines). 2-color arrays hybridized against a common reference pool of genomic DNA from 8 normal individuals. This dataset represents the aCGH component of the study.

2011-12-15 | E-GEOD-25273 | biostudies-arrayexpress

Comparative genomic hybridization of Enterococcus faecalis isolates from European hospital environments

Project description:Comparative genomic hybridization of 15 strains isolated in European hospital environments and selected for CGH based on MLST sequence types

2010-08-01 | E-TABM-905 | biostudies-arrayexpress

Patient-derived xenografts and matched cell lines identify pharmacogenomic vulnerabilities in colorectal cancer

Project description:Patient-derived xenografts and matched cell lines identify pharmacogenomic vulnerabilities in colorectal cancer

| PRJEB33640 | ENA

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

Genomic environments scale the activities of diverse core promoters

Project description:Genomic environments scale the activities of diverse core promoters

| PRJNA726578 | ENA

Genomic environments scale the activities of diverse core promoters

Project description:One model for how cells integrate cis-regulatory information is that housekeeping and developmental core promoters respond specifically to certain types of enhancers or chromatin features at different chromosomal locations. We tested this model using a genome-integrated massively parallel reporter assay (MPRA) to measure the activity of hundreds of diverse core promoters at four genomic locations While genomic locations had large effects on expression, the relative strengths of core promoters were preserved across locations regardless of promoter class, suggesting that their intrinsic activities are scaled at different genomic locations. We further show that core promoter scaling is a genome-wide phenomenon by testing six core promoters at thousands of locations across the genome. While the rank order of core promoters is preserved, the scaling of expression across the genome is non-linear and depends on the genomic location and the strength of the core promoter, but not on its class, suggesting that housekeeping and developmental promoters do not make different interactions with the surrounding genomic environment. Instead, our results support a modular genome in which genomic environments containing different enhancers and chromatin features scale the activities of core promoters in an independent, but non-linear manner.

2021-05-01 | GSE173678 | GEO

Expression data from patient and primary xenografts esophageal tumour samples

Project description:Microarrays were used to assess differences between 1) human tumours that did and did not engraft, 2) human tumours and their matched primary xenografts, 3) early and late passage primary xenografts and 4) small and large primary xenografts for a series of esophageal patient and primary xenograft tumours

2015-01-11 | GSE58870 | GEO

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