CoLabs offers numerous genomic approaches for UCSF and external investigators. We provide library construction and analysis tools for a variety of bulk and single cell genomic applications.
Our Genomics CoLab website lists recharge rates for our assays and services. To get started, please contact Genomics CoLab to discuss your project. From there, you may work with additional CoLabs Teams. Along with genomic methods, you can take advantage of the complementary platforms, expertise, and collaborative culture at CoLabs. Our labs are located near each other to streamline communication and workflows.
Working within the CoLabs Community
If you are interested in spatial transcriptomics, please visit our Spatial Omics platform section. If you require sorting for single cell applications, Flow Cytometry CoLab has a variety of sorters and Disease to Biology CoLab can assist with sample preparation and panel design. To combine results from several sources, Data Science CoLab can provide help with data integration and analysis. For large-scope projects, you can establish a multidisciplinary collaboration (“CoProject”) between you and multiple CoLabs Teams. CoProjects is also a conduit for CoLabs to develop customized methodologies.
Consultations prior to the start of the experiment are highly encouraged. Discussion topics include experimental design, sample processing, DNA/RNA extraction methods, nucleic acid quality control, NGS library preparation, sequencing strategies, and bioinformatic analysis methods.
CoLabs prepares libraries for sequencing with Illumina platforms and with 10x Genomics as an official Service Provider partner. Library preparation includes quality control, normalization, and pooling. We offer some sample processing services. Please contact us if you require a higher level of support.
Common assays are listed below, and more information (including costs) can be found on the Genomics CoLab website.
| Bulk genomics | Single cell genomics |
|---|---|
| Total RNA-seq PolyA RNA-seq Small RNA-seq ATAC-seq DNA-seq/ChIP-seq Exome-seq Microbiome-seq CUT&Tag |
scRNA-seq snRNA-seq CITE-seq snATAC-seq TCR, BCR, Feature Barcode Multiplexed assays are available |
For assays conducted in CoLabs, Genomics CoLab offer standard analysis support that includes genomic alignments, quality control and normalization, and identification of differentially expressed genes. If you plan to incorporate results from multiple platforms, please contact Data Science CoLab to learn about possible collaborations for data integration and analysis.
For genomic data generated elsewhere, Genomics CoLab may be able to provide stand-alone analysis service depending on the nature of the analysis and staff availability. Please contact us to discuss options.
One of the goals of CoLabs is to promote standardized protocols and data sharing. In collaboration with our Disease to Biology and Data Science CoLabs, we have developed methods and analysis tools for genomic experiments. We welcome collaborations to customize protocols for sample processing and data integration. Please contact us to discuss options.
In addition, many genomic datasets are available at the UCSF Data Library, which is curated and maintained by our Data Science CoLab. These datasets are open for researchers to explore and analyze.
1. Can you help me prepare my samples? Can I run my samples myself?
We offer guidance on sample preparation and encourage a meeting prior to receiving samples to ensure samples meet assay requirements. Please contact us if you require a higher level of assistance. Generally, instruments are not available for independent use.
2. What if I don’t see the approach that I need for my research? Can CoLabs manage instruments purchased by UCSF labs or programs?
The Genomics CoLab is enthusiastic about partnering with UCSF investigators and programs to develop new protocols and obtain and manage additional equipment to augment our capacity and bring novel capabilities to UCSF research community. Please contact us to get started.
3. Who do I contact for more information on assays, questions about sample preparation, help with analysis, etc?
GenomicsCoLab@ucsf.edu
Medical Sciences Building S813
513 Parnassus Ave (map)
Additional information can be found at the Genomics CoLab website.