Director: Xinmin Li

Mailing Address
38-123 CHS
650 Charles Young Dr.
Los Angeles, CA 90095
UCLA Mail Code 173517

Telephone: (310) 206-3945
Fax: (310) 825-3570
Email: sequencing@mednet.ucla.edu
Website: http://pathology.ucla.edu

Overview

The UCLA Jonsson Comprehensive Cancer Center Genomics Shared Resource (GSR) is a fully automated, high-throughput genomic Center equipped with all major next generation sequencing and microarray platforms. The GSR provides state-of-the-art genomics technologies, comprehensive services, specialized expertise and a wide range of trainings, enabling these services in a cost-effective and timely manner to serve basic science and translational/clinical research. In addition, The GSR provides pre-experiment consultation and post-experiment support, including preparation of grant applications, publications, and strategic planning for additional research steps. The GSR also provides educational training to faculty, staff, and students to raise awareness of new directions and major discoveries in the areas of genomics and bioinformatics.

Goals and Mission

1. To provide long and short read sequencing (third-generation and next generation/second-generation) and microarray-based genomic services to the research community
2. To develop and maintain the highest quality and reliability for the genomic services that we offer
3. To lead in establishing quality standards for genomic services (e.g., sample processing, data analysis and interpretation)
4. To advance the relatively new specialty area of personalized medicine through education, research, and publications

Major Services

• Long Read Sequencing/Oxford NANOPORE GridIONX5
• Next Generation Sequencing
  • Library construction: one to three days
  • Sequencing: three days to three weeks
• 10X Single Cell Sequencing:
  • Library construction: one to three days
• Sequencing: three days to three weeks
• Microarray: three to five days
• Data analysis: three days to one week
• DNA/RNA Isolation: one to two days
• Quality Control: same day or next day
• QRT-PCR (case by case basis)

Long Read Sequencing (Third Generation) and Next Generation Sequencing (Second Generation)

DNA and RNA sequencing is the process of determining the nucleotide order of a given DNA fragment. The nucleotide sequence encodes the necessary information that allows living things to survive and reproduce. Determining the sequence is therefore useful in researching into how organisms live. Our core facility provides many sequencing options to meet your individual needs, utilizing (a) Oxford NanoPore GridIONx5 Long-Read Sequencing (by reading the nucleotide sequences at the single molecule level), and (b) Illumina Short-Read Sequencing (by massive parallel sequencing of millions of DNA fragments and yielding substantially more throughput reads quickly).

• Whole transcriptome sequencing (RNA-Seq)
• Small RNA sequencing (miRNA-Seq)
• Whole exome sequencing
• Targeted resequencing
• Whole genome sequencing
• Chromatin immunoprecipitation sequencing (ChIP-Seq)
• Methylation sequencing (Methyl-Seq)
• Copy number variation sequencing (CNV-Seq)
• ATACseq

10X Single Cell Sequencing

The Chromium 10x genomics 3’ Single Cell Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling of hundreds to tens of thousands of cells. The Chromium Single Cell Immune Profiling simultaneously examines the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in human or mouse tissue on a cell-by-cell basis. The newest one is the Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin), which accelerates the understanding of the regulatory landscape of the genome, providing insights into cell variability.

• Chromium™ Single Cell 3’ Library Construction
• Chromium™ Single Cell 5’ Immune Library Construction (Single Cell V(D)J + 5’ Gene Expression)
• Chromium™ Single Cell ATAC Solution

Microarray Analysis

The human genome contains approximately 25,000 genes, and each cell of the human body contains a copy of every gene. At a given moment, each cell has a combination of genes that are turned on and off. This combination of genes that are "on/off" can change at any time depending on internal and external stimuli.

Thus, it can be very important to determine which genes are turned on and off. Microarray analysis allows us to do this. The TCGB is equipped with various platforms to meet your research needs.

• Gene expression profiling
• SNP genotyping
• Copy number variation analysis
• Global methylation
• ChIP-ChIP analysis
• miRNA profiling
• Advanced microarray data analysis
• QRT-PCR confirmation

Advanced Data Analysis

The TCGB has various academic and commercial data mining software and other resources for genomic data analysis, including Partek flow, VarSeq, Ingenuity Pathway Analysis, Falcon automated genomic analysis system,Hoffman2 data analysis clusters, UCLA CASS server, Illumina basespace Sequencing Hub professional, Amazon cloud HIPAA compliant research computing, and storage system server.

• Standard NGS & Microarray data analysis
• Advanced and customized data analysis
• Online data delivery, long term storage and data retrieval
• Data analysis tutorial

Other Services

Educational workshops are offered annually. Our core facility also provides RNA/DNA extraction; RNA/DNA quality control and quantification; cDNA synthesis for quantitative-PCR; and QRT-PCR.

Equipment

The GSR occupies approximately 2,568 square feet of laboratory space on the third floor of the Center for Health Sciences, CHS 38-123, 38-126 and 33-388. It is operated by eleven experienced genomic scientists. The GSR is a high throughput genomic center utilizing the equipment listed below. In addition to offering wet-lab services, the GSR has developed a broad informatics infrastructure and an efficient means for data acquisition, storage, and analysis. We have access to advanced software including Partek flow, VarSeq, Ingenuity Pathway Analysis, and Falcon automated system, which significantly enhance the overall capacity of TCGB to rapidly process and transform the large quantity of data into novel findings.

NGS

Oxford NANOPORE GriDIONx5 Sequencing System, Illumina NovaSeq™ 6000 Sequencing System, 10X Genomics Chromium™ Controller Single Cell Sequencing System, Illumina HiSeq 3000 Sequencing System, Illumina HiSeq 2500 Sequencing System, Illumina NextSeq 500 Sequencing System, Illumina MiSeq Personal Sequencer System, Ion Torrent PGM for research applications, IntegenX Apollo 324 for automated NGS library preparation, Beckman Coulter ArrayPlex for fully automated workstation, Fluidigm Access Array System for target-enrichment, Covaris M220 for DNA shearing

Microarray

Affymetrix GeneChip System, Affymetrix GeneAtlas System, Agilent microarray system

Nucleic Acid Isolation Robotics

Roche MagNa Lyzer instrument for automated tissue homogenization, Biochain AnaPrep Automated Nucleic Acid Preparation System, Qiagen QIAcube HT Automated mid- to high-throughput Nucleic Acid Purification System, QIAcube Connect for small scale nuclei acid isolations.

Quality Control

Agilent 2100 Bioanalyzer, Agiletn 2200 Tapestation, NanoDrop 8000, Qubit 2.0 Fluorometer, Fragment Analyzer, Varioskan Lux Plate Reader

Data Analysis and Management

Partek flow, VarSeq, Ingenuity Pathway Analysis, Falcon automated genomic analysis system, Hoffman2 data analysis clusters, UCLA CASS server, Illumina base space Sequencing Hub professional, Amazon cloud HIPAA compliant research computing and storage system

Other Equipment

Applied Biosystems 7500 Fast Real-Time PCR system, Bio-Rad C1000 Touch Thermal Cycler, Thermo Scientific DNA120 Speedvac Concentrator

Operational Policies/Procedures

The GSR has the following operational policies:

• Before each experiment, the director and co-director schedule two meetings with the investigator and their staff. The first meeting is to discuss experimental strategy and the second meeting is to discuss technical issues and expenses
• When a sample arrives, the GSR performs vigorous quality control before, during, and after each experiment. When quality meets established standards, the lab manager delivers the data to the investigator and saves a copy on the GSR data storage server for a minimum of two years
• After completion of the experiment, the GSR assists investigators in data analysis, publication, and grant application preparation, on request

To ensure the highest quality services, the GSR has the following use policies:

• Quality assurance: Data quality assurance occurs when initial samples pass GSR quality controls (QC). The GSR follows strict QC guidelines to ensure data quality equal to or above that of quality specifications by instrument or kit manufacturers.
• Flexibility: Investigators can use GSR services at any stage they choose. As an example, GSR services can start from tissue and deliver analyzed data or start from a pre-constructed library and deliver raw data. The GSR will make every effort to meet investigators’ specific scientific needs.
• Hours of operations: The GSR is accessible from 7:30 AM to 5:30 p.m., Monday through Friday. Users can access the GSR after-hours by arrangement with the lab manager.
• Turnaround time: GSR automation enables quick turnaround times in general. Although the GSR prioritizes JCCC investigators projects, 85% of NGS samples process within two weeks, and 100% of microarray samples process within one week of receipt for JCCC, non-JCCC, and non-UCLA users alike.
• Priority: JCCC members are given highest priority, non-JCCC UCLA investigators have second priority, and outside users are assigned the lowest priority. However, amongst outside users, cancer researchers from other cancer centers receive preferable scheduling.
• Low price: The GSR has three price tiers for each service. The fees for the majority of services are below or similar to reagent costs for JCCC members, and are below or similar to “reagent costs + labor” for non-JCCC UCLA investigators. The large number of outside users make these preferential prices possible for JCCC investigators (for a full list of prices, see http://pathology.ucla.edu/tcgb).

Pricing

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