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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
Published on: June 8, 2020
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An optimized method to obtain high-quality RNA from cassava storage root.
Lulu Guan1, Xiaowen Ma1, Xiaoxia Zhou1
1Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China.
3 Biotech
|March 12, 2019
Summary
A new modified TM (MTM) method efficiently extracts high-quality RNA from cassava storage roots, overcoming challenges posed by polysaccharides and polyphenols. This cost-effective technique is suitable for downstream applications like qPCR and transcriptome sequencing.
Area of Science:
- Plant Molecular Biology
- Biochemistry
Background:
- High-quality RNA extraction is vital for eukaryotic molecular biology.
- Cassava storage roots present extraction challenges due to high polysaccharide and polyphenol content.
Purpose of the Study:
- Evaluate four RNA extraction methods for cassava storage roots.
- Identify an efficient, cost-effective method for high-quality RNA isolation.
Main Methods:
- Comparative analysis of four RNA extraction protocols.
- Assessment of RNA yield, purity (A260/280), and integrity (RIN).
- Validation using quantitative PCR (qPCR) and transcriptome sequencing.
Main Results:
- The modified TM (MTM) method proved superior in yield and quality.
- MTM yielded 4.18-5.94 µg RNA/g fresh weight with A260/280 ratios of 2.14-2.17.
- RIN values ranged from 7.2 to 8.0, indicating high integrity suitable for sequencing.
Conclusions:
- MTM is an efficient, time-saving, and low-cost method for cassava RNA extraction.
- The isolated RNA is of sufficient quality for downstream molecular analyses, including qPCR and transcriptome sequencing.
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