The Genomics Shared Resource (GSR) is a fully automated, high-throughput genomic Center equipped with all major bulk sequencing, single cell multiomics and spatial genomics technologies. The GSR provides state-of-the-art technologies, comprehensive services, and specialized expertise, 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
- To provide long and short read sequencing (third-generation and next generation/second-generation) to the research community
- To develop and maintain the highest quality and reliability for the genomic services that we offer
- To lead in establishing quality standards for genomic services (e.g., sample processing, data analysis, and interpretation)
- To advance the relatively new specialty area of personalized medicine through education, research, and publications
- Long Read Sequencing/Oxford Nanopore GridIONX5
- Next Generation Sequencing
- Library construction: 1-3 days
- Sequencing: 3 days- 3 weeks
- Single Cell Multiomics
- Library Construction: 2-3 days
- Sequencing 3 days-3 weeks
- Spatial Genomics
- Library Construction:
- 10x Visium: 2 days
- GeoMx DSP: 3 days
- CosMx SMI: 2 days
- Sequencing: 3 days – 3 weeks
- Data Analysis: 1-3 days
- DNA/RNA Isolation: 1-2 days
- Quality Control: same day or next day
- QRT-PCR (case by case basis)
- Library Construction:
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)
Single cell multiomics
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.
The new BD Rhapsody™ HT Xpress System is a higher-throughput platform with a robust microwell-based single-cell partitioning technology which is especially feasible for fragile and heterogenic cell population. It is capable of capturing and barcoding single cells, allowing for the capture of over 320,000 cells per cartridge. This advancement enables researchers to conduct studies involving millions of individual cells.
- Chromium™ Single Cell 3’ Library Construction (3’ Gene Expression + FB (Feature Barcode))
- Chromium™ Single Cell 5’ Immune Library Construction (5’ Gene Expression + Single Cell V(D)J + FB (Feature Barcode))
- Chromium™ Single Cell ATAC Solution
- Chromium Single Cell Multiome ATAC + 3’ Gene Expression
- BD Rhapsody Scanner/HT Express
Each organ of a complex organism consists of diverse cell types that often interact in highly structured manners under distinct microenvironments. Such highly structured spatial heterogeneity enables the organism to function correctly and efficiently. To fully understand gene functions in a given cell type, one must study gene expression in the context of the location of the cells in the tissue. Spatial transcriptomics is a recently developed transformative technology that combines the strengths of the global transcriptional analysis of bulk RNAseq and In-stiu hybridization, providing transcriptomics data in the context of spatial locations of the cells in stiu.
Three spatial transcriptomics technologies are currently available today:
1. The 10X Visium Spatial Transcriptomics from 10X Genomics:
- Profiles the whole transcriptome and is compatible with fresh or FFPE tissues
- Services include:
- 10X Visium Gene Expression (GEX) + Protein Expression (PEX)
- 10X Visium Tissue Optimization (TO)
2. CosMx SMI for Single-Cell Imaging from NanoString technologies:
- Offers various RNA panels for single-cell imaging
- Services include:
- CosMx Hs Univ RNA Panel (2 or 4 Slides/RUN)
- CosMx Hs Immuno-oncology RNA Panel (2 or 4 Slides/RUN)
- CosMx Mm Neuro RNA Panel (2 or 4 Slides/RUN)
3. GeoMx digital spatial profiler (GeoMx DSP) from Nanostring Technologies:
- Profiles both RNA and protein for transcriptome or targeted panels
- Services include:
- GeoMx® Cancer Transcriptome Atlas (CTA) (1833 genes)
- GeoMx Human Whole Transcriptome Assay (WTA) (>20000 genes)
- GeoMx Mouse Whole Transcriptome Assay (>21000 genes)
- GeoMx Immune Pathways Panel (96 genes)
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 consultation and software tutorial
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.
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 eighteen genomics and bioinformatics staff. 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, Hoffman2 data analysis clusters, UCLA CASS server, Illumina basespace Sequencing Hub professional, Amazon cloud HIPAA compliant research computing, and storage system server, which significantly enhance the overall capacity of TCGB to rapidly process and transform the large quantity of data into novel findings.
Oxford NANOPORE GriDIONX5 Sequencing System, Illumina NovaSeq™ X Plus Sequencing System, Illumina NovaSeq™ 6000 Sequencing System, 10X Genomics Chromium™ Controller Single Cell Sequencing System, Illumina NextSeq 500 Sequencing System, Illumina MiSeq Personal Sequencer System, Complete Genomics DNBseq T7 Sequencing System, IntegenX Apollo 324 and Beckman Coulter BioMek i7 for automated NGS library preparation, Covaris M220 for DNA shearing
Single cell multiomics
Chromium Controller/IX/Connect for 10x Single-cell sequencing (3’ GEX + FB, TCR/BCR, 5’GEX+ FB, 5’GEX+V(D)J, 5’GEX + TCR/BCR + FB, Multiome 3’GEX+ ATAC), BD Rhapsody Scanner/HT Express for Rhapsody Multiomics
10X Visium/CytAssist Spatial Multiomics System, Nanostring GeoMx DSP Spatial Multiomics System, and Nanostring CosMx SMI Spatial Multiomics 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.
Agilent 2100 Bioanalyzer, Agilent 2200 Tapestation, NanoDrop 8000, Qubit 2.0 Fluorometer, Qubit Flex 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
Applied Biosystems 7500 Fast Real-Time PCR system, Bio-Rad C1000 Touch Thermal Cycler, Thermo Scientific DNA120 Speedvac Concentrator
Operational policies and 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 8:00 AM to 6:00 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 below).
A price list for above services can be downloaded here