As a collaborative laboratory (CoLab) plug-in, our mission is to foster connections among interdisciplinary researchers who share a common interest in discovering the biomedical potential of the microbiome. The Microbial Genomics CoLab Plug-in represents a new model for research and training at UCSF, offering collaborative data generation and analytical support for intramural and extramural investigators in parallel with embedded, experiential training opportunities in sequence-based microbiome profiling.
By providing collaborative expertise in next-generation sequencing, we facilitate the exploration of microbiome membership, gene content and transcriptional activity in relation to host outcomes and environmental exposures. We believe this approach in conjunction with complementary tools available within the Benoiff Center for Microbiome Medicine will lead to identification of actionable microbial targets and add a powerful new dimension to the diagnosis and treatment of medical conditions with unmet needs.
Our team has the expertise to offer assistance in the following areas: - Project planning and management - Sample collection, handling and storage recommendations - Nucleic acid extraction - Quantitative PCR - Library preparation and sequencing - Data interpretation - Dissemination of findings
As a centralized facility, we are a cost-effective resource for basic, clinical and translational studies. We have developed streamlined workflows and optimized protocols for individual sample types. Our technology hub is located in the Medical Science Building. Infrastructure for microbiome analyses includes dedicated pre- and post-PCR spaces, Illumina NextSeq and MiSeq instruments, Oxford Nanopore MinION and access to HiSeq and NovaSeq platforms and HPC cluster.
We recognize that collaboration is bi-directional. Shadowing opportunities and workshops are available to investigators upon request.
The core provides experimental design consultation, bioinformatics processing, and biostatistical analysis for microbiome and host-microbiome data. Additionally, the core embedded training on microbiome sequencing data analysis and data management support.
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DNA and RNA extraction (QIAGEN powerFecal kit)
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DNA extraction
We have experience working with a range of sample types including intestinal, skin, oral, nasal, blood or vaginal and are happy to work with investigators to develop extraction protocols for new sample types.
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Dual RNA sample processing (LibPrep and ribodeplete)
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Dual RNA seq
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Inactive - Technician Prep (Snr)
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Inactive - WGS Rapid 96
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ITS2 library preparation
This is the most economical, rapid and computationally feasible method for microbiota profiling in both pilot studies and projects involving large volumes of samples. Resultant data will reveal the types and distribution of organisms that make up the microbiota and provide insights on the complexity and structure of these communities. We have the capability to profile V1-V3 and V4 hypervariable regions of the 16S rRNA gene (bacteria) and ITS2 region (fungi).
Aside from DNA-based sequencing which captures live, dormant and dead microbial cells, we can apply a novel method developed in the Lynch Lab, where RNA is used to produce cDNA from which16S rRNA and ITS amplicons are generated. This permits assessment of transcriptionally active members of the microbiome, reducing the noise to signal ratio in associating microbial taxa with phenotypes of interest.
Internal
$35.90
each
External not for profit
$47.75
each
External for profit
$52.52
each
UC Rate
$35.90
each
Library Prep (Shotgun Metagenomics)
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Miseq (16S/ITS, 0-300)
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Miseq Micro (30-100)
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Miseq Nano (Fewer than 30)
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Miseq run only
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Nextseq (300-7200)
Kit charged separately as pass-through special consumables cost
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Nextseq run only
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Project management
Our team has the expertise to assist with all aspects of microbiome profiling, from study design, sample collection and preservation, sample processing, selection of appropriate sequencing method, generation of quality reads to data analysis. We work with investigators across disciplines to plan and coordinate studies involving the gut, oral, skin, vaginal microbiomes and many more. The first half hour of consultation is free of charge, subsequent project management services are invoiced at an hourly rate to support personnel time and administrative tasks.
Inquire
Shotgun Metagenomic Sequencing
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Technician Prep (Jr)
We can help investigators prepare microbiome collection kits and develop new protocols to address ongoing challenges in the field.
Our team has the expertise to assist with all aspects of microbiome profiling, from study design, sample collection and preservation, sample processing, selection of appropriate sequencing method, generation of quality reads to data analysis. We work with investigators across disciplines to plan and coordinate studies involving the gut, oral, skin, vaginal microbiomes and many more. The first half hour of consultation is free of charge, subsequent project management services are invoiced at an hourly rate to support personnel time and administrative tasks.
Inquire
Technician Prep (Jr)
We can help investigators prepare microbiome collection kits and develop new protocols to address ongoing challenges in the field.
We have experience working with a range of sample types including intestinal, skin, oral, nasal, blood or vaginal and are happy to work with investigators to develop extraction protocols for new sample types.
Inquire
Dual RNA sample processing (LibPrep and ribodeplete)
This is the most economical, rapid and computationally feasible method for microbiota profiling in both pilot studies and projects involving large volumes of samples. Resultant data will reveal the types and distribution of organisms that make up the microbiota and provide insights on the complexity and structure of these communities. We have the capability to profile V1-V3 and V4 hypervariable regions of the 16S rRNA gene (bacteria) and ITS2 region (fungi).
Aside from DNA-based sequencing which captures live, dormant and dead microbial cells, we can apply a novel method developed in the Lynch Lab, where RNA is used to produce cDNA from which16S rRNA and ITS amplicons are generated. This permits assessment of transcriptionally active members of the microbiome, reducing the noise to signal ratio in associating microbial taxa with phenotypes of interest.
Internal
$35.90
each
External not for profit
$47.75
each
External for profit
$52.52
each
UC Rate
$35.90
each
The core provides experimental design consultation, bioinformatics processing, and biostatistical analysis for microbiome and host-microbiome data. Additionally, the core embedded training on microbiome sequencing data analysis and data management support.
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