The joint Call for Collaborative Science between EMSL and the Joint Genome Institute (JGI) is open from December 20, 2013 to April 7, 2014 for Letters of Intent. Both user facilities, which are stewarded by the Department of Energy Office of Biological and Environmental Research, play critical roles in supporting DOE’s energy, environment and basic research missions. This call represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.
Applications for this Collaborative Science program follow a proposal package, schedule, and review process that is tailored to meet both EMSL and JGI requirements. Details regarding this proposal process and schedule are available on the joint EMSL and JGI website, and returning users especially are advised to carefully review the unique elements of this joint program.
Successful applications will focus on high risk/high payoff projects in the focused topic areas that can be completed in 18 months, utilize a broad range of the capabilities of each facility, and generate datasets unique to these two facilities and beyond what each could generate by itself. An individual application should not request more than 300 Gb of DOE-JGI sequencing, in addition to the EMSL resources necessary for the proposed work. Accepted projects must broadly address DOE/BER missions, but proof of concept for the demonstration of a technology that would be applicable to a DOE mission is appropriate.
Focused Topic Areas
- Biogeochemistry – Projects that enhance our understanding of the relationship between microbial community structure-function and the biogeochemistry of metal contaminants, including radionuclides.
- Carbon Cycling – Projects that elucidate the signaling and metabolic pathways in the rhizosphere and their potential impacts on carbon storage in terrestrial ecosystems.
- Biofuels Production – Projects that link metabolism with microbial compartmentalization or organelle development in fungi to enable improved metabolic modeling for production of biofuel and chemical intermediates.
EMSL provides a wide range of unique and state-of-the-art resources that can be applied to proposals under this Call. Applications may request any combination of resources, but must provide adequate information to demonstrate the plan for integration and justify the amount requested. Applicants are strongly urged to discuss their resource needs with the respective Capability Leads or Instrument Scientists prior to responding to the Call. Contact information for these individuals is available on the resource description pages, or interested applicants may contact the EMSL User Support Office for assistance.
Researchers interested in learning more about EMSL and specific instruments can now view a dozen different instruments in four of EMSL’s laboratories through a panning 360-degree virtual tour. The tour includes lab and instrument overviews available through text, images, video and web pages. It features EMSL’s surface science instruments, nuclear magnetic resonance spectrometers, ion mobility mass spectrometers, and cell isolation and surface analysis tools. Recent sustainability projects, such as a solar array, also are highlighted.
DOE-JGI primarily employs next-generation short-read sequencing platforms, augmented by 3rd generation single-molecule/long-read capabilities (3kb up to 10kb). The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:
DOE-JGI Core Capabilities Include:
- De novo sequencing of plant, fungal, bacterial, and archaeal genomes
- Resequencing for variation detection
- Single-cell DNA sequencing
- Microbial community DNA/RNA sequencing
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Target enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including FAIRE, and histone modifications through ChIP-seq
- DNA/gene synthesis
- Analysis pipelines for the datasets above
DOE-JGI also has limited capacity for the following developing capabilities:
- 3rd generation single-molecule sequencing
- Fluorescence activated cell sorting, including single-cell sorting and amplification of genomic DNA
- Transposon mutagenesis of bacteria
- Custom genome analysis of generated datasets