PUBLICATION
Direct-TRI: High-throughput RNA-extracting Method for All Stages of Zebrafish Development
- Authors
- Ujibe, K., Nishimura, K., Kashima, M., Hirata, H.
- ID
- ZDB-PUB-211005-12
- Date
- 2021
- Source
- Bio-protocol 11: e4136 (Journal)
- Registered Authors
- Hirata, Hiromi
- Keywords
- Gene expression, High throughput, RNA isolation, RNA-Seq, Zebrafish
- MeSH Terms
- none
- PubMed
- 34604443 Full text @ Bio Protoc
Citation
Ujibe, K., Nishimura, K., Kashima, M., Hirata, H. (2021) Direct-TRI: High-throughput RNA-extracting Method for All Stages of Zebrafish Development. Bio-protocol. 11:e4136.
Abstract
Recent popularization of next-generation sequencing enables conducting easy transcriptome analysis. Nevertheless, substantial RNA isolation work prior to RNA sequencing, as well as the high cost involved, still makes the routine use of large-scale transcriptome analysis difficult. For example, conventional phenol-chloroform RNA extraction cannot be easily applied to hundreds of samples. Therefore, we developed Direct-TRI, a new cost-effective and high throughput RNA-extraction method that uses a commercial guanidine-phenol-based RNA extraction reagent and a 96-well silica column plate. We applied Direct-TRI to zebrafish whole larvae and juvenile samples and obtained comparable RNA qualities by several different homogenization methods such as vortexing, manual homogenizing, and freezing/crushing. Direct-TRI enabled the extraction of 192 RNA samples in an hour with a cost of less than a dollar per sample. Direct-TRI is useful for large-scale transcriptome studies, manipulating hundreds of zebrafish individuals, and may be used with other animal samples.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping