Optimising RNA extraction for paddy bulk soil samples for metatranscriptome sequencing
Upon evaluation, the RNA extraction protocol by Peng et al., 2018 (method B3) was optimized by incorporating 20% and 30% PEG-based precipitation to remove carry-over pigmentation. Comparative testing showed that 20% PEG produced the highest quality RNA, yielding pigment-free RNA (> 100 ng/µl, integrity > 7, and A260/A280 of 2.02 ± 0.02). Metatranscriptome sequencing and analysis with Trinity, BUSCO, and Kraken2 confirmed superior quality and higher bacterial read assignment for RNA extracted with 20% PEG, highlighting its effectiveness for downstream microbial transcriptomic applications.
Authors
- Bent Petersen (ORCID: https://orcid.org/0000-0002-2472-8317)
- Ganesan Vadamalai
- Heera Rajandas (ORCID: https://orcid.org/0000-0001-5963-3441)
- Sumitra Sivaprakasam (ORCID: https://orcid.org/0009-0001-1373-9918)
- Sivachandran Parimannan (ORCID: https://orcid.org/0000-0002-0101-1858)
- Thomas Sicheritz‐Pontén (ORCID: https://orcid.org/0000-0001-6615-1141)
- Yukgehnaish Kumarasan
- Erneeza Mohd Hata (ORCID: https://orcid.org/0000-0002-4918-9049)
- Tan Yee Fan
Institutions
- University of Copenhagen (DK)
- Universiti Putra Malaysia (MY)
- AIMST University (MY)
Publication Details
- Journal
- BMC Research Notes
- Published
- 2025-07-05
- DOI
- https://doi.org/10.1186/s13104-025-07342-9
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Asian Institute of Medicine, Science and Technology
- Core Research for Evolutional Science and Technology