The CCR DNA Sequencing and Digital Gene Expression Core Facility, located within the Laboratory of Experimental Carcinogenesis, provides NCI intramural investigators with rapid and accurate sequencing of DNA samples. The DNA and Digital Gene Expression Core is an "open access" facility that has been in operation since April 1997 and has processed approximately 400,000 samples. The Core also processes samples for genomic protocols. Facility staff members provide expertise in the use of software and help in troubleshooting sequencing reactions and results. The mission of the DNA Sequencing Core is to combine the efficiency and quality of a centralized facility with the speed and convenience of a dedicated laboratory instrument. A major emphasis is placed on maximizing the use of the sequencers and minimizing the time between sample submissions and processing. Samples are accepted in which the reaction has already been completed by the user, as well as samples in which the sequencing reaction has yet to be done.
The core provides digital gene expression using the NanoString's nCounter Analysis System. The nCounter Analysis System utilizes a novel digital technology that is based on direct multiplex measurement of gene expression and offers high levels of precision and sensitivity. The technology uses molecular "barcodes" and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.
In 2012, the Core made its first venture into next generation sequencing with the MiSeq system. MiSeq utilizes reversible terminator-based sequencing by synthesis chemistry that delivers read lengths of up to 2x300bp and 15Gb of data output within days. Core staff will see each experiment through from beginning to end, offering experimental design, library preparation, and bioinformatics services, as well as partnering with OSTP to provide investigators with financial support. In the past year, the Core has worked on projects with a variety of applications, including targeted custom cancer panels, highly multiplexed PCR amplicon sequencing, T-cell receptor sequencing, viral profiling in patients and the search for novel viruses, whole bacterial genome sequencing, and 16S metagenomics.
In addition to services provided by the core, the core is home to several instruments where people can sign up on a calendar controlled by the core at no cost and use the instruments. These instruments include the Agilent DNA Microarry scanner and oven, a 2100 Bioanalyzer and the Stratagene Mx3005 Real Time PCR instrument.
Sample Size and Turnaround for sequencing
The Core is specifically designed for small to intermediate sample numbers. The average sample size is approximately 13, we average about 350 samples per day, and, as many as 1600 samples can be run per day. The Core does handle larger projects, but these need to be scheduled with our staff (see Contact Us). The usual time between submission of samples and delivery of data is currently less than one (1) business day. A database keeps track of sample submission and processing, the order in which samples may most efficiently be processed, and the costs. The Core's database is also used to control the distribution of finished data sets and to inform users when their data is ready.