Welcome!
| 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. |
| Name | Title | Phone | |
| Rahim Khan, PhD | Manager | rahim.khan@ucsf.edu |
| Hours | Location | ||
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| Name | Role | Phone | Location | |
|---|---|---|---|---|
| Rahim Khan |
Manager
|
rahim.khan@ucsf.edu
|
| Service list |
| ► Project and Method Development (3) | |||
| Name | Description | Price | |
|---|---|---|---|
| Project management |
|
Inquire | |
| Technician Prep (Jr) |
|
Inquire | |
| Technician Prep (Snr) | Inquire | ||
| ► Sample Processing (3) | |||
| Name | Description | Price | |
| 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. |
Inquire | |
| Dual RNA sample processing (LibPrep and ribodeplete) | Inquire | ||
| RNA processing surcharge |
Additional steps such as RNA isolation and cDNA synthesis can be performed to support transcriptomics projects. |
Inquire | |
| ► Bacterial 16S rRNA Sequencing (2) | |||
| Name | Description | Price | |
| V1-3 library preparation | Inquire | ||
| V4 library preparation | Inquire | ||
| ► Fungal ITS sequencing (1) | |||
| Name | Description | Price | |
| ITS2 library preparation | Inquire | ||
| ► Shotgun Metagenomics (2) | |||
| Name | Description | Price | |
| Library Prep (Shotgun Metagenomics) | Inquire | ||
| Shotgun Metagenomic Sequencing | Inquire | ||
| ► Analysis (1) | |||
| Name | Description | Price | |
| Data analysis |
Each analysis package is customized to the project and includes a written report with figures, methods and sequence data files. Analysis is charged based on an hourly rate. Although the actual cost will depend on the total number of samples, the complexity of the study design and analytical approach, most projects can expect to spend $2000+ for analyses. |
Inquire | |
| ► Sequencing (9) | |||
| Name | Description | Price | |
| Dual RNA seq | Inquire | ||
| Miseq (16S/ITS, 0-300) | Inquire | ||
| Miseq Micro (30-100) | Inquire | ||
| Miseq Nano (Fewer than 30) | Inquire | ||
| Miseq run only | Inquire | ||
| Nexteseq run only | Inquire | ||
| Nextseq (300-7200) | Inquire | ||
| WGS Rapid 24 | Inquire | ||
| WGS Rapid 96 | Inquire | ||
