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.

Identification of viruses infecting sweet potato in southern China by small RNA deep sequencing and PCR detection

2018 ◽  
Vol 85 (2) ◽  
pp. 122-127 ◽  
Author(s):  
Siqi Ma ◽  
Qiufeng Zheng ◽  
Jiajie Ye ◽  
Wendi Feng ◽  
Guohui Zhou ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Deep Sequencing ◽  
Small Rna ◽  
Southern China ◽  
Pcr Detection ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

scholarly journals Analysis of miRNAs in the Heads of Different Castes of the Bumblebee Bombus lantschouensis (Hymenoptera: Apidae)

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 349 ◽  
Author(s):  
Liu ◽  
Huang ◽  
Zhang ◽  
Liu ◽  
An
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Solexa Sequencing ◽  
Biological Functions ◽  
Putative Target ◽  
Differentially Expressed Mirnas ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing ◽  
Go Terms

Bumblebees are important insect pollinators for many wildflowers and crops. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate different biological functions in insects. In this study, the miRNAs in the heads of the three castes of the bumblebee Bombus lantschouensis were identified and characterized by small RNA deep sequencing. The significant differences in the expression of miRNAs and their target genes were analyzed. The results showed that the length of the small RNA reads from males, queens, and workers was distributed between 18 and 30 nt, with a peak at 22 nt. A total of 364 known and 89 novel miRNAs were identified from the heads of the three castes. The eight miRNAs with the highest expressed levels in males, queens, and workers were identical, although the order of these miRNAs based on expression differed. The male vs. queen, male vs. worker, and worker vs. queen comparisons identified nine, fourteen, and four miRNAs with significant differences in expression, respectively. The different castes were clustered based on the differentially expressed miRNAs (DE miRNAs), and the expression levels of the DE miRNAs obtained by RT-qPCR were consistent with the read counts obtained through Solexa sequencing. The putative target genes of these DE miRNAs were enriched in 29 Gene Ontology (GO) terms, and catalytic activity was the most enriched GO term, as demonstrated by its association with 2837 target genes in the male vs. queen comparison, 3535 target genes in the male vs. worker comparison, and 2185 target genes in the worker vs. queen comparison. This study highlights the characteristics of the miRNAs in the three B. lantschouensis castes and will aid further studies on the functions of miRNAs in bumblebees.

Small RNA Deep Sequencing and the Effects of microRNA408 on Root Gravitropic Bending in Arabidopsis

2015 ◽  
Vol 27 (6) ◽  
pp. 495-503 ◽  
Author(s):  
Huasheng Li ◽  
Jinying Lu ◽  
Qiao Sun ◽  
Yu Chen ◽  
Dacheng He ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

scholarly journals Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing

BioTechniques ◽  
2010 ◽  
Vol 49 (4) ◽  
pp. 751-755 ◽  
Author(s):  
Mitsuoki Kawano ◽  
Chika Kawazu ◽  
Marina Lizio ◽  
Hideya Kawaji ◽  
Piero Carninci ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing

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

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