Comparison of EGF and PDGF driven glioblastomas. - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001001900		Other

Study ID

Alternative Stable ID

Type

EGAS00001001900

Other

Study Description

Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor. Epidermal growth-factor (EGF) and platelet-derived growth-factor (PDGF) receptors are frequently amplified and/or possess gain-of-function mutations in these tumors. Despite years of research into tyrosine-kinase inhibitors, clinical trials have shown disappointing efficacy. One of the underlying reasons is intra-tumor heterogeneity. To assess the effect of intra-tumor heterogeneity on gene expression, we derived a general approach to map single-cell expression profiles to sequentially-acquired mutations identified from exome sequencing. Using 288 single cells, we constructed high-resolution phylogenies of EGF-driven and PDGF-driven GBMs, modeling transcriptional kinetics during tumor evolution. A deletion in a PDGF-receptor domain involved in dimerization correlated to an up-regulation of the PI3K/AKT pathway in a proneural GBM, and ectopic expression of this mutant PDGFRA in vitro enhanced proliferation and invasiveness. Descending the phylogenetic tree of the PDGFR-driven tumor ... (Show More)

Dataset ID	Description	Technology	Samples
EGAD00001002269	We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers. We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers.	Illumina HiSeq 4000	1
EGAD00001002270	We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002271	We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002272	We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells. We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.	Illumina HiSeq 2500	1
EGAD00001002273	We performed bulk exome-seq on a primary GBM and a blood sample from SF10345 We performed bulk exome-seq on a primary GBM and a blood sample from SF10345	Illumina HiSeq 2500	1
EGAD00001002274	We performed bulk exome-seq on a primary GBM and a blood sample from SF10360 We performed bulk exome-seq on a primary GBM and a blood sample from SF10360	Illumina HiSeq 2500	1
EGAD00001002275	We performed bulk exome-seq on a primary GBM and a blood sample from SF10282 We performed bulk exome-seq on a primary GBM and a blood sample from SF10282	Illumina HiSeq 2500	1

Dataset ID

Description

Technology

Samples

EGAD00001002269

We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers.

Illumina HiSeq 4000

EGAD00001002270

We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Illumina HiSeq 2500

EGAD00001002271

We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Illumina HiSeq 2500

EGAD00001002272

We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

Illumina HiSeq 2500

EGAD00001002273

We performed bulk exome-seq on a primary GBM and a blood sample from SF10345

Illumina HiSeq 2500

EGAD00001002274

We performed bulk exome-seq on a primary GBM and a blood sample from SF10360

Illumina HiSeq 2500

EGAD00001002275

We performed bulk exome-seq on a primary GBM and a blood sample from SF10282

Illumina HiSeq 2500

Study

Study Description

Study Datasets 7 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.