The technique, which pairs RIKEN’s Cap Analysis of Gene Expression (CAGE) protocol with the Helicos® Genetic Analysis System developed by Helicos BioSciences Corporation, opens the door to the detailed analysis of gene expression networks and rare cell populations.
In recent years, next-generation DNA sequencers have produced an increasingly detailed picture of how genes are expressed at the molecular level. The transcriptional output of these genes – the RNA copies produced from DNA – has revealed a richness of complexity in transcript structure and function, providing insights into the molecular-level properties of cancers and other diseases.
One of the most powerful methods for analyzing RNA transcripts is the Cap Analysis of Gene Expression (CAGE) protocol developed at the RIKEN OSC. A unique approach, CAGE enables not only high-throughput gene expression profiling, but also simultaneous identification of transcriptional start sites (TSS) specific to each tissue, cell or condition.
With HeliScopeCAGE, the OSC research team has adapted the existing CAGE protocol for use with the revolutionary HeliScopeTM Single Molecule Sequencer. Unlike earlier sequencers, the HeliScope Sequencer does not employ polymerase chain reaction (PCR) amplification to multiply a small number of DNA strands for analysis, a process which can introduce biases into data. Instead, the HeliScope Sequencer actually sequences the DNA strand itself, enabling direct, high-precision measurement.In a paper published in Genome Research, RIKEN researchers confirm that this direct approach reduces biases and generates highly reproducible data from between 5 micrograms to as little as 100 nanograms of total RNA. A comparison using a leukemia cell line (THP-1) and a human cervical cancer cell line (HeLa) further shows that results from the technique are closely correlated to those from traditional microarray analysis. By making possible high-precision gene expression analysis from tiny samples, HeliScopeCAGE greatly expands the scope of research at the OSC, strengthening the institute’s role in Japan as a hub for next-generation genome analysis.
Here at the RIKEN Omics Science Center, we are developing a versatile analysis system, called the “Life Science Accelerator (LSA)”, with the objective of advancing omics research. LSA is a multi-purpose, large-scale analysis system that rapidly analyzes molecular networks. It collects various genome-wide data at high throughput from cells and other biological materials, comprehensively analyzes experimental data, and thereby aims to elucidate the molecular networks of the sample. The term “accelerator” was chosen to emphasize the strong supporting role that this system will play in supporting and accelerating life science research worldwide.
Microscope measures muscle weakness
16.11.2018 | Friedrich-Alexander-Universität Erlangen-Nürnberg
Good preparation is half the digestion
16.11.2018 | Max-Planck-Institut für Stoffwechselforschung
Researchers at the University of New Hampshire have captured a difficult-to-view singular event involving "magnetic reconnection"--the process by which sparse particles and energy around Earth collide producing a quick but mighty explosion--in the Earth's magnetotail, the magnetic environment that trails behind the planet.
Magnetic reconnection has remained a bit of a mystery to scientists. They know it exists and have documented the effects that the energy explosions can...
Biochips have been developed at TU Wien (Vienna), on which tissue can be produced and examined. This allows supplying the tissue with different substances in a very controlled way.
Cultivating human cells in the Petri dish is not a big challenge today. Producing artificial tissue, however, permeated by fine blood vessels, is a much more...
Faster and secure data communication: This is the goal of a new joint project involving physicists from the University of Würzburg. The German Federal Ministry of Education and Research funds the project with 14.8 million euro.
In our digital world data security and secure communication are becoming more and more important. Quantum communication is a promising approach to achieve...
On Saturday, 10 November 2018, the research icebreaker Polarstern will leave its homeport of Bremerhaven, bound for Cape Town, South Africa.
When choosing materials to make something, trade-offs need to be made between a host of properties, such as thickness, stiffness and weight. Depending on the application in question, finding just the right balance is the difference between success and failure
Now, a team of Penn Engineers has demonstrated a new material they call "nanocardboard," an ultrathin equivalent of corrugated paper cardboard. A square...
09.11.2018 | Event News
06.11.2018 | Event News
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16.11.2018 | Health and Medicine
16.11.2018 | Life Sciences
16.11.2018 | Life Sciences