Genomics

Services

DNA/RNA Isolation - 1 to 2 days
Quality Control - Same day or next day
Single Cell Multiomics
- 10X Single Cell - 1 to 3 days
- BD Rhapsody - 2 to 3 days
Spatial Genomics
- 10X Visium - 2 days
- Visium HD - 1 week
- GeoMx DSP - 3 days
- CosMx SMI - approximately 1 week
- Xenium - 2 to 3 days
- StereoSeq - 1 week

* Please note that sequencing will be separate for Visium, GeoMx, and StereoSeq

Bulk Sequencing
- Long Read Sequencing/Oxford NANOPORE GridIONX5 - 2 to 3 days
- Next Generation Sequencing - 1 to 3 weeks
Data Analysis - 1 to 3 days
Others (including QRT-PCR) - variable based on request

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)
Copy Number Variation Sequencing (CNV-Seq)
Small RNA Sequencing (miRNA-Seq)
Chromatin Immunoprecipitation Sequencing (Chip-Seq)
Methylation Sequencing (Methyl-Seq)

Single Cell Multiomics

10X Single Cell Library Construction

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.

3’ GEX Library Prep (Fresh Cell)
3’ GEX Fixed/FFPE RNA Profiling (FRP) Library Prep
3’ GEX + FB (Single Cell Hashing) Library Prep
TCR Library Prep
5’ GEX + TCR Library Prep
5’ GEX + TCR + BCR Library Prep
5’ GEX + FB (Single Cell Hashing) Library Prep
ATAC Library Prep
Multiome (ATAC + 3’GEX) Library Prep

BD Rhapsody

The BD Rhapsody™ Single-Cell Analysis System offers a fast and easy way to collect a wealth of information about individual cells, including their genes and proteins. This is achieved through a unique cartridge system and a sophisticated barcoding technique. The collected data can then be used to create specialized libraries for next-generation sequencing (NGS), a powerful tool for analysing massive amounts of genetic information. By analysing these NGS libraries, researchers gain a deep understanding of individual cells, uncovering hidden patterns and insights invisible to traditional methods.

BD Rhapsody™ WTA Library Prep
BD Rhapsody™ WTA + Sample Tag Library Prep
BD Rhapsody™ WTA + Sample Tag + AbSeq Library Prep

Spatial Genomics

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-situ hybridization, providing transcriptomics data in the context of spatial locations of the cells in situ.

Six spatial transcriptomics technologies are commercially available today: (1) The 10X Visium spatial transcriptomics from 10X Genomics (2) Visium HD spatial gene expression from 10X Genomics (3) GeoMx digital spatial profiler (GeoMx DSP) from NanoString Technologies (4) CosMx SMI for single-cell imaging from NanoString Technologies (5) Xenium single cell spatial imaging platform from 10X Genomics and (6) Stereo-seq Transcriptomics Solution from STOmics. Fresh or FFPE tissues can be applied to 10X Visium, GeoMx DSP, and CosMx and fresh or PFA fixed tissues to Stereo-seq:

10X Visium

Visium Gene Expression (GEX)
Visium Tissue Optimization (TO)
Visium Whole Transcription Analysis (WTA) with CytAssist
Visium Whole Transcription Analysis + Protein Expression (WTA + PEX)

Visium HD

Human or Mouse Whole Transcription Analysis (WTA)

GeoMx DSP

GeoMx Whole Transcriptome Analysis for Human & Mouse
GeoMx Cancer Transcriptome Analysis for Human
GeoMx Protein Profiling

CosMx SMI

CosMx Universal RNA Panel for Human
CosMx Immuno-oncology RNA Panel for Human
CosMx Neuro RNA Panel for Mouse

Xenium

10X Xenium Panel (users provide specific gene panel)

StereoSeq

Whole Transcriptome Analysis for Any Species

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, Illumina basespace Sequencing Hub professional, Amazon cloud HIPAA compliant research computing, and storage system server.

Standard NGS Analysis
Advanced and customised data analysis, including 10X single cell and spatial data analysis
Online data delivery, long term storage and data retrieval
Data analysis tutorial
BioTuring

Other Services

The TCGB hosts not only informative seminars on cutting-edge technologies every one to two months but also annual educational workshops offering comprehensive learning experiences. Our core facility also provides:

RNA/DNA extraction
RNA/DNA quality control and quantification
RNA/DNA Purification
cDNA synthesis for quantitative-PCR
QRT-PCR
qPCR Library Quantification
Covaris Fragmentation
Size-selection
Vacuum Concentration

Equipment

The TCGB 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 seventeen experienced genomic scientists. The TCGB is a high throughput genomic center utilizing the equipment listed below. In addition to offering wet-lab services, the TCGB 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, 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.

Next-Generation Sequencing

OxfordNANOPORE GriDIONx5 Sequencing System
10X Genomics Chromium™ Controller Single Cell Sequencing System
10x Genomics Chromium Connect
GeoMx DSP (Nanostring)
CosMx SMI (NanoString)
10X Visium
Visium HD
Xenium
StereoSeq
NovaSeqTM X Plus Sequencing System
Illumina NextSeq 500 Sequencing System
Illumina MiSeq Personal Sequencer System
IntegenX Apollo 324 for automated NGS library preparation
Beckman Coulter BioMek i7 for fully automated workstation
Fluidigm Access Array System for target-enrichment
Covaris M220 for DNA shearing

Nucleic Acid Isolation

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

Quality Control

Agilent 2100 Bioanalyzer
Agilent 2200 Tapestation
NanoDrop 8000
Qubit 3.0 Fluorometer
Fragment Analyzer
Varioskan Lux Plate Reader

Other

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

Data Analysis (Software) / Other Resources

Partek flow
VarSeq
Falcon automated genomic analysis system
Hoffman2 data analysis clusters
Illumina base space Sequencing Hub professional
Amazon cloud HIPAA compliant research computing and storage system

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).

Pricing

Download price list for above services