Dataset Information

Genome wide transcriptome analysis of patient matched prostate cancer using NGS technology

ABSTRACT: Purpose: The goal of present study is to compare transcript level changes between normal and tumor of same individual Methods: Total RNA was isolated, strand specific RNA seq was performed after Ribosomal RNA removal, global transcript profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq. Initial quality check was performed using FASTQC, Alignment was performed using Hisat2 against human hg19 genome. Raw read count was performed using SummarizedExperiment (R package). Differential analysis was done using DEseq2 Results: This study provides insights in terms of global trancriptome changes between normal and tumor of same patient. Conclusions: This study provides in depth analysis of transcriptomoc data in patient specific manner.

ORGANISM(S): Homo sapiens

PROVIDER: GSE133626 | GEO | 2019/07/02

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Modern molecular genetic methods, massive parallel sequencing in particular, allow for genotyping of various pathogens with the aim of their epidemiological marking and improvement of molecular epidemiological surveillance of actual infections, including cytomegalovirus infection. The aim of the study is to evaluate the next-generation sequencing (NGS) technology for genotyping clinical isolates of cytomegalovirus (CMV).Materials and methodsThe object of the study were samples of biological substrates (leukocyte mass, saliva, urine) taken from patients who underwent liver and kidney transplantation. Detection of CMV DNA was carried out by a real-time PCR using commercial diagnostic AmpliSense CMV-FL test systems (Central Research Institute for Epidemiology, Moscow, Russia). DNA extraction was performed using DNA-sorb AM and DNA-sorb V kits (Central Research Institute for Epidemiology) in accordance with manufacturer's manual. The quality of the prepared DNA library for sequencing was assessed by means of the QIAxcel Advanced System capillary gel electrophoresis system (QIAGEN, Germany). Alignment and assembly of nucleotide sequences were carried out using CLC Genomics Workbench 5.5 software (CLC bio, USA). The sequencing results were analyzed using BLAST of NCBI server.ResultsCMV DNA samples were selected for genotyping. The two variable genes, UL55(gB) and UL73(gN), were used for CMV genotype determination, which was performed using NGS technology MiSeq sequencer (Illumina, USA). Based on the exploratory studies and analysis of literature sources, primers for genotyping on the UL55(gB) and UL73(gN) genes have been selected and the optimal conditions for the PCR reaction have been defined. The results of sequencing the UL55(gB) and UL73(gN) gene fragments of CMV clinical isolates from recipients of solid organs made it possible to determine the virus genotypes, among which gB2, gN4c, and gN4b were dominant. In some cases, association of two and three CMV genotypes has been revealed.ConclusionThe application of the NGS technology for genotyping cytomegalovirus strains can become one of the main methods of CMV infection molecular epidemiology, as it allows for obtaining reliable results with a significant reduction in research time.

Dataset Information

Genome wide transcriptome analysis of patient matched prostate cancer using NGS technology

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets