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Oral specimens as a tool for metagenomic analysis

ABSTRACT: Oral specimens as a tool for metagenomic analysis: A pilot study

PROVIDER: PRJEB64500 | ENA |

REPOSITORIES: ENA

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Oral specimens as a tool for metagenomic analysis

Project description:Oral specimens as a tool for metagenomic analysis: A pilot study

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Oral specimens as a tool for accurate metagenomic analysis: A pilot study.

Project description: Not available

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HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.

2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress

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2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress

Oral dysplasias and oral squamous cell carcinoma

Project description:Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization Whole genome tiling-path array CGH profiles of 94 formalin-fixed paraffin-embedded oral specimens.

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Oral Samples (HOMIM-v.02); A Characterization of the Oral Microbiome in Allogeneic Stem Cell Transplant Patients

Project description:The purpose of this study is to describe the effects of allogeneic stem cell transplant on oral microbiota and to examine differences in those patients who acquired respiratory complications. Forty-five patients were consented for the study and followed for 100 days post-transplant. Eleven patients represented by 115 speciment had specimens collected before and after transplant were subjected to further analysis. The Human Oral Microbe Identification Microarray was used for this analysis. In these 11 patients, five developed respiraotry complications after transplant and six did not develop this complication. Cluster analysis was used to identify patterns in the data. 115 specimens are included from 11 patients. These specimens were collected before and after transplant. There are no duplicate samples.

2012-10-01 | E-GEOD-34439 | biostudies-arrayexpress

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