| Title: | Methodologies for discovery and quantitative profiling of sRNAs in potato |
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| Authors: | ID Križnik, Maja (Author)
ID Zagorščak, Maja (Author)
ID Gruden, Kristina (Author) |
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| Files: |  PDF - Presentation file, download (1,17 MB)
MD5: F0DA6D3450D8B48289FF39A52B51B80A
 URL - Source URL, visit https://link.springer.com/protocol/10.1007/978-1-0716-1609-3_11
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| Language: | English |
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| Typology: | 1.16 - Independent Scientific Component Part or a Chapter in a Monograph |
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| Organization: |  NIB - National Institute of Biology
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| Abstract: | Small RNAs (sRNAs) are short noncoding RNAs involved in the regulation of a wide range of biological processes in plants. Advances in high-throughput sequencing and development of new computational tools had facilitated the discovery of different classes of sRNAs, their quantification, and elucidation of their functional role in gene expression regulation by target transcript predictions. The workflow presented here allows identification of different sRNA species: known and novel potato miRNAs, and their sequence variants (isomiRs), as well as identification of phased small interfering RNAs (phasiRNAs). Moreover, it includes steps for differential expression analysis to search for regulated sRNAs across different tested biological conditions. In addition, it describes two different methods for predicting sRNA targets, in silico prediction, and degradome sequencing data analysis. All steps of the workflow are written in a clear and user-friendly way; thus they can be followed also by the users with minimal bioinformatics knowledge. We also included several in-house scripts together with valuable notes to facilitate data (pre)processing steps and to reduce the analysis time. |
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| Publication status: | Published |
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| Publication version: | Author Accepted Manuscript |
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| Publication date: | 01.01.2021 |
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| Year of publishing: | 2021 |
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| Number of pages: | str. 221-260 |
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| PID: | 20.500.12556/DiRROS-23222  |
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| UDC: | 632 |
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| COBISS.SI-ID: | 76787203 |
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| Publication date in DiRROS: | 06.08.2025 |
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| Views: | 387 |
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| Downloads: | 178 |
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| Metadata: |    |
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