Product Offerings - DOE Joint Genome Institute (original) (raw)
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 product offerings, 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 sequencing products below. In addition, JGI will submit raw sequence data to SRA at NCBI once the standard analysis is complete. Raw metabolomics data is submitted to the MassIVE repository.
Not all products are available for all proposal calls. Please review the call language carefully to ensure that your request is appropriate for that call.
Learn more about the average base outputs for each product.
For custom requests not on this list, or to discuss experimental design for a proposal, we encourage you to contact the relevant JGI program leads to discuss available options.
Note: In 2021, we conducted an extensive internal product audit to analyze the scientific value, demand, and costs of current offerings in the JGI product catalog. As a result certain products have been discontinued, including smRNA, bisulfite sequencing, and ChIP-seq.
| Scientific Program | Product | Brief Description | Deliverables | Actual cycle time between July 1-Sep 30, 2024 (median), days* | Actual cycle time between July 1-Sep 30, 2024 (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 | 89 | N/A |
| 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 | 84 | N/A |
| 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 | depends on project | N/A |
| 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 | depends on project | N/A |
| 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 | depends on project | N/A |
| Fungal | Minimal Draft | Lower coverage short-read whole genome shotgun sequencing | Assembly, annotation (Mycocosm) | 354 | 382 |
| Fungal | Standard Draft | Whole genome shotgun sequencing using long-read sequencing. Exact library types and quality of finished product depend on genome. Selected genomes will be improved based on feasibility and scientific merit | Assembly, annotation (Mycocosm) | 354 | 382 |
| 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 | 237 | 237 |
| Fungal | Transcriptome | RNA for expression profiling and genome annotation (single organism). Note: smRNA sequencing is no longer supported. | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files | 208 | 205 |
| 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. | 62 | 138 |
| 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. | 62 | 138 |
| Metagenome | MetatranscriptomeReference guide | Environmental transcript sequence from prokaryotes and/or eukaryotes | Assembly, annotation (IMG/M), mapping to metagenome if applicable | 249 | 524 |
| Metagenome | Cell Enrichments Reference guide | 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) | 47 | 86 |
| Metagenome | Minimal DraftReference guide | Lower-coverage short-read assembly & annotation of environmental DNA (note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M), binning | 217 | 265 |
| Metagenome | Standard DraftReference guide | Short-read assembly & annotation of environmental DNA. (Note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M), binning | 217 | 265 |
| Metagenome | Improved DraftReference guide | Long-read assembly & annotation of environmental DNA. | Assembly, annotation (IMG/M), binning | 217 | 265 |
| Metagenome | Stable Isotope Probing (SIP)Reference guide SIP webinar | Used for the identification of active groups of organisms within a community. Individual samples are fractionated using a density gradient, and a metagenome library is prepared and sequenced for each fraction. | individual assembly, combined assembly of related fractions originating from the same sample, annotation (IMG/M), binning | depends on project | depends on project |
| Microbial | Minimal Draft, Isolate | Draft quality microbial assembly of short-read sequence data, many unordered contigs. | Assembly, annotation (IMG) | 280 | 298 |
| Microbial | Improved Draft, Isolate | High quality draft assembly of long-read sequence data, computationally analyzed and improved. Semi-manual. | Assembly, annotation (IMG), methylation analysis | 131 | 176 |
| Microbial | Single Particle Sort | Draft quality assembly of amplified genomes from sorted cell(s)/particle(s), many unordered contigs. | Assembly, annotation (IMG/M) | 150 | 150 |
| 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 | 114 | 114 |
| Microbial | Transcriptome | RNA for expression profiling (single organism). Note: smRNA sequencing is no longer supported. | For counting: text file of gene counts (mapped against reference transcriptome), alignment files | 133 | 133 |
| Viral | Minimal Draft | Draft quality viral assembly, many unordered contigs. | Assembly, annotation (IMG) | 111 | 159 |
| Viral | Single Particle Sort | Draft quality assembly of amplified genomes from sorted viral particles, unordered contigs | Assembly, annotation (IMG/M) | 162 | 167 |
| Viral | Enrichment | Draft quality assembly from virus pools/plaques obtained from a single host, many unordered contigs. | Assembly, annotation (IMG) | 162 | 167 |
| Plant and Algal | 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. Arizona Genomics Institute will produce high molecular weight DNA as needed for these projects. | Assembly, annotation for (Phytozome for plant, Phycocosm for algae) | depends on genome | depends on genome |
| Plant and Algal | 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 | 213 | 213 |
| Plant and Algal | Transcriptome | RNA for expression profiling and genome annotation (single organism). Note: smRNA sequencing is no longer supported. | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files | 144 | 245 |
| Plant, Algal, Fungal, and Microbial | DAP-seq | Used for genome-wide identification of transcription factor binding sites. | TF binding sites and motifs | project-dependent | project-dependent |
* Cycle times listed above are based on actual cycle times for projects completed over the previous quarter. In general, projects that do not require any rework will have the fastest cycle times, so please ensure your DNA/RNA sample quality is as high as possible to minimize failure.