The JGI has diverse capabilities in DNA and RNA sequencing, sample and library preparation, DNA synthesis and pathway engineering, and mass spectrometry based metabolomics. Below is a table of standard sequencing and synthesis products, including a description of the product and deliverables as well as target cycle times from sample receipt to completion of standard analysis. (Note: raw data is provided for all products below. In addition, JGI will submit raw sequence data to SRA once the standard analysis is complete.)
For custom requests not on these lists, we encourage you to contact the relevant program leads to discuss available options.
| Scientific Program | Product | Brief Description | Deliverables | FY20 target cycle time (median), days* | FY20 target cycle time (75th %), days* |
|---|---|---|---|---|---|
| DNA Synthesis | Constructs <5kb in size | Single gene or multiple small genes assembled to less than 5kb in length, cloned into vector of choice | Glycerol stock of sequence verified clone | 80 | 80 |
| DNA Synthesis | Constructs 5-10kb in size | Single gene or multiple small genes assembled totaling 5-10kb in length, cloned into vector of choice | Glycerol stock of sequence verified clone | 100 | 100 |
| DNA Synthesis | Constructs >10kb in size | Gene clusters or pathways totaling more than 10kb in length assembled together, cloned into vector of choice | Glycerol stock of sequence verified clone | 160 | 160 |
| DNA Synthesis | Combinatorial libraries | Multiple genes synthesized and cloned into a vector of choice in various combinations | Glycerol stock of sequence verified clones if low number of variants, or pool of variants with sample sequencing to predict the number of successful variants made | 200 | 200 |
| DNA Synthesis | Complex libraries | Multiple variants of sgRNA or a small coding gene assembled together in various combinations and cloned into a vector of choice; up to 210,000 variants can be made | Pool of variant libraries; sample sequencing to determine coverage of variants | 200 | 200 |
| Fungal | Minimal Draft | Lower coverage whole genome shotgun sequencing | Assembly, annotation (Mycocosm) | 300 | 475 |
| Fungal | Resequencing | SNP and short indel calls, rearrangement detection, population analysis | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files | 215 | 300 |
| Fungal | Standard Draft | Whole genome shotgun sequencing. Exact scope items and quality of finished product depend on genome. Selected genomes will be improved based on feasibility and scientific merit | Assembly, annotation (Mycocosm) | 300 | 475 |
| Fungal | Transcriptome | RNA for expression profiling and genome annotation (single organism) | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files | 215 | 270 |
| Metabolomics | Polar metabolite analysis | Relative abundance profiling of polar (e.g. amino acids, nucleosides, etc) metabolites using normal phase chromatography coupled to tandem mass spectrometry (detailed description) | Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. | based on experimental design | based on experimental design |
| Metabolomics | Non-polar metabolite analysis | Relative abundance profiling of non-polar (e.g. secondary metabolites, lipids, etc) metabolites using reverse phase chromatography coupled to tandem mass spectrometry (detailed description) | Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. | based on experimental design | based on experimental design |
| Metagenome | Metatranscriptome | Environmental transcript sequence from prokaryotes and/or eukaryotes | Assembly, annotation (IMG/M), mapping to metagenome if applicable | 175 | 215 |
| Metagenome | Cell Enrichments |
Obtained by physical separation of a biologically relevant unit from a microbial community, such as a microcolony, microbial aggregate, or a specific subset of free-living cells. Due to the low biomass of cell enrichments, the extracted DNA may be amplified using whole-genome amplification prior to sequencing. | Assembly, annotation (IMG/M) | 240 | 430 |
| Metagenome | Minimal Draft | Lower-coverage assembly & annotation of environmental DNA (note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M) | 200 | 220 |
| Metagenome | Standard Draft | Assembly & annotation of environmental DNA. Selected metagenomes will be improved based on feasibility and scientific merit. (Note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M) | 200 | 220 |
| Microbial | Improved Draft, Isolate | High Quality Draft assembly computationally analyzed and improved. Semi-manual. | Assembly, annotation (IMG), methylation analysis | 260 | 380 |
| Microbial | Minimal Draft, Isolate | Lowest quality microbial draft product, many unordered contigs. | Assembly, annotation (IMG) | 240 | 430 |
| Microbial | Minimal Draft, Single Cell | Lowest quality microbial draft product, many unordered contigs. | Assembly, annotation (IMG) | 240 | 430 |
| Microbial | Single Particle Sort | Draft assembly of whole genome amplified sorted cell(s)/particle(s) | Assembly, annotation (IMG/M) | 240 | 430 |
| Microbial | Resequencing | SNP and short indel calls, rearrangement detection, population analysis. | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files | 150 | 180 |
| Microbial | Transcriptome | RNA for expression profiling (single organism). | For counting: text file of gene counts (mapped against reference transcriptome), alignment files | 150 | 180 |
| Microbial | Transcriptome – smRNA | smRNA sequencing (size range: 30-200 bp) | mapping to reference genome, identifying known miRNAs and predicting novel miRNAs (miRDeep2 software). | 150 | 180 |
| Plant | Resequencing | SNP and short indel calls, rearrangement detection, population analysis. | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files | 95 | 140 |
| Plant | Standard Draft | Whole genome shotgun sequencing. Sequencing generated for initial evaluation varies depending on genome characteristics, availability of external resources and project goals. Selected genomes will be improved based on feasibility and scientific merit. | Assembly, annotation (Phytozome) | depends on genome | depends on genome |
| Plant | Transcriptome | RNA for expression profiling and genome annotation (single organism). | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files | 210 | 280 |
| Plant | Bisulphite-seq | Used for genome-wide analysis of DNA methylation patterns. | Genome-wide methylation calls and summary statistics of fraction of genome methylated in different sequence contexts | ||
| Plant and Fungal | ChIP-seq | Used for genome-wide analysis of in vivo binding sites for DNA associated proteins to assess their role in temporal and spatial patterns of gene expression and chromatin remodeling. | protein binding sites | ||
| Plant and Fungal | Transcriptome – smRNA | smRNA sequencing (size range: up to 35 bp ) | mapping to reference genome, identifying known miRNAs and predicting novel miRNAs (miRDeep2 software). | 175 | 225 |
* FY20 actual cycle times may be affected by JGI’s move to its new facility in FY20 Q1. If your project will be delayed by the move, your project manager will contact you with more information.