Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species
Studying transcriptomic changes in plants is crucial for the understanding of many plant biological processes. In this study, a method is proposed that aims to cheaply and efficiently multiplex RNA-seq libraries without the need of RNA barcoding, by using only conventional bioinformatical tools from...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Final Year Project (FYP) |
| Language: | English |
| Published: |
Nanyang Technological University
2023
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/169871 |
| _version_ | 1811678546899238912 |
|---|---|
| author | Boon, Chong Jun |
| author2 | Marek Mutwil |
| author_facet | Marek Mutwil Boon, Chong Jun |
| author_sort | Boon, Chong Jun |
| collection | NTU |
| description | Studying transcriptomic changes in plants is crucial for the understanding of many plant biological processes. In this study, a method is proposed that aims to cheaply and efficiently multiplex RNA-seq libraries without the need of RNA barcoding, by using only conventional bioinformatical tools from typical RNA-seq analyses for demultiplexing. Arabidopsis thaliana, Brachypodium distachyon, and Oldenlandia corymbosa were chosen to create the multiplexed RNA sequence libraries in this study. Firstly, HISAT2 and Kallisto were compared for their ability to demultiplex the RNA libraries sequenced. HISAT2 was proven to be superior in de-multiplexing compared to Kallisto. HISAT2 also offered better optimisation capabilities. Secondly, it has been demonstrated that using O. corymbosa to spike transcripts can be used as a viable internal reference for count normalisation. Both methods have potential applications beyond plant stress research, which can offer cost savings and enhanced accuracy in RNA sequencing studies with a large sample quantity. Further optimisation of the demultiplexing process can also be achieved using HISAT2 parameters, allowing for more efficient and accurate RNA sequencing research. |
| first_indexed | 2024-10-01T02:54:59Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/169871 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:54:59Z |
| publishDate | 2023 |
| publisher | Nanyang Technological University |
| record_format | dspace |
| spelling | ntu-10356/1698712023-09-12T07:52:11Z Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species Boon, Chong Jun Marek Mutwil School of Biological Sciences mutwil@ntu.edu.sg Science::Biological sciences::Botany Science::Biological sciences::Genetics Studying transcriptomic changes in plants is crucial for the understanding of many plant biological processes. In this study, a method is proposed that aims to cheaply and efficiently multiplex RNA-seq libraries without the need of RNA barcoding, by using only conventional bioinformatical tools from typical RNA-seq analyses for demultiplexing. Arabidopsis thaliana, Brachypodium distachyon, and Oldenlandia corymbosa were chosen to create the multiplexed RNA sequence libraries in this study. Firstly, HISAT2 and Kallisto were compared for their ability to demultiplex the RNA libraries sequenced. HISAT2 was proven to be superior in de-multiplexing compared to Kallisto. HISAT2 also offered better optimisation capabilities. Secondly, it has been demonstrated that using O. corymbosa to spike transcripts can be used as a viable internal reference for count normalisation. Both methods have potential applications beyond plant stress research, which can offer cost savings and enhanced accuracy in RNA sequencing studies with a large sample quantity. Further optimisation of the demultiplexing process can also be achieved using HISAT2 parameters, allowing for more efficient and accurate RNA sequencing research. Bachelor of Medicine (Chinese Medicine) Bachelor of Science in Biomedical Sciences 2023-08-10T07:05:29Z 2023-08-10T07:05:29Z 2023 Final Year Project (FYP) Boon, C. J. (2023). Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species. Final Year Project (FYP), Nanyang Technological University, Singapore. https://hdl.handle.net/10356/169871 https://hdl.handle.net/10356/169871 en application/pdf Nanyang Technological University |
| spellingShingle | Science::Biological sciences::Botany Science::Biological sciences::Genetics Boon, Chong Jun Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title | Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title_full | Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title_fullStr | Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title_full_unstemmed | Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title_short | Revolutionizing plant stress response studies: developing a novel method for high-throughput analysis of multiple plant species |
| title_sort | revolutionizing plant stress response studies developing a novel method for high throughput analysis of multiple plant species |
| topic | Science::Biological sciences::Botany Science::Biological sciences::Genetics |
| url | https://hdl.handle.net/10356/169871 |
| work_keys_str_mv | AT boonchongjun revolutionizingplantstressresponsestudiesdevelopinganovelmethodforhighthroughputanalysisofmultipleplantspecies |