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MRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis

ABSTRACT: mRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis

PROVIDER: PRJNA475228 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7280700.fastq.gz	Fastqsanger.gz
	SRR7280710.fastq.gz	Fastqsanger.gz
	SRR7280701.fastq.gz	Fastqsanger.gz
	SRR7280711.fastq.gz	Fastqsanger.gz
	SRR7280702.fastq.gz	Fastqsanger.gz

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mRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis

Project description:Treatment of neuroepithelial cancers remains a daunting clinical challenge, particularly due to an inability to address rampant invasion deep into eloquent regions of the brain. Given the lack of access, and the dispersed nature of brain tumor cells, we explore the possibility of electric fields inducing directed tumor cell migration. In this study we investigate the properties of populations of brain cancer undergoing electrotaxis, a phenomenon whereby cells are directed to migrate under control of an electrical field. We investigate two cell lines for glioblastoma and medulloblastoma (U87mg & DAOY, respectively), plated as spheroidal aggregates in matrigel-filled electrotaxis channels, and report opposing electrotactic responses. To further understand electrotactic migration of tumor cells, we performed RNA-sequencing for pathway discovery to identify signaling that is differentially affected by the exposure of direct-current electrical fields.

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Project description:The goal of this study was to profile the total proteome and transcriptome of the established medulloblastoma cell lines, Daoy and UW228, using label-free nano-LC-MS/MS-based quantitative proteomics and high-throughput RNA sequencing (RNA-Seq), coupled with pathway analysis to identify differentially expressed genes, proteins and signaling pathways with potential as prognostic markers. A total of 14250 and 12870 transcripts were detected for Daoy and UW228, respectively. Proteomic profiling identified 2630 and 1235 proteins in Daoy and UW228, representing 18% and 10% of detected transcripts, respectively. Interestingly, Daoy proteome included >50% unique proteins, while almost 90% of proteins expressed by UW228 were commonly expressed in Daoy. Differential expression of a number of adhesion, cytoskeletal and signaling molecules were observed between the two cell lines. Upregulation of a number of proteins and enrichment of key signaling pathways, including WNT, Sonic hedgehog (SHH) and integrin signaling pathways, were uniquely observed in MB cell lines, in particular in Daoy.

2017-10-27 | PXD002659 | Pride

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Project description:To investigate the role of miR-211 in medulloblastoma, next-generation sequencing analysis of RNA extracted from DAOY, D425, and CHLA01 cells expressing vector only (V/O) or miR-211 were performed.

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Daoy gene expression

Project description:Using measurements of absolute protein and mRNA concentrations in cellular lysate from a Daoy medulloblastoma cell line, we quantitatively evaluate the influence of absolute transcript levels and a large number of sequence-encoded regulatory elements on steady-state human protein expression levels.

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Daoy gene expression

2010-04-22 | E-GEOD-20492 | biostudies-arrayexpress

BioID proximity labelling of MAP4K4 interactors in DAOY medulloblastoma cells

Project description:Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) is Ser/Thr protein kinase highly expressed in medulloblastoma (MB) patient samples which promotes cell migration and invasiveness downstream of growth factor receptors. Although MAP4K4 implication in the control of the membrane protrusions at the leading edge of cells during migration and invasion in MB is established, its downstream effectors governing and mediating this process in MB have not been identified. In this study we explored the proteomic neighborhood of MAP4K4 in MB cells and to identify candidate potentially affecting its activity and pro-migratory functions. Towards this aim, we expressed BioID fused versions of MAP4K4 (N- and C-terminal) in DAOY cells under presence of biotin. In the control setup, we expressed the BioID enzyme alone. After Streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions.

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Project description:DNase-seq on cell line Daoy (polygonal cell from 4 year old male human cerebellum, desmoplastic cerebellar medulloblastoma) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

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