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.
Symbiotic bacteria: from hitchhiker to beetle bodyguard
28.04.2017 | Johannes Gutenberg-Universität Mainz
Nose2Brain – Better Therapy for Multiple Sclerosis
28.04.2017 | Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik IGB
More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.
Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...
Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.
"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...
The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.
Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...
The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...
Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.
Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...
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28.04.2017 | Life Sciences