DNA Analysis Researcher Pouring Liquid

Genomics

Providing state-of-the-art equipment, expertise, and next-generation sequencing services.

The Genomics Core at SBP in La Jolla 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 also provides full-service Quantitative real-time PCR (Q-PCR) analysis, predominantly utilizing SYBR green, as well as amplification-free analysis of RNA expression using the NanoString nCounter.  Additional Core services include full service Human cell line authentication, utilizing short tandem repeat analysis (STR), as well mycoplasma testing.  The Core provides a variety of shared genomics-related analytical instruments and training in their use, for SBP investigators.  The Genomics Core also provides its services to investigators outside of SBP.

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.

Human cell line authentication and mycoplasma testing services

are 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).

Quantitative real-time PCR (Q-PCR) service

is predominantly SYBR green-based analysis, but hybridization probe (e.g. TaqMan) approaches are also supported.  Starting with RNA, the facility will utilize primers from investigators, or design custom primers and perform Q-PCR.   The facility provides control primers and assists with experimental design, as well as providing basic relative quantitation analysis. Q-PCR analysis in the facility can also provide gene, RNA, or viral copy number data.

Ion Torrent sequencing

is available on the PGM, or Ion Proton platform.  Contact Brian James for more information and pricing.

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.

• NetSeq 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.

• Ion Proton Sequencer
The Ion Proton sequencer from Life Technologies offers up to 10 Gb of sequence data
with the PI and read lengths up to 200 bases .

• 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.

• Agilent 2100 Bioanalyzer
The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA and RNA.  The 2100 Bioanalyzer is 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.

• 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)

• BioRad Experion (BioAnalyzer equivalent)

• 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 Price List, please call (858)646-3100 ext. 4084 or email us.

Leadership

Scientific Supervisor
Facility Director

Contact

Brian James
Brian James directs the Genomics core and provides DNA sequencing and downstream bioinformatic analysis. Dr. James started with SBP 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


Jian Xing, B.S.
Research Technician II
Jian performs QPCR assays and also assists in NextGen sequencing sample preparation
(858)646-3100 ext. 3457
Email Jian Xing

 

Please call (858)646-3100 ext. 4084 or use the button below to send us an email.

Contact the Facility

 

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