Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses

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Bioinformatics and Genomics

Main article text

 

Introduction

Material and Methods

Clinical UTUC specimen characteristics

Next-generation sequencing

miRmap database analysis for microRNA target predicting

Gene Expression Omnibus database and statistical analysis

Oncomine database analysis

Ingenuity®Pathway Analysis

TargetScan and miRDB analyses

Western blot analysis

Quantitative real time reverse transcriptase-PCR (qRT-PCR)

Immunohistochemistry

Results

Identification of significant miRNA expression in renal pelvis cancer

Identification of significant miRNA–mRNA interactions and genes

Identification of differentially expressed genes in UTUC and the potentially involved pathways

Identifying correlations among PDE5A, CYBRD1, and ZEB2 by an in vitro study

Discussion

Supplemental Information

Raw data

mRNA expression of PDE5A, CYBRD1, and ZEB2 in UC and UTUC cells.

DOI: 10.7717/peerj.11343/supp-1

Fig. 9 raw data

PDE 5A expression through real-time PCR.

DOI: 10.7717/peerj.11343/supp-2

Full-length uncropped blots

DOI: 10.7717/peerj.11343/supp-3

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Hsiang-Ying Lee and Bi Wen Yeh conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Ching-Chia Li, Ya-Ling Hsu, Hung-Lung Ke, Chun-Nung Huang, Chien-Feng Li and Wen-Jeng Wu conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Wei-Ming Li and Hsin-Chih Yeh analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Po-Lin Kuo conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The Kaohsiung Medical University Hospital granted Ethical approval to carry out the study within its facilities (KMUHIRB-E(I)-20170018; KMUH107-7R56).

Data Availability

The following information was supplied regarding data availability:

Data is available at NCBI GEO: GSE159824.

Funding

This study was supported by grants from the Ministry of Science and Technology (MOST 106-2314-B-037-029), the Kaohsiung Medical University Hospital (KMUH 106-6R53), Kaohsiung Municipal Ta-Tung Hospital (kmtth-108-R003) and partially by the Kaohsiung Medical University Grant (KMU-KI109002), the Regenerative Medicine and Cell Therapy Research Center Grant (KMU-TC108A02), and the Cohort Research Center (KMU-TC108B07). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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