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
BRC Sequencing Core at UBC
https://bme.ubc.ca/home/sequencing-facility/
Located on campus at the Biomedical Research Center, the BRC Sequencing Core (BRC-Seq) brings greater sequencing accessibility to all researchers at UBC and beyond. BRC-Seq provides researchers with quality data — from standardized sample preparation to sequencing to QC to analysis — and a quick turnaround time.
Services include:
- Bioanalyzer sizing and QC: RNA samples are run on the Agilent Bioanalyzer to ensure RNA is of sufficient quality and quantity for library preparation. DNA libraries are quantified by Qubit, sized on the Agilent Bioanalyzer, and quantified by qPCR using the NEBNext Library Quant Kit for Illumina.
- Library Preparation: RNA or DNA samples are prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. We offer both poly(A) mRNA and ribodepletion selection.
- Single Cell Capture: Using the 10x Genomics Platform, cells are captured using either the 3’ RNA, 5’VDJ, ATAC or Multiome kit, with the option to include Total-Seq or Cite-Seq applications.
- Sequencing: Depending on experimental requirements, libraries are quantified, pooled and ran on either the Illumina MiSeq or NextSeq2000, with customizable sequencing fragment read length and depth.
Instrumentation:
- 10X Genomics Chromium Single Cell Controller
- Illumina NextSeq2000 & Illumina MiSeq
- Agilent 2100 Bioanalyzer
- Covaris M220
- ViiA 7 Real-Time PCR System
- epMotion 5075t
- Invitrogen Qubit
Contact:
E: tstach [at] brc.ubc.ca
P: (604) 827-3381
Scientific Director: Dr. Michael T. Underhill
Facility Manager: Tara Stach
Sequencing Technician: Yvonne Chung
Bioinformatic Technician: Bernie Zhao
Address: Biomedical Research Centre – Room 300
2222 Health Sciences Mall, University of British Columbia
Vancouver, BC, V6T 1Z3
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
David Levy-Booth, PhD, Bioinformatics Specialist
Sunita Sinha, PhD, Research Manager
E: sequencing.centre [at] 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, LAGA and BGI@VPC
P: 604-875-4506
E: slebihan [at] prostatecentre.com
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.
Informatics on High Throughput Sequencing Data - CBW 2018
https://bioinformatics.ca/workshops/2018-informatics-on-high-throughput-sequencing-data/
Video (YouTube) and slide decks (PDF) of lectures from the two-day Canadian Bioinformatics Workshops on Informatics on High Throughput Sequencing Data, May 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.
Lectures include: Genome Visualization; Genome Alignment; Small-variant calling and annotation; Structural variation; De Novo Assembly.
Informatics for RNA-seq Analysis - CBW 2018
https://bioinformatics.ca/workshops/2018-informatics-for-RNA-seq-analysis/
Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Informatics for RNA-seq Analysis, May 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.
Lectures include: Introduction to RNA sequencing and analysis; RNA-seq alignment and visualization; Expression and differential expression; Reference free alignment; Genome Guided and Genome-Free Transcriptome Assembly; Functional Annotation and Analysis of Transcripts.
Bioinformatics for Cancer Genomics - CBW 2018
https://bioinformatics.ca/workshops/2018-bioinformatics-for-cancer-genomics/s
Video (YouTube) and slide decks (PDF) of lectures from the six-day Canadian Bioinformatics Workshops on Bioinformatics for Cancer Genomics, March 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.
Lectures include: Introduction to Cancer Genomics; Ethics of Data Usage and Security; Databases and Visualization Tools; Genome Alignment; Genome Assembly; Somatic Copy Number Changes; Somatic Mutations and Annotations; Gene Expression Profiling; Gene Fusion Discovery and Genomic Rearrangements; Sharing and Scaling a VM; Working Reproducibly in the Cloud; Big Data Analysis in the Cloud; Genes to Pathways; Variants to Networks; Integration of Clinical Data.
Pathway and Network Analysis of -omics Data - CBW 2018
https://bioinformatics.ca/workshops/2018-pathway-and-network-analysis-of-omics-data/
Video (YouTube) and slide decks (PDF) of lectures from the three-day Canadian Bioinformatics Workshops on Pathway and Network Analysis of -omics Data, June 2018. Canadian Bioinformatics Workshops past workshop content is available under a Creative Commons License.
Lectures include: Introduction to pathway and network analysis; Finding over-represented pathways in gene lists; Network visualization and analysis with Cytoscape; More Depth on Pathway and Network Analysis; Gene Function Prediction; Regulatory Network Analysis.
