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RNA sequencing analysis of stable medulloblastoma DAOY, D425, and CHLA01 cells expressing vector only (V/O) or miR-211

ABSTRACT: RNA sequencing analysis of stable medulloblastoma DAOY, D425, and CHLA01 cells expressing vector only (V/O) or miR-211

PROVIDER: PRJNA780435 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16947270.fastq.gz	Fastqsanger.gz
	SRR16947271.fastq.gz	Fastqsanger.gz
	SRR16947272.fastq.gz	Fastqsanger.gz
	SRR16947273.fastq.gz	Fastqsanger.gz
	SRR16947274.fastq.gz	Fastqsanger.gz

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RNA sequencing analysis of stable medulloblastoma DAOY, D425, and CHLA01 cells expressing vector only (V/O) or miR-211

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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.

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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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