| Title: | RNA sequencing analyses for deciphering potato molecular responses |
|---|
| Authors: | ID Ramšak, Živa (Author)
ID Petek, Marko (Author)
ID Baebler, Špela (Author) |
|---|
| Files: |  PDF - Presentation file, download (3,14 MB)
MD5: 0135C58F4F9D6EBA14A9DFA5C1E97EB9
 URL - Source URL, visit https://link.springer.com/protocol/10.1007/978-1-0716-1609-3_3
|
|---|
| Language: | English |
|---|
| Typology: | 1.16 - Independent Scientific Component Part or a Chapter in a Monograph |
|---|
| Organization: |  NIB - National Institute of Biology
|
|---|
| Abstract: | Understanding the molecular mechanisms of potato development and responses to environmental stressors is of utmost importance for achieving stable crop yields. RNA sequencing (RNA-Seq) provides an insight into responses of all of the organism genes to the environmental and developmental cues and thus provides insights into underlying modes of action. In this chapter, we guide a researcher through some of the most important steps in the analysis of transcriptomics data. The initial topic of experimental design is followed by a more wet-lab-oriented section on RNA-Seq sample preparation. Next, we present intermediate steps of data retrieval, quality control, mapping, and differential expression of the dataset and a section on how to expose your data to the public (i.e., public repositories) and make it findable, accessible, interoperable, and reusable (FAIR). In the last four sections, we describe specific tools or Web applications, which ease the exploration of generated results in the context of their gene function and network-based visualizations, specifically GoMapMan, GSEA, DiNAR, and Biomine Explorer. All sections are accompanied by potato dataset examples and include general hints and tricks, as well as potato specificities that one should be aware of. |
|---|
| Publication status: | Published |
|---|
| Publication version: | Author Accepted Manuscript |
|---|
| Publication date: | 01.01.2021 |
|---|
| Year of publishing: | 2021 |
|---|
| Number of pages: | str. 57-94 |
|---|
| PID: | 20.500.12556/DiRROS-23221  |
|---|
| UDC: | 632 |
|---|
| COBISS.SI-ID: | 76791043 |
|---|
| Publication date in DiRROS: | 06.08.2025 |
|---|
| Views: | 384 |
|---|
| Downloads: | 189 |
|---|
| Metadata: |    |
|---|
|
:
|
Copy citation |
|---|
| | | | Share: |  |
|---|
Hover the mouse pointer over a document title to show the abstract or click
on the title to get all document metadata. |
