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McGill University and Genome Quebec Innovation Centre

Montreal, Quebec, CA

The McGill University and Génome Québec Innovation Centre is a world-class research facility for genomics. Founded in 2002, the Centre has developed a world-renowned expertise in complex genetic disorders such as cardiac disease, asthma and Type 2 diabetes, and has become a technical resource and a networking site for various research initiatives in human health, forestry, infectious diseases, agriculture and environment.

Ambitious projects in recent years are a testimony of the ability of Génome Québec to provide data of exceptional quality in the pursuit of various genomics studies. The Innovation Centre provides complete DNA and RNA analysis services, from a few samples to several tens of thousands per week. Large-scale genomics services at the Innovation Centre are articulated around sequencing (including massively parallel sequencing), genotyping and expression profiling supported by a solid infrastructure,... Show more »

The McGill University and Génome Québec Innovation Centre is a world-class research facility for genomics. Founded in 2002, the Centre has developed a world-renowned expertise in complex genetic disorders such as cardiac disease, asthma and Type 2 diabetes, and has become a technical resource and a networking site for various research initiatives in human health, forestry, infectious diseases, agriculture and environment.

Ambitious projects in recent years are a testimony of the ability of Génome Québec to provide data of exceptional quality in the pursuit of various genomics studies. The Innovation Centre provides complete DNA and RNA analysis services, from a few samples to several tens of thousands per week. Large-scale genomics services at the Innovation Centre are articulated around sequencing (including massively parallel sequencing), genotyping and expression profiling supported by a solid infrastructure, tools (Nanuq) and unique expertise in bioinformatics.

All services work in parallel to provide comprehensive, reliable services to the Québec, Canadian and international scientific community as well as the private sector. Located on the campus of McGill University in the heart of Montreal, the Innovation Centre acts as a vast resource of knowledge and technology to the academic and industrial sectors.

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McGill University and Genome Quebec Innovation Centre has not listed any services.

Homozygosity Mapping
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SMRT Sequencing
Single Molecule Real-Time Sequencing
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The PacBio RS II Single Molecule Real-Time (SMRT ® ) sequencing technology produces thousands of base pairs from single molecules in real time, allowing observations of structural and cell type variation not accessible with other technologies. These unique capabilities of the PacBio RS II system are ideally suited for a variety of... Show more »

The PacBio RS II Single Molecule Real-Time (SMRT ® ) sequencing technology produces thousands of base pairs from single molecules in real time, allowing observations of structural and cell type variation not accessible with other technologies. These unique capabilities of the PacBio RS II system are ideally suited for a variety of applications:

  • from de novo assembly of small genomes (ex. bacterial or fungal)
  • targeted sequencing of long cDNA molecules
  • detecting base modifications
  • RNA sequencing

As more scientists adopt the SMRT ® technology, we expect numerous other applications of sequencing to become feasible for the first time.

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PacBio RS II
SNP Genotyping
Single Nucleotide Polymorphism Genotyping
Price on request

Different technologies are available for genotyping bi-allelic markers such as SNPs (Single Nucleotide Polymorphisms) and indels (insertion/deletion polymorphisms) depending on the number of markers to test in parallel and the desired applications, .

Genotyping Technologies

  • Interrogate between 1 and over 5M loci (SNP,... Show more »

Different technologies are available for genotyping bi-allelic markers such as SNPs (Single Nucleotide Polymorphisms) and indels (insertion/deletion polymorphisms) depending on the number of markers to test in parallel and the desired applications, .

Genotyping Technologies

  • Interrogate between 1 and over 5M loci (SNP, indel, or CNV)
  • Custom genotyping for studying focused genomic regions of interest on any species
  • Commercial arrays with standard content

Applications

  • Candidate-gene studies
  • SNP discovery validation
  • Fine-mapping of candidate association regions
  • Linkage analysis for mapping the location of phenotype causing loci
  • Admixture mapping
  • Genome-wide association studies (GWAS) for mapping genetic variation across populations to identify variants associated with a phenotype
  • Copy Number Variation (CNV) Analysis
  • Cytogenetic studies
  • Homozygosity mapping
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RNA Sequencing
Price on request

The Innovation Centre offers transcriptome analysis by performing cDNA library constructions from total RNA to allow subsequent sequencing using the HiSeq 2000/2500/4000 from Illumina. To learn more about this service please consult the Next-Generation Sequencing services section.

Library preparation services include the... Show more »

The Innovation Centre offers transcriptome analysis by performing cDNA library constructions from total RNA to allow subsequent sequencing using the HiSeq 2000/2500/4000 from Illumina. To learn more about this service please consult the Next-Generation Sequencing services section.

Library preparation services include the following types of RNA-Seq libraries:

  • Eukaryotic protein coding transcripts (mRNA stranded libraries)
  • Prokaryotic long transcripts (bacterial rRNA-depleted libraries)
  • Eukaryotic long non coding and coding transcripts (rRNA-depleted libraries)
  • Prokaryotic and eukaryotic long non coding and coding transcripts for metagenomic studies (rRNA-depleted libraries)
  • All transcripts (total RNA)
  • Eukaryotic small transcripts (<200 nt)
  • Eukaryotic miRNA (enriched in species 22-50 nt)
  • Targeted human protein coding transcripts (minimum of 48 samples)
  • Human protein coding transcripts from FFPE samples (minimum of 48 samples)

All libraries are strand-specific.

Ribosomal RNA depletion yields vary according to species. Consult Illumina web site to verify expected % of depletion. If the species of interest is not listed, it might be a good idea to use RNAMatchmaker.

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Affymetrix RNA Microarray
Price on request

GeneChip® expression arrays enable the measurement of expression levels of transcripts both quantitatively and qualitatively. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer... Show more »

GeneChip® expression arrays enable the measurement of expression levels of transcripts both quantitatively and qualitatively. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

Arrays are currently available for many biologically relevant model organisms.

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RNA Quality Control
Price on request

The verification of RNA integrity and concentration is crucial for all samples coming to the Innovation Centre for expression analysis. However, it is possible to bring your samples to have their quality checked without requiring other services. For this you'll need to fill the request form for Bioanalyzer only.

*Available... Show more »

The verification of RNA integrity and concentration is crucial for all samples coming to the Innovation Centre for expression analysis. However, it is possible to bring your samples to have their quality checked without requiring other services. For this you'll need to fill the request form for Bioanalyzer only.

Available technologies

  • NanoDrop (Thermoscientific): The NanoDrop ND 1000 is used in the lab to verify the concentration of RNA samples. This spectrophotometer is working with 1 uL of RNA sample and will measure the absorbance at 260, 280 and 230 nm. The detection limit is 2 ng/uL.
  • Bioanalyzer 2100 (Agilent): The Agilent Bioanalyzer 2100 in concert with the Agilent RNA 6000 nano or pico kit is a microfluidics-based platform used for quality control and integrity checks of RNA samples.
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Agilent Bioanalyzer
SNP Discovery Sequencing
Price on request

The Innovation Centre offers a custom SNP Discovery service and a service of de novo sequencing of complete plasmids by primer walking.

Full SNP Discovery/Validation services by Next-Generation Sequencing (NGS) include:

  • Designing and ordering primers to amplify target regions.
  • Target region amplification using the... Show more »

The Innovation Centre offers a custom SNP Discovery service and a service of de novo sequencing of complete plasmids by primer walking.

Full SNP Discovery/Validation services by Next-Generation Sequencing (NGS) include:

  • Designing and ordering primers to amplify target regions.
  • Target region amplification using the Fluidigm Access Array System.
  • Sequencing of PCR products using various NGS Technologies (Illumina HiSeq or MiSeq, PacBio).
  • Transmission of a SNP report.

Full SNP Discovery services include:

  • Designing and ordering primers to amplify target regions
  • PCR amplification of target regions from genomic DNA of test samples based on Sanger Sequencing
  • Detection of variations in test samples or between test samples and a reference sequence
  • Preparation and transmission of a SNP report including several annotations on the variations.

The de novo sequencing service includes:

  • Sanger sequencing with any entry primer
  • Designing and ordering all primers needed to sequence entire plasmids or regions
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Sanger Sequencing
Price on request

The Innovation Centre offers a Sanger Sequencing Service using Applied Biosystem's 3730xl DNA Analyzer technology.

In addition to the regular service, the Innovation Centre also offers the 24hr BaseXpress Sequencing Service.

Sanger sequencing is often used to proofread plasmid DNA sequence to verify the integrity of a... Show more »

The Innovation Centre offers a Sanger Sequencing Service using Applied Biosystem's 3730xl DNA Analyzer technology.

In addition to the regular service, the Innovation Centre also offers the 24hr BaseXpress Sequencing Service.

Sanger sequencing is often used to proofread plasmid DNA sequence to verify the integrity of a gene inserted into an expression vector or to re-sequence targeted regions of a genome with the purpose of finding genetic variations.

Sanger sequencing is most suitable for small to medium range sequencing projects. For large scale sequencing projects, please contact the Client Management Office to help select the most suitable Next-Generation sequencing technology.

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DNA Extraction
Price on request

The McGill University and Génome Québec Innovation Centre offers services for DNA extraction and sample preparation to academic and industrial researchers.

Genomic DNA extraction*

The Innovation Centre offers a genomic DNA isolation service from blood, saliva, buffy coat, bacteria and cultured cells.

DNA can be isolated... Show more »

The McGill University and Génome Québec Innovation Centre offers services for DNA extraction and sample preparation to academic and industrial researchers.

Genomic DNA extraction*

The Innovation Centre offers a genomic DNA isolation service from blood, saliva, buffy coat, bacteria and cultured cells.

DNA can be isolated from a range of sample volumes of 0.2 to 2 mL, and can be used for various types of genetic analyses including genotyping and sequencing.

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Illumina Sequencing
Price on request

Among others, the Innovation Centre NGS fleet included 18 HiSeq 2000/2500/4000/X instruments.

Various library types are available for Illumina HiSeq and MiSeq sequencing, including:

  • Shotgun DNA libraries (Kapa BioSystems and Illumina TruSeqPCRfree) for the sequencing of large size genomes - de novo assemblies and SNP... Show more »

Among others, the Innovation Centre NGS fleet included 18 HiSeq 2000/2500/4000/X instruments.

Various library types are available for Illumina HiSeq and MiSeq sequencing, including:

  • Shotgun DNA libraries (Kapa BioSystems and Illumina TruSeqPCRfree) for the sequencing of large size genomes - de novo assemblies and SNP calling
  • Various Nextera libraries (Illumina) for the sequencing of large to small genomes - de novo assemblies
  • ChIP-Seq libraries
  • Whole genome bisulfite libraries - identification of methylation sites
  • Reduced genome libraries
    • Exome captures (Agilent SureSelect; Roche Nimblegen SeqCap; Illumina Nextera Exome)
    • Custom panels (Roche Nimblegen SeqCap; Illumina Nextera Capture)
    • Methylation (Roche Nimblegen SeqCapEpi)
    • RNA-Seq
  • Custom Amplicons, 16S
  • RNA-Seq

Most library preparation pipelines have been automated to increase robustness and cost efficiency.

Libraries can be sequenced in either single-read of paired-end formats and for read lengths of 50, 100, 150, or 250 bases (up to 300 bases for the MiSeq). On average, 15M reads can be obtained on the MiSeq and from 120M to over 250M reads can be obtained on a single lane of HiSeq flowcell depending on the sequencing mode selected.

Sequences are downloadable directly from Nanuq. Sequence reads will be delivered as bam files for human, rat and mouse and as fastq for the other species.

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Illumina
Microsatellite Instability Testing
Price on request

This technology performs genotyping of microsatellite markers for Genome-Wide Scans and Fine Mapping. Both methods are powerful options for mapping genes of Mendelian-type inheritance due to the highly informative nature of these markers compared to SNPs.

Available Technologies

This technology performs genotyping of microsatellite markers for Genome-Wide Scans and Fine Mapping. Both methods are powerful options for mapping genes of Mendelian-type inheritance due to the highly informative nature of these markers compared to SNPs.

Available Technologies

  • Genome-Wide Scan: A set of 400 highly polymorphic microsatellite markers spaced at an average distance of 8.7 cM throughout the human genome is currently used. Each marker is amplified individually followed by pooling of 8 markers together in a panel. The genotyping results are obtained using an ABI-3730XL DNA Analyzer.
  • Fine-Mapping: The personnel of the service is available to facilitate in the choice, panel design and ordering of microsatellite markers to suit the chromosomal region and density requirements.

    Note that the optimization and the production of PCR reactions is no longer supported since January 2009, except for markers already validated or from the genome-wide scan set. Detailed information on the design of the labelled PCR primers can be obtained by contacting the Client Management Office.

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Transcriptome Sequencing and Profiling
Price on request

Arrays

  • GeneChip® Human Transcriptome Array 2.0 (HTA 2.0)
  • GeneChip® Mouse Transcriptome Array 1.0 (MTA 1.0)

Tens of thousands of human genes contain hundreds of thousands of exons, which produce hundreds of thousands of different transcript isoforms. These transcript isoforms are produced when the exons of a gene may... Show more »

Arrays

  • GeneChip® Human Transcriptome Array 2.0 (HTA 2.0)
  • GeneChip® Mouse Transcriptome Array 1.0 (MTA 1.0)

Tens of thousands of human genes contain hundreds of thousands of exons, which produce hundreds of thousands of different transcript isoforms. These transcript isoforms are produced when the exons of a gene may be included within, or excluded from, the final, processed messenger RNA produced from that gene. Until now, measuring and analyzing these transcript isoforms has been nearly impossible due to technology limitations, sample input requirements, and lack of analysis capabilities/tools.

Designed to empower next-generation expression profiling studies, GeneChip� Human Transcriptome Array 2.0 (HTA 2.0) provides the ability to go beyond gene-level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene.

The robustness of the technology has been demonstrated by over 25,000 publications. This means you do not need to worry about technology development and may focus on biological analysis. Moreover, Affymetrix provides a freely available analysis software, so data analysis can be performed easily in any lab.

Comprehensive transcriptome analysis requires combining transcript diversity from multiple data sources

Most genes produce multiple transcript isoforms, and measuring changes in the relative abundance of each isoform provides new insights into disease and biology. HTA 2.0 has combined multiple data sources to ensure you are able to independently analyze the broadest collection of transcript isoforms available.

Overall, the main advantage of the HTA arrays is the actual time to results which is much shorter compared to RNA-Seq experiments.

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Biology
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Biochemistry & Molecular Biology
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Nucleic Acid Services
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DNA Services
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Genotyping Services
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DNA Sequencing
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Next Generation Sequencing (NGS)
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DNA Extraction and Purification
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RNA Services
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RNA Microarray
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RNA Microarray Platforms
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Sequencing Data Analysis
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Sequencing Data Analysis Services

Sequencing Data Analysis Services

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2017-09-02 06:40:21 +1200

Net Promoter Score of 9 received for DNA Extraction.

Additional Ratings: satisfaction with deliverable: 9, satisfaction with timeliness: 9.

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