Genomics includes assessment of genome-wide phenomena involving DNA, RNA and epigenetic marks. Applications of high throughput sequencing include: sequencing or resequencing of whole or targeted regions of genomes from a single cell to microbial communities to whole organisms (genomics); capturing the complete expression profile of protein-coding genes as well as noncoding RNAs by RNA-sequencing (transcriptomics); genome-wide profiling of DNA-protein interactions (ChIP-Seq), epigenetic marks, and chromatin structure (epigenomics); and analysis of microbiome genetic potential and gene expression.
LSI Genomics Directors Don Moerman & Corey Nislow
High Throughput Sequencing
Biofactorial (Bio!) Core at LSI
https://lsi.ubc.ca/biofactorial/
Many unanswered questions in biology require large, multifactorial experiments that demand automation systems or extreme miniaturization to offset the high costs of essential reagents. The High Throughput Biology Facility, Biofactorial (Bio!), bridges critical gaps in automation infrastructure for academia and small to mid-size enterprises (SMEs). It provides researchers within and beyond UBC access to cutting-edge automation, enabling deeper scientific insights at new economies of scale. Biofactorial is a member of the Global Biofoundries Alliance (GBA) and promotes the adoption of common standards and open science initiatives.
Services Include
- Compound Screening: Compound screening is at the heart of many probe and drug discovery projects. Biofactorial enables investigators to access small volumes of compounds for screening projects performed at the facility, and can support activities from assay design, screening, secondary assay screening, through to preliminary SAR. Small molecule libraries include bio-actives and screening collections.
- High Content Screening: Offering the Cellomics ArrayScan VTi and the CellInsight CX5, our high content screening platforms allow for quantitative cellular imaging and analysis in 96 or 384 well format. Access to an EVOS FL Auto with an onstage incubator, allowing florescence and transmitted light applications under modified environmental conditions (humidity, carbon dioxide, and oxygen controls).
- Environmental-DNA (E-DNA) Screening: The facility has access to a large library of metagenomic samples. These resources are available for use by clients to explore novel protein or biosensor discovery, and opens the door to unique enzyme discovery for synthetic biology applications.
- Automation Equipment for High Through-put Processes:
- QPix Colony Picker - allows for picking, replicating, and re-arraying colonies from agar plates to 96- and 384-well plates
- KingFisher Apex - an automated magnetic-particle processing system for the extraction of DNA, RNA, and proteins in 24- and 96-well formats
- QuantStudio qPCR - real time PCR machine in 96- and 384- well formats
- Agilent Bravo - a liquid handling platform used for DNA and RNA purification for NGS
- Labcyte Access Workstation - including an Echo for tip-less acoustic liquid dispensing for small volume reactions.
- Illumina Miseq - typically used for amplicon sequencing but can also be used for low coverage shotgun sequencing applications
- New Equipment:
- Meso Sector S 600: High sensitivity electrochemi-luminescence immunoassay imager capable of multiplexing in 96- and 384-well formats.
- On-Chip Sort: Chip-based microfluidic sorter capable of gently sorting cells or emulsion droplets with improved cell viability and growth.
- To see additional equipment, screening libraries, and pricing, visit our website: https://lsi.ubc.ca/biofactorial/
Contact
- Tom Pfeifer, Automation Manager
- E: tom.pfeifer@ubc.ca
- Address: #2505-2350 Health Sciences Mall, Vancouver, BC V6T 1Z3
SBME Sequencing Core (formerly BRC-Seq)
https://bme.ubc.ca/home/sequencing-facility/
The School of Biomedical Engineering (SBME) Sequencing Core (formerly BRC-Seq) is dedicated to providing Single-Cell and Next-Generation Sequencing Services and training to the Research Community. We work collaboratively with the Michael Smith Genome Sciences Center and the Michael Smith Laboratories, and are located at the Biomedical Research Center at UBC.
Turnaround time is ~ 3 – 4 weeks, depending on request. Please expect 3-5 days for QC results.
Services include
- Quality Control
- Illumina library qPCR quantification
- Agilent Bioanalyzer & TapeStation DNA & RNA sizing & quality assays
- Next Generation Sequencing Library Prep
- mRNA Seq & Ribodepletion prep available
- DNA prep
- 10x Genomics Single Cell Prep
- Illumina NextSeq2000 Sequencing runs
- Bioinformatic Analysis
Contact
Sequencing and Bioinformatics Consortium (SBC)
http://sequencing.ubc.ca/
The Sequencing and Bioinformatics Consortium in the Pharmaceutical Sciences building at UBC provides experimental design consultation, next generation (Illumina) sequencing, Sanger sequencing, genotyping, and bioinformatics analysis. Their expertise and experience allows them to develop and utilize customized solutions for sequencing and bioinformatics analysis with rapid turnaround times. Their website provides clear descriptions of services, costs and turnaround times.
The SBC provides high throughput sequencing on Illumina MiSeq and NextSeq instruments, including sample QC and library preparation (genomic, RNA, 16S, amplicon, and custom protocols), with results provided as FASTQ and/or BAM files. Custom analysis is available for projects with unique needs.
Contacts
Christine Yanta, MSc, Bioinformatics Specialist
Sunita Sinha, PhD, Research Manager
E: sequencing.centre@ubc.ca
Pharmaceutical Sciences Building
University of British Columbia
3124 – 2405 Wesbrook Mall
Vancouver, BC V6T 1Z3
Genome Sciences Centre - Sequencing
http://www.bcgsc.ca/services
The GSC, Canada's Michael Smith Genome Sciences Centre, is the largest capacity genomics centre of its type in Canada. The GSC specializes in high-throughput, large-scale genome research activities encompassing cancer genetics, bioinformatics, LIMS, DNA sequencing, data analysis, genome mapping, gene expression profiling, proteomics and technology development. The GSC has services available for sequencing, bioinformatics platform services, proteomics and in-silico drug design.
GSC services are in high demand, and performed on a "first in, first on" basis. All work is put in a queue based on the date of receipt, and turnaround times vary. Please see their terms and conditions or submit inquiries about collaborative services here.
Sequencing services include:
- Nucleic acid extraction and library construction
- Whole genome, whole transcriptome, epigenome, ChIP, exome capture, miRNA, long reads, linked reads, customized
Instrumentation:
- Illumina HiSeqX, HiSeq2500, NextSeq500, MiSeq
- Oxford Nanopore MinION, PromethION
- MGI DNBSEQ-G400
Contact
Leslie Alfaro, PhD, PMP, Projects Team Leader
P: (604) 707-5800 x 675244
E: lalfaro [at] bcgsc.ca
Genome Sciences Centre, BC Cancer Agency
Suite 100, 570 West 7th Ave
Vancouver, BC, V5Z 4S6
Laboratory for Advanced Genome Analysis
https://www.prostatecentre.com/node/255
Vancouver Prostate Centre genomics core facility
Expertise: The Laboratory for Advanced Genome Analysis (LAGA) specializes in the acquisition, processing, statistical analysis, integration, and visualization of next-generation sequencing and microarray data. Our highly trained technicians interpret complex data and offer important recommendations for the best possible use of genomics and transcriptomics technology. LAGA prides itself on providing clients with solutions that are rapid, economical and tailored to their needs. From 2011 to 2017, LAGA’s performance has been rewarded by >20 peer-reviewed publications arising directly from work performed by Dr. Collins’ group and close collaborators.
LAGA has unique capabilities in the following areas:
- Translational genomics, where genomics, computer science, and clinical science converge in diagnostics and therapeutics
- Combined use of microarray and sequencing technologies
- Advanced bioinformatics and data visualization
- Comparative oncogenomics, where tumours from different organ sites converge on common genome structures as they progress toward metastasis
Services: PC-TRiADD’s Laboratory for Advanced Genome Analysis supports small and large-scale projects across Canada and internationally for the following applications:
Microarray Platform
- Agilent catalog and custom design microarray
Microarray Applications
As a Certified Service Provider, all Agilent microarray applications are supported; LAGA specializes in:
- Gene, exons and non-coding expression
- Array Comparative Genomic Hybridization with CGH probes for genome-wide DNA copy number variation and SNP probes for copy neutral aberrations
Next Generation Sequencing Platforms
- Life Technologies Ion Proton
- Illumina MiSeq
Next Generation Sequencing Applications
- Exome sequencing for integrative analysis of SNVs and CNVs
- 16S rRNA genes
- Target capture sequencing
- RNA sequencing (gene expression analysis)
- RNA sequencing (whole transcriptome analysis)
- Small RNA sequencing
- ChIP-seq; ATAC-seq
- Microbial and viral whole genome sequencing, including metagenomics
Bioinformatics
- Acquisition, processing, statistical analysis, integration, and visualization of high-density genomic and transcriptome data from simple to complex experimental designs using one of several platforms
- Utilization of software that allows seamless cross-platform integration and analysis of expression, genomic, and next generations sequence data making possible extremely powerful and comprehensive studies
Contact
Research:
Colin Collins, PhD
Professor, Dept. Urological Sciences
University of British Columbia
Senior Research Scientist
Director, LAGA and BGI@VPC
P: 604-779-9287
E: ccollins [at] prostatecentre.com
Services:
Stéphane LeBihan, PhD
Manager, Genomics Core
P: 778-991-4506
E: slebihan [at] mail.ubc.ca
Vancouver Prostate Centre
2660 Oak Street
Vancouver, BC, Canada V6H 3Z6
Single Cell Genomics
Bigelow Laboratory Single Cell Genomics Center
https://scgc.bigelow.org/
The Single Cell Genomics Center (SCGC) is a nonprofit research and service center at Bigelow Laboratory for Ocean Sciences, with its primary focus on microbial single cell genomics for applications in microbial ecology, evolution, bioprospecting and human health. SCGC offers a comprehensive suite of single cell genomics services, from single cell separation through genome sequencing and bioinformatics and can provide advice on environmental sample collection and storage protocols and post-sequencing analyses.
Contact
Ramunas Stepanauskas, Director
Brian Thompson, Manager
P: 207-315-2567, ext. 517
F: 207-315-2329
E: bthompson [at] bigelow.org
Single Cell Genomics Center
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive
East Boothbay, Maine 04544-0380 USA
Other
GENEWIZ Dropbox
https://www.genewiz.com/
LSI researchers can drop off samples for GENEWIZ in a dropbox in LSC Shipping and Receiving on level B2. GENEWIZ provides services including Next Generation and Sanger Sequencing, gene and oligo synthesis, and many more. Samples from the dropbox are picked up daily between 2:00 - 2:30pm.
Genomics Training and Online Resources
SEQanswers Forum
http://seqanswers.com/forums/index.php
SEQanswers was founded to be an information resource and user-driven community focused on all aspects of next-generation genomics including next generation sequencing technology discussion and education. The site attempts to cater to everyone, regardless of scientific background or knowledge.
