Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER
These videos have been matched automatically. Contact us if they are not relevant.
These videos have been matched automatically. Contact us if they are not relevant.
View abstract on PubMed
Summary
This summary is machine-generated.RISER is a new biochemical-free technology that enriches RNA detection during direct RNA sequencing. It depletes abundant RNA classes in real-time, improving the detection of weakly expressed RNA molecules.
Area Of Science
- Genomics and Molecular Biology
- Bioinformatics and Computational Biology
Background
- Cellular transcriptomes are complex, making it difficult to detect low-abundance RNA classes obscured by abundant ones.
- Existing biochemical methods for RNA enrichment/depletion are costly, time-consuming, and can degrade RNA integrity.
Purpose Of The Study
- To introduce RISER, a novel biochemical-free technology for real-time RNA class enrichment or depletion during direct RNA sequencing.
- To demonstrate RISER's ability to improve the detection of low-abundance RNA by reducing interference from dominant RNA species.
Main Methods
- RISER utilizes deep learning to identify RNA classes from nanopore signals in real-time.
- It selectively rejects unwanted RNA molecules by communicating directly with sequencing hardware.
- The technology is modular, retrainable, and features a user-friendly command-line interface.
Main Results
- RISER depleted dominant messenger and mitochondrial RNA classes by over 85%, increasing sequencing depth for long non-coding RNAs by 47%.
- In whole blood, RISER reduced globin mRNA reads by over 90%, increasing non-globin reads by 16%.
- RISER processing is faster than GPU-accelerated basecalling and mapping.
Conclusions
- RISER offers an efficient, real-time, and adaptable solution for targeted RNA depletion or enrichment in direct RNA sequencing.
- This technology overcomes limitations of traditional biochemical methods, enhancing the study of complex transcriptomes.
- RISER's speed and flexibility make it valuable for various RNA analysis applications.
These videos have been matched automatically. Contact us if they are not relevant.
These videos have been matched automatically. Contact us if they are not relevant.
Related Concept Videos
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...