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Genomics (GSR)

Dr. Xinmin LiDirector: Xinmin Li

38-123 CHS
650 Charles Young Dr.
Los Angeles, CA 90095
(Mail Code 173517)

Telephone: (310) 206-3945
Fax: (310) 825-3570
E-mail: cmc@mednet.ucla.edu

Website: http://pathology.ucla.edu/body.cfm?id=126

Overview

The GSR provides comprehensive next generation sequencing and microarray services in a cost-effective and timely manner to serve the JCCC’s basic, translational and clinical researchers. The GSR assists JCCC members with bioinformatic analyses to facilitate the transformation of genomic data into novel findings. The GSR also provides educational training to students, staff, and faculty to raise awareness of new directions and major discoveries in the areas of genomics and bioinformatics.

News Announcement

3/15/2013: JCCC Genomics Shared Resource/UCLA Clinical Microarray Core is pleased to announce a five-day Next Generation Sequencing and Data Analysis Workshop to be held June 17-21, 2013. Click here for details and registration.

The JCCC’s Genomics Shared Resource (GSR) and Biostatistics, Analytical Support & Evaluation (BASE) are pleased to announce a formal strategic partnership to significantly strengthen the JCCC's next generation sequencing/microarray and data analysis capabilities. GSR will perform the wet-lab sequencing/microarray and initial/standardized data analysis whereas BASE will now offer advanced, customized data analysis.

For details, visit our website or contact Dr. Xinmin Li at xinminli@mednet.ucla.edu or Dr. Gang Li at vli@ucla.edu for more information.

Goals & Mission

  • To provide next generation sequencing- and microarray-based genomic services for prevention, early diagnosis, and management of cancer
  • To build and maintain the highest quality and reliability for the services that we offer
  • To play a leadership role in establishing quality and standards for the genomic services, including sample processing, data analysis, and data interpretation
  • To advance the relatively new specialty area of personalized medicine through education, research, and publications

Services

With the state of the art instruments, the GSR offers a wide range of genomic services and continuously develops new services when needs are identified. Current services include:

  1. Pre-experiment consultation
  2. Whole Transcriptome sequencing (RNA-Seq)
  3. Small RNA sequencing (miRNA-Seq)
  4. Whole exon sequencing
  5. Targeted resequencing
  6. Methylation sequencing (Methy-Seq)
  7. Chromatin Immunoprecipitation sequencing (ChIP-Seq)
  8. Large-scale gene expression profiling
  9. SNP genotyping
  10. Genome-level copy number variation analysis
  11. Genome-level methylation and chip-chip analysis
  12. miRNA profiling
  13. QRT-PCR confirmation
  14. RNA/DNA quality evaluation
  15. Advanced data analysis
  16. Data analysis software tutorial and consultation
  17. Assistance with grant applications and publications
  18. Post experiment support, including developing integrated strategies for following–up microarray experiments
  19. Educational training

The GSR has developed a broad bioinformatics infrastructure and an efficient means for data acquisition, storage and analysis. The GSR has access to various advanced software including GeneSpring 11.0, Partek Genomics Suite 6.5, D-chip, SAM and Ingenuity Pathway Analysis. The well-established data management, data analysis and data integration systems have significantly enhanced the overall capacity of the GSR to assist the investigators in rapidly digesting and transforming large quantities of data into new findings.

Equipment

The GSR is a fully automated and high-throughput facility with the following instrumentation:

The Illumina HiSeq 2500 Sequencing System is the latest member of Illumina HiSeq family, which can be switched between a high output run mode and rapid turnaround run mode. In high output mode, the HiSeq 2500 can deliver 600 Gb data/run similar to HiSeq2000. In rapid run mode, the HiSeq 2500 can sequence a 30× genome in a day, which no other available NGS instruments are comparable. The fast turn-around-time (TAT) is critically important for many time sensitive NGS projects.

Illumina HiSeq 2500 Sequencing System

The Illumina MiSeq Personal Sequencer System enables researchers to go from sample to analyzed data in as little as eight hours with a revolutionary workflow and the flexibility to undertake the widest range of applications. Capable of generating greater than 7 Gb at 2 X 250bp read length per run, MiSeq is the only next-generation sequencer that integrates amplification, sequencing, and data analysis in a single instrument with a footprint of less than two-feet square. Coupled with optimized sample prep workflows, Illumina’s proven TruSeq™ chemistry, and the BaseSpace™ cloud-based analysis solution, the MiSeq system is the ideal platform for rapid, cost-effective genetic analysis.

Illumina MiSeq Personal Sequencer System

Ion Torrent Personal Genome Machine System (PGM™) is a revolutionary next generation sequencing platform, which combines semiconductor sequencing technology with natural biochemistry to directly translate chemical information into digital data. The system leverages the exponential improvements in the semiconductor industry (known as Moore’s Law) to provide scalability and flexibility for various applications including small genome sequencing, targeted resequencing, miRNA-Seq, RNA-Seq, and ChIP-Seq. Direct, real time sequencing detection provides sequencing results typically in less than three hours.

Ion Torrent Personal Genome Machine System (PGM)

The Apollo 324™ NGS Library Prep System is a benchtop system that automates next-generation sequence library preparation workflows by using bead technology to execute high-performance isolation and purification of nucleic acids (DNA, RNA, plasmid and so on) and proteins. The system automates end-repair, A-tail addition, adapter ligation and final double-bead-based cleanup and size selection.

Apollo 324 NGS Library Prep System

The Fluidigm Access Array™ System is the first high-throughput, target-enrichment system designed to work with all of the major next-generation sequencing instruments. The Access Array System enables the user to enrich multiple unique targets (such as exons) from a large number of samples, all at one time. The system combines the library construction and target enrichment into one automated step, ideal for sequencing a small number of genes from a large number of samples.

Fluidigm Access Array System

The Affymetrix GeneChip® System 3000Dx v.2 is 510(k) cleared and CE marked for in vitro diagnostic use. This second-generation system includes GeneChip® Scanner 3000Dx v.2, the GeneChip® Fluidics Station 450Dx v.2, GeneChip Hybridization Oven 645 and Workstation with Affymetrix Molecular Diagnostics Software (AMDS). The fully integrated platform performs both DNA and RNA analysis for genetic testing, personalized medicine, and pharmacogenomic analyses.

Affymetrix GeneChip System 3000Dx

The Affymetrix GeneChip® System is a Research-Use-Only system for genome-level DNA and RNA analyses. It includes GeneChip® Scanner 3000 7G, the GeneChip® Fluidics Station 450, GeneChip Hybridization Oven 640 and Workstation with Affymetrix Command Console software. The system can be used for all Affymetrix arrays as well as arrays developed by Affymetrix Partner.

Affymetrix GeneChip System

Affymetrix GeneAtlas™ Personal Microarray System The GeneAtlas™ System is a new member of Affymetrix gene expression family. It utilizes an entirely new array format—the array strip, with four arrays per strip. The system has a streamlined hybridization/washing/staining procedure, and provides the comparable data quality with the gene expression gold standard—Affymetrix Genechip system, but with a significantly reduced cost.

Affymetrix GeneAtlas™ Personal Microarray System

Agilent Microarray System can process a wide range of Agilent catalog microarrays as well as customized microarrays to enable the widest possible range of experimentation. Using eArray, an easy-to-use web-based application, researchers can rapidly design custom microarrays in a secure online environment at no additional cost. CMC supports a variety of formats, probes, genomic applications, and species, from which researchers can determine the right combination of options to meet specific experimental needs.

Agilent Microarray System Agilent Microarray System

Roche NimbleGen Microarray System presents a complete, optimized workflow for NimbleGen DNA microarrays. This optimized workflow includes MS 200 Microarray Scanner and Hybridization System 12. The MS 200 Microarray Scanner is a high-sensitivity laser scanner that reproducibly acquires two-color fluorescent image data down to two micron pixel resolution and allows completely automatic high-throughput image processing. The Hybridization System 12 can process 1 to 144 samples (up to twelve 12x135K arrays) simultaneously to speed your experiments and publication of data. This system has been heavily used for global methylation studies.

Roche NimbleGen Microarray System Scanner Roche NimbleGen Microarray System Hybridization System

Beckman Coulter's ArrayPlex for automatic microarray target preparation for large-scale gene expression and genotyping studies. The ArrayPlex features:

  • Hgher Throughput: Automated target RNA sample processing in 36 hours—six times that of a single technician holding an manual pipettor
  • Flexibility: Filtration or magnetic bead cleanup steps and compatible with both Affymetrix and Enzo IVT labeling reagents
  • Scalability: Process experimental and control samples in batches of eight, up to 96 in a full microplate
  • Reliability: Fully validated robust solution; increased performance of GeneChip hybridization

ArrayPlex

Roche's MagNA Pure Compact Nucleic Acid Purification System is the solution for fully automated nucleic-acid purification. The System incorporates a variety of protocols using different specimen (100­-1000 µl) and elution (50­-200 µl) volumes for a broad variety of sample materials.

Roche MagNA Pure Compact Nucleic Acid Purification System

Roche's MagNA Lyser Instrument is an ideal instrument for automated tissue homogenization prior to automated nucleic acid purification using the MagNA Pure Compact System. It can efficiently homogenize a wide variety of sample materials and prevent nucleic acid degradation with the benchtop cooling block.

Roche MagNA Lyser Instrument

Agilent 2100 Electrophoresis Bioanalyzer System for rapid determination of quality and quantity of RNA and DNA with one ul sample up to a dozen samples in 30 minutes. Compliance Services allow work within regulated environment.

Agilent 2100 Electrophoresis Bioanalyzer

NanoDrop-8000 is a full-spectrum UV/Vis spectrophotometer that measures one ul samples, up to eight at a time, allowing measurement of 96 samples in six minutes. The high absorbance capability (dynamic range: 2-3700 ng/ul) eliminates the need for dilutions in most cases.

 

NanoDrop-8000

Applied Biosystems 7500 Fast Real-Time PCR System offers maximum performance in the minimum time. Fully optimized for fast cycling, the 7500 Fast delivers high-quality results in as little as 30 minutes.

7500 Fast Real-Time PCR System

DNA Engine Tetrad 2 Thermal Cycler is a completely redesigned and updated version of the original Tetrad chassis. Real-time displays of block, sample and lid temperatures provide quality assurance that the thermal cycler is performing as directed. Superior software features, such as error tracking logs, run tracking files, problem resolution trees and file management tools, offer invaluable information for troubleshooting during high throughput runs.

DNA Engine Tetrad 2 Thermal Cycler

Staffing, Organization and Operational Policies/Procedures

The GSR, directed by Dr. Xinmin Li, includes a staff of six and is overseen by a faculty advisory committee.

The GSR has the following operational policies:

  • Quality guarantee: The GSR guarantees results if RNA samples passe our quality controls.
  • Flexibility: The GSR makes every effort to meet investigators’ individual needs. We can provide start-to-finish solution or provide partial services.
  • Turnaround time: The GSR delivers 90 percent of service requests within one week, and 99 percent within two weeks.
  • Priority: All University investigators have access to the facility. Non-UCLA users are accommodated at a lower priority. In the rare instance where scheduling difficulties arise, priority will be given to JCCC members.

Pricing

A price list for above services can be downloaded here (Microsoft Excel format).

 

Last updated: 12/17/2014 4:28:55 PM