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Microbiomics & Functional Genomics Core


The Microbiomics and Functional Genomics Core in the San Diego Digestive Diseases Research Center provides advanced microbiomics and genomics services to Center members. It also offers consultation and training in genomics technologies to enhance the ability of members to implement these technologies in their research.

Dr. David Pride, Professor of Medicine, is the Core Director. Dr. Sven Heinz, an expert in functional genomics, is the Core Co-Director. Dr. Kristen Jepsen serves as co-investigator and is the director of the IGM Genomics Center at UCSD, which performs all sequencing-based assays for the Core. Dr. Brin Rosenthal serves as co-investigator and the executive director of the Center for Computational Biology & Bioinformatics (CCBB), which provides all bioinformatics analyses that result from sequencing-based assays.

Services Offered by the Core

Microbiomics Services

The Core processes raw samples submitted by Center investigators. The SDDRC offers Microbiomics services including 16S/ITS/18S rRNA and metagenomic shotgun sequencing of microbial communities. Prior to preparing and submitting samples, Center members are asked to send microbiomics service requests to:

Functional Genomics Services

The SDDRC offers genomics services through an arrangement with the UCSD Institute for Genomics Medicine (IGM) Genomics Center, which provides a variety of genomics services, including sequencing library preparation, RNA-Seq (including single-cell transcriptomics), miRNA-Seq, ChIP-Seq and scATAC-Seq. Prior to preparing and submitting samples, new customers are encouraged to email the IGM Genomics Core Director Dr. Kristen Jepsen. Samples must be submitted in approved tubes and appropriate manifest.

Bioinformatics Services

The SDDRC offers Bioinformatics services through an arrangement with the UC San Diego’s Center for Computational Biology & Bioinformatics (CCBB). CCBB is a collaborative center that provides investigators with bioinformatics expertise to analyze large molecular datasets and develop novel algorithms. It has expertise in genomics, transcriptomics, epigenomics, microbiomics, systems biology, and translational medicine. The CCBB center services include data analysis, biological interpretation, grant writing, and training. Prior to study execution, investigators are encouraged to discuss the study design with the CCBB Director Dr. Brin Rosenthal. Investigators must fill out a consultation request form. CCBB offers a variety of analytical services, including NGS analyses, transcriptomics, genomics, epigenomics, metagenomics, microbiome, CRISPR screens, network analysis, grant consultations, and custom analytical pipelines and algorithm development. Training in specific experimental and analytical techniques related to microbiomics and functional genomics is available. To obtain services, please visit CCCB’s services page.