Ontology highlight
ABSTRACT:
PROVIDER: PRJNA788683 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17225339.fastq.gz | Fastqsanger.gz | |||
| SRR17225340.fastq.gz | Fastqsanger.gz | |||
| SRR17225341.fastq.gz | Fastqsanger.gz | |||
| SRR17225342.fastq.gz | Fastqsanger.gz | |||
| SRR17225343.fastq.gz | Fastqsanger.gz |
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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:The purpose of this study was to characterize the transcriptomic alterations accompanying the inflammation involved in feline chronic gingivostomatitis (FCGS). Towards this goal next-generation sequencing (NGS)-based gene expression profiling (RNA-Sequencing; RNA-Seq) was performed on matched pairs of FCGS diseased and healthy tissues obtained from three feline subjects.
2020-09-25 | GSE149881 | GEO
Project description:Small RNA sequencing of urine-derived PS.
| PRJNA644397 | ENA
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Purpose:MicroRNAs (miRNAs) are members of a rapidly growing class of small endogenous non-coding RNAs that play crucial roles in post-transcriptional regulator of gene expression in many biological processes. Feline Panleukopenia Virus (FPV) is a highly infectious pathogen that causes severe disease in pets, economically important animals and wildlife in worldwide. However, the molecular mechanisms underlying the pathogenicity of FPV have not been completely clear. To study the involvement of miRNAs in the FPV infection process, miRNAs expression profiles were identified via deep sequencing in the feline kidney cell line (F81) infected and uninfected with FPV. Methods:miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol Results:As a result, 673 known miRNAs belonging to 210 families and 278 novel miRNAs were identified. Then we found 57 significantly differential expression miRNAs by comparing the results between uninfected and FPV-infected groups. Furthermore, stem-loop qRT-PCR was applied to validate and profile the expression of the randomly selected miRNAs; the results were consistent with those by deep sequencing. Furthermore, the potential target genes were predicted. The target genes of differential expression miRNAs were analyzed by GO and KEGG pathway. Conclusions:The identification of miRNAs in feline kidney cell line before and after infection with Feline Panleukopenia Virus will provide new information and enhance our understanding of the functions of miRNAs in regulating biological processes.
2020-12-20 | GSE122381 | GEO
Project description:Small RNA sequencing of urine-derived ADO2-iPSCs
| PRJNA553161 | ENA
Project description:Urinary extracellular vesicle (EV)-derived microRNAs (miRNAs) have emerged as promising noninvasive biomarkers for disease prediction. However, fluctuations in urine concentration throughout the day may influence miRNA abundance and profiles, potentially limiting their clinical utility. To ensure the broader applicability of urinary miRNAs in disease prediction, it is essential that their profiles remain stable regardless of collection time. In this study, we systematically examined factors influencing urinary miRNA abundance and assessed the stability of miRNA profiles. We collected serial urine samples from healthy individuals over three days, and performed small RNA sequencing to analyze urinary miRNA profiles in relation to various urine concentration parameters. Total miRNA counts were negatively correlated with urine volume and positively correlated with urine concentration indicators, including specific gravity and creatinine levels. miRNA profiles remained stable across different times and days when samples with low miRNA counts were excluded. These findings indicate that urine dilution—primarily due to fluid intake—is a major cause of variation in urinary miRNA abundance. Our results highlight the importance of collecting adequately concentrated samples and provide foundational insights for developing standardized urine collection protocols to enhance the reliability of urinary miRNAs as biomarkers.
2025-07-31 | GSE297465 | GEO
Project description:Induced pluripotent stem cells (iPSCs) are a valuable resource in veterinary regenerative medicine and cellular therapy, particularly for advancing species-specific applications such as feline medicine. This study employs RNA sequencing (RNA-seq) to investigate the transcriptomic profiles of feline iPSCs generated using the Sendai virus method and mesenchymal stem cells (MSCs) derived from these iPSCs. The comparative analysis reveals unique expression patterns linked to the Sendai virus reprogramming approach, identifying key regulatory pathways and gene networks characteristic of Sendai virus-derived iPSCs. Furthermore, the distinct transcriptome of iPSC-derived MSCs showcases markers associated with mesenchymal lineage commitment and MSC functionality. These findings provide valuable insights into the impact of Sendai virus reprogramming on feline iPSC properties and contribute to advancing stem cell-based therapies tailored to feline-specific needs.
2024-11-27 | GSE282965 | GEO
Project description:Small non-coding RNA profiling of urine exosomal total RNA from patients with or without prostate cancer were performed using Affymetrix GeneChip miRNA 4.0 to identify small non-coding RNA profile that can be used for prostate cancer diagnosis.
2020-07-29 | GSE138740 | GEO