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.
Project description:We performed single cell transcriptomic analysis on 17 urine samples obtained from five subjects at two different occasions using both spot and 24-hour urine collection. In addition, we used a combined spot urine samples of five healthy individuals as a control sample. We sequenced a total of 71,667 cells. After quality control and downstream analysis, we found that epithelial cells were the most common cell types in the urine. We were also able to identify most kidney cell types in the urine, such as podocyte, proximal, and collecting duct (CD), in addition to macrophages, monocytes and lymphocytes.
Project description:Genome wide DNA methylation profiling of urine and blood samples from patients with diabetic chronic kidney disease. The Illumina Infinium MethylationEPIC BeadChip kit was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples included two urine and four buffy coat samples from adults with diabetic chronic kidney disease.
Project description:Fifty patient urine samples diagnosed as high-grade urothelial carcinoma (HGUC) or benign were evaluated for bladder cancer via urine cytology. RNA was isolated and analyzed by microarray to identify a panel of biomarkers differentially expressed in HGUC and benign.
Project description:Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
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.
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.
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.
Project description:Growth in urine of cranberry extract-treated volunteers did not markedly affect the transcirptome of UPEC strain UTI89. Expression of bacterial adhesin determinants (P fimbriae, S fimbrae, curli) was not markedly changed upon growth in the urine samples, while a slight, but non-significant upregulation of type 1 fimbriae was observed.