Healthy Female Urine Microbiota
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REPOSITORIES: ENA
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Project description:Female Catheterized Urine Targeted loci
| PRJNA1025276 | ENA
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
Project description:Antibody microarray based profiling of twelve urine samples.<br>3 healthy female<br>3 heatlhy male<br>3 female with pancreatic cancer<br>3 male with pancreatic cancer<br>
2012-05-03 | E-MEXP-3006 | biostudies-arrayexpress
Project description:Analysis of induced nephron progenitor cells from female/male urine cells (iNPC-F/INPC-M) by defined transcription factors vs. ESC derived nephron progenitor cell (ESC-NPC_H9/ESC-NPC_BG01) and female/male urine cells (UC-F/UC-M). Results provide insight into molecular similarities between induced nephron progenitor cells and human ESC derived nephron progenitor cell
2021-12-29 | GSE134145 | GEO
Project description:Analysis of induced keratinocyte stem cells from male/female urine cells (MiKSC/FiKSC) by defined transcription factors vs. foreskin derived primary human neonatal epidermal keratinocytes (pKC) and male/female urine cells (MUC/FUC). Results provide insight into molecular similarities between induced keratinocyte stem cells and human foreskin derived primary human neonatal epidermal keratinocytes.
2019-04-11 | GSE129316 | GEO
Project description:We performed genome-wide 5hmC Methylated DNA Capture (5hMethylCap-seq) on one pooled RCC tissue sample (n=3) and the corresponding matched normal kidney tissue (NAT) (n=3), and we also performed 5hMethylCap-seq on one pooled urine sample obtained from RCC patients (n=52) along with another pooled urine sample obtained from control patients without malignancy (n=65). Global 5hmC levels were dramatically reduced in RCC tissues compared to matched normal adjacent kidney tissues, and although we detected low levels of 5hmC in urine samples, we also observed reduction of 5hmC in urine samples compared to tissue samples. Through assessing histone marked regions we found that 5hmC levels were enriched in H3K9me3 marked repressive genomic regions of normal adjacent kidney compared to RCC tissue tissues. Given the lower 5hmC signal in other genomic regions in cancer tissues, this upregulated 5hmC levels in H3K9me3 marked regions were also clearly identified comparing urine samples from RCC patients to control patients without RCC. We used Caki1 and Caki2 RCC cells to established stable cells with low H3K9me3 expression by knocking down the SUV39H1 gene. We found that low global H3K9me3 causes major upregulation of 5hmC at H3K9me3 marked regions and minor downregulation of 5hmC at genebody regions without change global 5mC and 5hmC levels.
2019-12-31 | GSE118922 | GEO
Project description:MicroRNA (miRNA) biomarkers for fragile X syndrome were searched by urine microRNA (miRNA) profiling using deep sequencing. The urine miRNA profile of twin boys who shared the same environment but one had a FXS full mutation and the other carried a premutation allele was compared based on the similar sequence reads. The urine of twin boys showed 28 differentiatially regulated miRNAs when 219 reliable identified miRNAs were compared.
2020-03-30 | GSE143347 | GEO