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ABSTRACT: Metagenomic sequencing of PF and Normal paocai

PROVIDER: PRJNA857191 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20314045_1.fastq.gz	Fastqsanger.gz
	SRR20314045_2.fastq.gz	Fastqsanger.gz
	SRR20314046_1.fastq.gz	Fastqsanger.gz
	SRR20314046_2.fastq.gz	Fastqsanger.gz
	SRR20314047_1.fastq.gz	Fastqsanger.gz

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Paocai

Project description:Metagenomic sequencing of Paocai

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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

Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

Project description:Pulmonary fibrosis (PF) is a form of chronic lung disease characterized by progressive destruction of normal alveolar gas-exchange surfaces and accumulation of extracellular matrix (ECM). In order to comprehensively define the cell types, mechanisms and mediators driving ECM deposition and fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNA-sequencing (scRNA-seq) of single-cell suspensions generated from non-fibrotic control and PF lungs. Analysis of over 114,000 cells from 20 PF and 10 control lungs identified 31 distinct cell types. We identified multiple distinct lineages directly contribute to ECM expansion, including a novel HAS1hi fibroblast subtype and a previously undescribed KRT5-/KRT17+, collagen and ECM-producing epithelial cell population that was highly enriched in PF lungs. Together these data provide high-resolution insights into the basic mechanisms of pulmonary fibrosis, and indicate a direct profibrotic role of the lung epithelium in PF pathogenesis.

2019-09-05 | GSE135893 | GEO

Metagenome and Viral Interrogation of a Moose Rumen Microbial Community

Project description:Proteomic data from moose fistulated rumen; metagenomic and viral sequencing performed; metabolic pathways reconstructed

2018-07-03 | PXD008667 | Pride

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

Project description:paocai metatranscriptome

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MuSt multiomics - Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.

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Project description:sichuan paocai brine microbial sequencing

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Pericardial Fluid of Patients with Coronary Artery Disease Can Drive Fibrosis via TGF-Beta Signalling Pathway

Project description:Pericardial fluid (PF) helps maintain homeostatic conditions that facilitate optimal heart function. We have yet to understand how cardiovascular pathologies affect the profile of PF. We hypothesized that human PF contains immune markers that can be affected by different pathologies and contribute to inflammatory-mediated processes, such as fibrosis. PF was collected from patients undergoing cardiac surgery. Multiplex analysis was performed to determine the composition of inflammatory markers and soluble mediators. A gel contraction assay was used to investigate the fibrotic potential of PF. RNA-sequencing was used to elucidate the mechanisms driving the pro-fibrotic properties of PF. With the results of these multiple approaches we show that the acellular component of PF has pro-fibrotic characteristics and suggest putative mechanisms that can explain such observations.

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