About This Call
The CSP New Investigator call seeks to target investigators and research initiatives new to the JGI, with an emphasis on providing pilot data to assess feasibility of a novel approach or form the foundation for a large-scale CSP proposal submission. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previously accepted JGI CSP or FICUS proposal. Sequence requests should not exceed 500 Gbp in total.
Proposals for this call may be submitted at any time as brief white papers and will be reviewed every six months. Applicants may submit up to two proposals per cycle (but may be listed as co-PI on an unlimited number of proposals). Proposals must be submitted using the web form available at (begin a new proposal document at http://proposals.jgi.doe.gov/ to see the proposal format).
All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions. Screened proposals will then be reviewed for scientific merit, DOE relevance, proposed data usage by the applicant/community, and track record of the applicant. After proposal approval, and at an established time (roughly two months after approval), the proposer will be asked to provide samples meeting JGI’s sample requirements. Samples that are not available at that time, or are of insufficient quality or quantity, will delay or potentially defer approval for sequencing.
For details on JGI product offerings see https://jgi.doe.gov/user-program-info/product-offerings/. For questions about the appropriateness of projects, program specifics or application process, please contact us.
Current Call (OPEN; proposals due March 1, 2018)
Bacterial and archaeal isolates and single cell draft genomes
The JGI will accept proposals for sequencing of collections of bacterial and archaeal genomes from cultivated isolates or physically isolated single cells. Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. Type strains, including proposed strains prior to publication, are highly encouraged. For single-cell sequencing projects, MDA products of single amplified genomes should be in hand at the time of proposal submission – JGI will not do sorting and genome amplification of single cells under this call. Between 48 and 92 isolates or single-cell genomes may be proposed. For projects with >92 genomes, please refer to the CSP Annual Call.
The JGI seeks proposals centered on resequencing of bacterial, archaeal and fungal isolates for which a reference genome exists. Projects may focus on natural population structure, understanding gene function under selective pressure or in mutagenized strains, or developing pan and core genomes. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose decomposition, fermentation of sugar substrates or degradation of environmental toxins for bacteria and fungi or biomass composition for plants. Between 36 and 72 samples may be proposed. For projects with >72 samples, please refer to the CSP Annual Call.
Plant genome size estimation
Proposals will be considered for low-pass short-read sequencing of plant genomes to assess genome size and complexity in preparation for large-scale genome sequencing projects. Between 1-6 samples may be proposed. For larger number of samples, please refer to the CSP Annual Call.
Bacterial, archaeal, fungal and plant RNA sequencing
The JGI solicits RNA sequencing projects for genomes for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (e.g. gene expression profiling of a bacterium during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions; for plants, projects using the standard conditions defined by the Plant Gene Atlas are specifically encouraged. Between 36 and 54 samples (including replicates) may be proposed. For projects with >54 samples, please refer to the CSP Annual Call.
Bacterial and archaeal epigenomes and high-quality draft genomes
Single molecule real time sequencing enables greater genome contiguity as well as assessment of DNA base modifications (6mA, 5mC, 4mC and others) of potential importance in host defense and gene regulation. The JGI will accept proposals including up to 12 samples for improved draft or epigenome sequencing. For projects with >12 samples, please refer to the CSP Annual Call.
Metagenomes and metatranscriptomes
JGI is accepting proposals that include up to 92 metagenomes or metatranscriptomes (in any combination) from environmental samples, laboratory enrichments or synthetic communities. Projects examining sample series across time or space as well as those targeting viruses are particularly encouraged.
The JGI has limited capacity (≤8 samples; 24 sequencing libs) for targeted sorting and metagenomic analysis of specific populations that can be fluorescently labeled, e.g. naturally pigmented cells, cells labeled with Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT), etc. This ‘mini-metagenomic’ approach does not require whole genome amplification assuming >10,000 target cells can be recovered, and target populations should be >1% of cells. Proposals should not include requests for single cell sorting and sequencing.
Note: JGI will be phasing out amplicon sequencing beginning September 2017, so iTag requests will no longer be supported.
DNA synthesis for functional assays
DNA/gene synthesis linked to sequence data generation, including codon optimization, refactoring, and assembly of biosynthetic pathways into appropriate vector systems for expression in heterologous hosts. (Use of this capability is encouraged, but synthesis-only projects should be directed to the call for stand-alone DNA synthesis proposals). JGI is accepting proposals for synthesis of up to 500 kb.
Metabolomics based functional analyses
Targeted and untargeted metabolomic technologies at JGI enable users to examine diverse polar and non-polar metabolites from plants, microbes, and environments. In addition, users may request targeted analysis of stable isotope labeling for specific metabolites. JGI is accepting proposals for up to 50 polar metabolite sample analyses or 150 non-polar metabolite sample analyses.
Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date. This call replaces the “Small Scale Microbial CSP call” which is no longer active.
Upcoming submission deadlines/review dates:
March 1, 2018/May 2018
September 4, 2018/November 2018
March 1, 2019/May 2019