Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: microbial sample sequencing

PROVIDER: PRJNA660096 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12549501_1.fastq.gz	Fastqsanger.gz
	SRR12549501_2.fastq.gz	Fastqsanger.gz
	SRR12549502_1.fastq.gz	Fastqsanger.gz
	SRR12549502_2.fastq.gz	Fastqsanger.gz
	SRR12545003_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Diurnal oscillations in human salivary microRNA and microbial transcription

Project description:We investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Eleven miRNAs and 11 microbial RNAs demonstrated consistent diurnal oscillation across the first 2 sample sets and accurately predicted collection time in the hold-out set based on multivariate logistic regression modeling. Associations among five circadian miRNAs and four circadian microbial RNAs were observed.

2018-07-06 | GSE116686 | GEO

Expression data from an in vitro growth of Methanobrevibacter smithii PS

Project description:RNA-sequencing is a powerful tool for exploring expression profiles of microbial species that does not require the production of a custom genechip. We used microarrays to compare our quantitative RNA-sequencing method to the standard expression quantification methods Methanobrevibacter smithii PS cultures were grown to stationary phase under 80% hydrogen, 20% CO2, with varying amounts of formate. RNA was extracted and purified, then divided into two aliquots per sample. One aliquot was prepared for hybridization on Affymetrix gene chips, the other was prepared for microbial RNA-sequencing.

2011-03-30 | E-GEOD-25535 | biostudies-arrayexpress

Project description:Microbial sample sequencing

| PRJNA1101844 | ENA

Project description:Microbial sample sequencing

| PRJNA639225 | ENA

Project description:soil microbial sample sequencing

| PRJNA799230 | ENA

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

An Open-Source QIIME2 and R Pipeline for Multi-Amplicon 16S rRNA Profiling: Validation and Application in Pediatric Microbiome Studies

Project description:This study presents a validated, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using multi-amplicon sequencing. It aims to overcome the limitations of commercial, closed-source tools by offering a standardized and reproducible workflow. The pipeline was benchmarked against proprietary software using five mock communities and 12 child–caregiver fecal sample pairs, showing nearly identical microbial profiles, greater sequencing depth, and improved taxonomic resolution. High reproducibility (R = 0.99, p < 0.0001) was achieved across all datasets. Application to pediatric cancer samples revealed distinct Bifidobacterium variants in children whose microbiota closely matched their caregivers’. This highlights the pipeline’s utility in studying microbial relationships. Overall, the pipeline supports transparent, adaptable, and accurate microbiome analysis, advancing research in both clinical and experimental settings while promoting open-source solutions for reproducible science.

2025-07-14 | GSE300047 | GEO

Mouse caecum vs faeces - Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse

Project description:We compared the microbiota of paired mouse caecal contents and faeces by applying a multi-omic approach, including 16S rDNA sequencing, shotgun metagenomics, and shotgun metaproteomics. The aim of the study was to verify whether faecal samples are a reliable proxy for the mouse colonic luminal microbiota, as well as to identify changes in taxonomy and functional activity between caecal and faecal microbial communities, which have to be carefully considered when using stool as sample for mouse gut microbiota investigations.

2017-03-31 | PXD004911 | Pride

Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China

Project description:We recruited 24 Mongolian volunteers,6 of which were T2D cases(sample T1-T6), 6 were prediabetes cases(sample P1-P6), and 12 were health cases(sample C1-C12). The metagenomic analysis of gut microbiota from the volunteers’ fecal samples was performed. We compared the microbial differences in the three groups, and analyzed the differences of the stool microbial function.

2022-07-30 | E-MTAB-11957 | biostudies-arrayexpress

Project description:Microbial sample

| PRJNA1205371 | ENA