Related Experiment Video
Updated: Mar 11, 2026
08:25
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
12.9K
cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs
Tobias Fehlmann1, Stefanie Reinheimer2, Chunyu Geng3
1Clinical Bioinformatics, Saarland University, 66125 Saarbrücken, Germany.
Clinical Epigenetics
|November 30, 2016
Summary
The BGISEQ-500 sequencer using combinatorial probe-anchor synthesis (cPAS) demonstrates high reproducibility for small non-coding RNA sequencing. This technology offers a valuable addition to existing methods for miRNome analysis.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The study introduces the BGISEQ-500 sequencer, which utilizes combinatorial probe-anchor synthesis (cPAS).
- Investigated the human small non-coding RNA repertoire using this novel sequencing technology.
Purpose of the Study:
- To evaluate the performance of the cPAS-based BGISEQ-500 sequencer for small non-coding RNA analysis.
- To compare its capabilities against established sequencing techniques.
Main Methods:
- Generated sequencing data from human tissues (brain, heart) and blood.
- Performed bioinformatic analysis including read mapping to the human genome and miRBase.
- Utilized miRDeep2 for novel miRNA prediction with stringent criteria.
Main Results:
- Achieved a median of 30.1 million reads per sample with high mapping rates to miRBase.
- Demonstrated high technical reproducibility with a median correlation of 0.98 among technical replicates.
- Showed good correlation with other platforms (HiSeq: 0.75, microarrays: 0.58), while noting potential biases in blood cell expression.
Conclusions:
- cPAS-based sequencing exhibits high technical reproducibility.
- This technology serves as a valuable supplement to existing platforms for miRNome profiling.
- While no single platform is ideal, cPAS offers a reliable option for specific analytical challenges.
Related Concept Videos
03:21RNA-seq
12.3K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.3K
03:00Next-generation Sequencing
100.3K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
100.3K
01:57Sanger Sequencing
777.0K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
777.0K
02:24Ribosome Profiling
4.3K
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...
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...
4.3K
02:35RACE - Rapid Amplification of cDNA Ends
7.5K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.5K