The Genomics Core at Sanford Burnham Prebys provides next-generation sequencing services, providing assistance with experimental design, sample QC, library preparation, sequencing, and data analysis through Illumina BaseSpace. The facility primarily provides high throughput sequencing on the Illumina NextSeq 500. The core provides full service library preparation, starting with DNA or RNA provided by the user. Services include, PolyA RNA-seq, whole transcriptome RNA-seq, high throughput 3’ RNA counting applications, ChIP-seq, Human Exome sequencing and targeted DNA seq. The core is also equipped with two single cell systems, the 10x Genomics Chromium Controller, and BioRad ddSeq single cell isolator. Additional Core services include full service Human cell line authentication, utilizing short tandem repeat analysis (STR), as well as amplification-free analysis of RNA expression using the NanoString nCounter. The Genomics Core also provides its services to investigators outside of the Institute.
Next gen sequencing
The facility provides high throughput sequencing on the Illumina NextSeq 500 sequencer, which is capable of producing up to 400 million reads per run, with run times ranging from 19-29 hours. The NextSeq 500 is very scalable allowing it to support several applications including, sequencing of small genomes, targeted sequencing, whole transcriptome, ChIP-seq, and whole exome sequencing. The core offers full service library preparation, and sample QC. Included in the cost of sequencing is basic bioinformatic analysis through Illumina BaseSpace (SNP/InDel calling, transcript abundance). The core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing. Advanced bioinformatic and systems biology analysis is available through the Bioinformatics Core in La Jolla.
Single cell RNA-SEQ and ATAC-SEQ
The core is equipped with two single cell systems, the 10x Genomics Chromium Controller, and BioRad ddSeq single cell isolator. Core staff can assist with processing single cell suspensions, library prep, sequencing, and basic informatic analysis.
Human cell line authentication services
Human cell line authentication is available through the Genomics core. The GenePrint 10 System from Promega is used to perform short tandem repeat (STR) analysis on genomic DNA submitted to the core. STR data is processed by the core in GeneMarker HID, and allele calls are returned to the customer. For commercially available cell lines, the core will search STR profiles against databases of know STR profiles (ATCC, RIKEN, JCRB, and DSMZ) and return the best match. Samples can be submitted as purified genomic DNA, or cells can be spotted directly on FTA cards in media or trypsin (FTA cards are available in the core).
Capillary DNA sequencing
has been outsourced for several years, with three vendors picking up samples at SBP and typically returning results within 24 hr.
Microarray based global analysis of gene expression (Discontinued)
Illumina has discontinued all gene expression arrays in light of the now cost-effective and deeper data from RNA-seq. For gene expression analysis, contact Brian James to discuss RNA-seq options.
Equipment & Resources
- Illumina NextSeq 500
The NextSeq 500 Sequencing System from Illumina provides the widest range of sequencing applications. The flexible, scalable system offers tunable read lengths and output options to support research needs. It can sequence 20 RNA-seq, or ChIP-seq libraries per day and supports Whole-Genome Sequencing and Exome Sequencing.
- 10X Genomics Chromium Controller Single Cell System
The Chromium is used to prepare single cell RNA-seq and ATAC-seq libraries from single cell suspensions provided by users. The Chromium is capable of processing from a few hundred to 5,000 cells per sample. Core staff can train users on the system, or assist with sample preparation.
- Bio-Rad ddSeq Single-Cell Isolator
Like the Chromium, the ddSeq is a single cell RNA-seq and ATAC-seq library preparation system. The ddSeq is well suited for pilot studies with less than 1000 cells targeted per sample.
- Eppendorf epMotion 7075 Liquid handling system
The epMotion 7075 is used for high throughput construction of RNA and DNA libraries for sequencing on the NextSeq 500.
- Agilent 2100 Bioanalyzer and Atilent TapeStation 4200
The Agilent 2100 Bioanalyzer and Agilent 4200 TapeStation systems provide sizing, quantitation and quality control of DNA and RNA. They are especially useful for assessing the integrity of submitted RNA samples.
- Qubit Fluorometer
The Qubit Fluorometer gives an extremely accurate measurement of DNA, RNA or protein.
- Nanostring nCounter-Amplification-free RNA Analysis
The nCounter is an excellent instrument for analyzing the expression of a substantial number (e.g., 100) of genes and micro RNAs in a large number of samples, such as validation of putative biomarkers in clinical samples, including FFPE samples.
- Roche LC480 real time QPCR instrument (interchangeable 96 or 384 well)
- Roche LC96 real time QPCR instrument
- Stratagene Mx3000p real-time QPCR instrument (96 well)
- Nanodrop Spectrophotometer
- Shared Instruments:
- Roche LC480 (2) QPCR (interchangeable 96 or 384 wells)
- LC96 (4) QPCR
- ABI 7900HT real time QPCR (interchangeable 96 or 384 wells)
- Nanodrop spectrophotometers (3)
For a complete list of services, please call (858) 646-100 ext. 4084 or email us.
Brian James directs the Genomics core and provides DNA sequencing and downstream bioinformatic analysis. Dr. James started with Sanford Burnham Prebys in 2013 after leaving the MD Anderson Cancer Center, where he ran the sequencing bioinformatic support service for the Department of Experimental Therapeutics Next-generation sequencing core. Dr. James received his Ph.D. in Molecular and Cellular Biology from the University of Arizona, where he studied development and integrin signaling in Drosophila melanogaster. Please contact Dr. James for advice on next-generation sequencing projects or experimental design for core services.
Kang Liu, Ph.D.
Dr. Liu is primarily involved in NextGen Sequencing
(858) 646-3100 ext. 3714
Email Kang Liu
Please call (858) 646-3100 ext. 4084 or use the button below to send us an email.