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| Status |
Public on Nov 15, 2019 |
| Title |
Small non-coding RNA discovery and profiling with sRNAtools based on high-throughput sequencing |
| Organism |
Populus deltoides |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Small non-coding RNAs (sncRNAs) are generated from different genomic loci and have important roles in biological processes, such as cell proliferation and regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNAs, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small interfering RNAs), piRNAs and plant specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all these diverse sncRNAs. A novel web server, sRNAtools (https://bioinformatics.sc.cn/sRNAtools), is presented that can be used in conjunction with high-throughput sequencing to discover, profile and functionally annotate sncRNAs, including miRNAs, isomiRs, piRNAs, tRFs, tRNAs, snRNAs, snoRNAs, rRNAs, phasiRNAs, and plant specific 24-nt siRNAs for 21 species. In this study, sRNAtools has been used in sncRNA profiling in poplar wood tissues, which identified many wood related sncRNAs expression patterns.We believe that sRNAtools will greatly benefit the scientific community as an integrated tool to study sncRNAs.
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| Overall design |
Woody plants provide large amounts of biomass, which can serve as raw material for the production of renewable energy and other commercial products. Poplar is a model system to study woody plants. miRNAs has been revealed playing important roles in the formation of poplar wood. To fully understand the characteristics of poplar sncRNAs, especially in wood formation, we used sRNAtools based on sRNA-seq to study sncRNAs in all poplar wood tissues (xylem, phloem, and cambium) and leaves.
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| Contributor(s) |
Lang X, Liu Q, Ding C, Su X |
| Citation(s) |
31885040 |
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| Submission date |
Nov 04, 2019 |
| Last update date |
Feb 14, 2020 |
| Contact name |
Qi Liu |
| Organization name |
Chinese Academy of Forestry
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| Department |
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry
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| Lab |
Su lab
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| Street address |
Dong xiaofu No 1, Xiangshan Road, Haidian District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
10091 |
| Country |
China |
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| Platforms (1) |
| GPL20012 |
Illumina HiSeq 2000 (Populus deltoides) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA587495 |
| SRA |
SRP228551 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE139897_RAW.tar |
386.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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