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Salk Institute Using WaferGen SmartChip System in 'Nano-qPCR' Core Lab

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WaferGen Biosystems said this week that the Salk Institute for Biological Studies has established a nano-qPCR core laboratory that will feature a WaferGen SmartChip system for high-throughput, real-time PCR studies.

A major focus of the core lab will be on designing and testing libraries of assays targeting receptors and transcriptional regulators for important functional pathways, thereby interrogating entire regulatory networks in a highly parallel fashion. It is also envisioned that the lab will be an important resource for the larger Salk community.

Ronald Evans, professor and chair of developmental biology at Salk Institute, will head the lab. Evans received the 2004 Albert Lasker Prize for Basic Medical Research and is a member of the National Academy of Sciences and a Howard Hughes Medical Institute Investigator.

In a statement, Evans said that his group has successfully tested the SmartChip system in a variety of gene expression experiments.

"The platform is ideal for follow-up studies to [chromatin-immunoprecipitation sequencing], and for de novo large-scale gene expression studies in precious clinical samples," Evans said, adding that the group chose SmartChip based on its ability to perform qPCR without pre-amplification and provide "the required throughput for measuring a series of longitudinal genomic events in cells." Evans said that the platform's flexibility was also a selling point.

Chromatin immunoprecipitation, or ChIP, is a technique whereby genomic regulatory sites bound by a specific factor of interest are enriched through antibody precipitation. ChIP sequencing uses next-generation sequencing to provide the nucleotide sequences of these regulatory sites.

Downstream studies have historically been conducted by designing qPCR assays targeting these elements, and have been restricted to small numbers of analytes due to the limited amounts of ChIP material, WaferGen said. SmartChip enables NGS researchers to quantitatively evaluate the presence of numerous elements across multiple ChIP samples, thus facilitating the validation of large ChIP-seq data sets and allowing researchers to conduct large studies of promoter occupancy dynamics, WaferGen said.

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