scholarly journals Oasis2.0: improved online analysis of small RNA-seq data

2017 ◽  
Author(s):  
Raza-Ur Rahman ◽  
Abhivyakti Gautam ◽  
Jörn Bethune ◽  
Abdul Sattar ◽  
Maksims Fiosins ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Small Rnas ◽  
Web Application ◽  
The Novel ◽  
Sequencing Data ◽  
Essential Information ◽  
Deep Sequencing Data ◽  
Small Rna Deep Sequencing ◽  
User Friendly

AbstractOasis 2 is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module. Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.Availability and Implementation: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at http://oasis.dzne.de

scholarly journals CPSS: a computational platform for the analysis of small RNA deep sequencing data

2012 ◽  
Vol 28 (14) ◽  
pp. 1925-1927 ◽  
Author(s):  
Yuanwei Zhang ◽  
Bo Xu ◽  
Yifan Yang ◽  
Rongjun Ban ◽  
Huan Zhang ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing ◽  
Computational Platform

scholarly journals Biases in small RNA deep sequencing data

2013 ◽  
Vol 42 (3) ◽  
pp. 1414-1426 ◽  
Author(s):  
Carsten A. Raabe ◽  
Thean-Hock Tang ◽  
Juergen Brosius ◽  
Timofey S. Rozhdestvensky
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

scholarly journals Oasis: online analysis of small RNA deep sequencing data

2015 ◽  
Vol 31 (13) ◽  
pp. 2205-2207 ◽  
Author(s):  
Vincenzo Capece ◽  
Julio C. Garcia Vizcaino ◽  
Ramon Vidal ◽  
Raza-Ur Rahman ◽  
Tonatiuh Pena Centeno ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Sequencing Data ◽  
Online Analysis ◽  
Deep Sequencing Data ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

scholarly journals Identification of Novel MicroRNAs in Primates by Using the Synteny Information and Small RNA Deep Sequencing Data

2013 ◽  
Vol 14 (10) ◽  
pp. 20820-20832 ◽  
Author(s):  
Zhidong Yuan ◽  
Hongde Liu ◽  
Yumin Nie ◽  
Suping Ding ◽  
Mingli Yan ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

scholarly journals deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

2015 ◽  
Vol 44 (D1) ◽  
pp. D196-D202 ◽  
Author(s):  
Ling-Ling Zheng ◽  
Jun-Hao Li ◽  
Jie Wu ◽  
Wen-Ju Sun ◽  
Shun Liu ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rnas ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Expression Evolution ◽  
And Function

scholarly journals Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

RNA ◽  
2009 ◽  
Vol 15 (12) ◽  
pp. 2147-2160 ◽  
Author(s):  
C. Cole ◽  
A. Sobala ◽  
C. Lu ◽  
S. R. Thatcher ◽  
A. Bowman ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rnas ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Identification of Circulating miRNAs in a Mouse Model of Nerve Allograft Transplantation under FK506 Immunosuppression by Illumina Small RNA Deep Sequencing

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Shao-Chun Wu ◽  
Cheng-Shyuan Rau ◽  
Johnson Chia-Shen Yang ◽  
Tsu-Hsiang Lu ◽  
Yi-Chan Wu ◽  
...  
Keyword(s):  
Sciatic Nerve ◽  
Deep Sequencing ◽  
Small Rna ◽  
Small Rnas ◽  
Biological Function ◽  
Circulating Mirnas ◽  
Serum Samples ◽  
Circulating Micrornas ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

Background. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation in the presence and absence of FK506 immunosuppression.Methods. A 1 cm BALB/c donor sciatic nerve graft was transplanted into the sciatic nerve gaps created in recipient C57BL/6 mice with or without daily FK506 immunosuppression [1 mg/(kg·d)]. At 3, 7, and 14 d after nerve allotransplantation, serum samples were collected for miRNA expression analysis by Illumina small RNA deep sequencing.Results. Sequence analysis showed that the dominant size of circulating small RNAs after nerve allotransplantation was 22 nucleotides, followed by 23-nucleotide sequences. Nine upregulated circulating miRNAs (let-7e-5p, miR-101a-3p, miR-151-5p, miR-181a-5p, miR-204-5p, miR-340-5p, miR-381-3p, miR-411-5p, miR-9-5p, and miR-219-2-3p) were identified at 3 d, but none was identified at 7 or 14 d. Among them, miR-9-5p had the highest fold-change of >50-fold, followed by miR-340-5p with 38.8-fold. The presence of these nine miRNAs was not significant at 7 and 14 d after nerve allotransplantation with or without immunosuppression, showing that these miRNAs are not ideal biomarkers for monitoring rejection of deep-buried nerve allografts, a response usually observed later.Conclusions. We identified nine upregulated circulating miRNAs, which may have a biological function, particularly during the early stages after nerve allotransplantation under FK506 immunosuppression.

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