Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metataxonomic analysis of the urine microbiome

ABSTRACT: The bacterial diversity of mid-flow first urine samples was determined using 16S rRNA gene inventories

PROVIDER: PRJEB4256 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR309936.fastq.gz	Fastqsanger.gz
	ERR309937.fastq.gz	Fastqsanger.gz
	ERR309938.fastq.gz	Fastqsanger.gz
	ERR309939.fastq.gz	Fastqsanger.gz
	ERR309940.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Single-Cell RNA-Seq Analysis of cells from human urine

Project description:Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.

2021-01-25 | GSE165396 | GEO

Escherichia coli global gene expression in urine from women with urinary tract infection

2010-11-12 | GSE24478 | GEO

Cell and microvesicle urine microRNA deep sequencing profiles from healthy individuals

Project description:Background: Urine is a potential source of biomarkers for diseases of the kidneys and urinary tract. RNA, including microRNA, is present in the urine enclosed in detached cells or in extracellular vesicles (EVs) or bound and protected by extracellular proteins. Detection of cell- and disease-specific microRNA in urine may aid early diagnosis of organ-specific pathology. In this study, we applied barcoded deep sequencing to profile microRNAs in urine of healthy volunteers, and characterized the effects of sex, urine fraction (cells vs. EVs) and repeated voids by the same individuals. Results: Compared to urine-cell-derived small RNA libraries, urine-EV-derived libraries were relatively enriched with miRNA, and accordingly had lesser content of other small RNA such as rRNA, tRNA and sn/snoRNA. Unsupervised clustering of specimens in relation to miRNA expression levels showed prominent bundling by specimen type (urine cells or EVs) and by sex, as well as a tendency of repeated (first and second void) samples to neighbor closely. Likewise, miRNA profile correlations between void repeats, as well as fraction counterparts (cells and EVs from the same specimen) were distinctly higher than correlations between miRNA profiles overall. Differential miRNA expression by sex was similar in cells and EVs. Conclusions: miRNA profiling of both urine EVs and sediment cells can convey biologically important differences between individuals. However, to be useful as urine biomarkers, careful consideration is needed for biofluid fractionation and sex-specific analysis, while the time of voiding appears to be less important.

2016-01-28 | GSE72183 | GEO

urine metagenome

Project description:Urine samples Metataxonomic analysis by 16S rRNA gene inventory

| PRJNA208706 | ENA

Escherichia coli global gene expression in urine from women with urinary tract infection

Project description:Examination of E. coli transcripts present in bacteria in urine samples from 8 patients attending a urology clinic with symptoms of cystitis, as compared to transcripts present in the same E. coli strains during mid-exponential growth in filter-sterilized human urine in vitro. A 48 array study using total RNA recovered from eight clinical E. coli isolates immediately following collection from women and following culture in pooled human urine ex vivo. Each array measures the expression of the 5,379 ORFs in the CFT073 genome, using an average of 14 60-mer probes per ORF. Arrays were performed in triplicate: biological replicates of the in vitro-cultured samples and technical replicates of the in vivo samples.

2010-11-12 | E-GEOD-24478 | biostudies-arrayexpress

microRNA expression profiling of urine and cancer tissues of patients with bladder cancer, and those from the controls with haematuria

Project description:Mid-stream urine was collected from bladder cancer patients prior to surgery. Both tumor tissue and normal bladder mucosa that are located at >3cm away from the tumor edge were obtained by cystoscopy. For the normal controls with haematuria, urine samples were collected from patients who had normal cystoscopic finding and absence of malignancy with >6 months follow-up. All urine samples were centrifuged at 2500 r.c.f. for 20 minutes and the urine supernatant was collected. Total RNA of urine supernatant and frozen tissue was extracted using MirVanaTM PARISTM Kit (Ambion) in accordance with the manufacturerâs recommended protocols. AgilentTM Human miRNA Microarray Chip (Release 13.0, Agilent Technologies, Santa Clara, CA, USA) was used to determine the microRNA expression profiles of the samples.

2014-04-16 | E-MTAB-2573 | biostudies-arrayexpress

Urine

Project description:Urine Raw sequence reads

| PRJNA850668 | ENA

urine metagenome

Project description:16S rRNA gene targeted metagenome sequencing of urine microbiome in kidney stone disease

| PRJNA398193 | ENA

urine metagenome

Project description:urine metagenome Metagenome

| PRJNA1032262 | ENA

urine metagenome

Project description:source-separated urine Metagenome