Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Shotgun Metagenomic Sequencing Analysis of Soil Microcosms

PROVIDER: PRJNA1189582 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31476626_1.fastq.gz	Fastqsanger.gz
	SRR31476626_2.fastq.gz	Fastqsanger.gz
	SRR31476627_1.fastq.gz	Fastqsanger.gz
	SRR31476627_2.fastq.gz	Fastqsanger.gz
	SRR31476628_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

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

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

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

Zearalenone-induced aberration in gut microbiome composition and function are associated with degeneration in ovary reserve

Project description:We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.

2019-11-09 | GSE140149 | GEO

Project description:16S Metagenomic Analysis of Soil Microcosms

| PRJNA1189583 | ENA

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Project description:Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate’s closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

2018-07-31 | MTBLS492 | MetaboLights

Project description:Shotgun sequencing of sediment microcosms

| PRJNA1050283 | ENA

Project description:Shotgun metagenomic analysis

| PRJNA1041042 | ENA

mWGS analysis of the fecal microbiota of WT and TCRb-/- mice

Project description:The gut microbiota plays an important role in host health. Microbiota dysbiosis has been implicated in the global epidemic of Metabolic Syndrome (MetS) and could impair host metabolism by noxious metabolites. It has been well established that the gut microbiota is shaped by host immune factors. However, the effect of T cells on the gut microbiota is yet unknown. Here, we performed a metagenomic whole-genome shotgun sequencing (mWGS) study of the microbiota of TCRb-/- mice, which lack alpha/beta T cells.

2024-05-06 | GSE262397 | GEO

The sample from anearobic sludge

Project description:ZVI Metagenomic shotgun sequencing analysis

| PRJNA957482 | ENA

Project description:Metagenomic shotgun sequencing of Rhizosphere soil

| PRJNA1221826 | ENA