Microbiomics and Functional Genomics Core

Overview

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.

The Core offers the following services:

  1. Conduct sequencing-based assays for microbiomics and functional genomics 
  2. Perform bioinformatics analyses of sequencing-based assays 
  3. Consult and advise in studies involving microbiomics and functional genomics
  4. Provide validated experimental protocols and training 

The Core is directed by Dr. Rob Knight, an internationally recognized expert in microbiomics, and co-directed by Dr. Christopher Glass, an expert in functional genomics.  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. Kathleen Fisch serves as co-investigator and the executive director of the Center for Computational Biology & Bioinformatics (CCBB), which provides all bioinformatics analyses that result from the sequencing-based assays.

Services Offered by the Core

Microbiomics and Functional Genomics services

1. 16S rRNA and metagenomic shotgun sequencing of microbial communities
2. RNA-seq (including single-cell transcriptomics), ChIP-seq, miRNA-Seq, GRO-Seq, Ribo-Seq, ATAC-Seq,  Whole Genome Sequencing, and Exome sequencing

The SDDRC offers genomics services through an arrangement with the UCSD Institue for Genomics Medicine (IGM) Genomics Center, which provides a variety of genomics services, including sequencing library preparation and sequencing on Illumina's MiSeq, HiSeq2500, HiSeq4000 and NovaSeq 6000. The Genomics Center supports single-cell sequencing on the 10X Genomics Chromium Controller. In addition, it processes Illumina Infinium Beadchips, which includes a variety of whole-genome genotyping (WGGT) arrays as well as the Infinium MethylationEPIC BeadChip. 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. For detailed information and instructions, please visit Sample Submission. For complete listing of services offered, please visit Genomics Center’s services page

Bioinformatics Services

  • Bioinformatics analyses of sequencing-based assays
  • Consultation and training in specific experimental and analytical techniques related to microbiomics and functional genomics.

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, 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 study design with the CCBB Director Dr. Kathleen Fisch.  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.  To obtain services, please visit CCCB’s services page.