Services and Nodes

Genomics Technologies: Nucleic Acid and Sequencing Technologies

1.  General NGS sequencing and library prep
   1. Library Preparation - The ACE Core provides a range of sequencing library preparation services. The following is a brief outline of some of the main types of sequencing library preps that we offer, but make sure to discuss all the details of your potential project with core staff.
      • General NGS Illumina DNA Prep Kit
        Applicable to a wide range of applications including sequencing of amplicons, plasmids and microbial species. This prep is also used in our 16S RNA sequencing service.
      • 16S rRNA Sequencing (metagenomics) or other Amplicon libraries. Used for metagenomic analysis, the 16sRNA region from available bacterial and archaeal DNA within a sample is PCR amplified so that it can be sequenced and species diversity within the sample can be known. We have in-house primers that target the V3-V4 region of the 16S rRNA gene outlined in the following publication. Custom primers for different regions can be used if provided along with a PCR protocol. This also applies to other custom amplicon projects. The core accepts both isolated genomic DNA and amplicons as samples for this service. 
      • Bulk RNA Sequencing
        • Illumina Stranded mRNA assay kits stocked
        • Illumina Truseq V2 still available to maintain consistency to previous or existing studies run with the HCA core
      • Single Cell Transcriptomics and other assays
      • Other assays and prep
        • The core has expertise in processing many specialised assay kits in the past. We’re happy to work with users and industry application scientists to process non-stocked kits at our standard rate of $50 per hour for labour. Keep in mind that troubleshooting may add considerable additional processing time over what a kit may outline in their workflow. Please contact core staff to discuss any specialised or customised library preparations you might be interested in processing.
   2. Sequencing
      • The ACE core houses an Illumina Miseq Sequencer. It excels at sequencing small capacity libraries like 16S RNA or other amplicon based preps. It is also useful at processing small specialised kits. We stock Miseq v3 600 cycle kits in the core, but can order any listed Miseq sequencing kits on a cost recovery basis. Please contact the core for current pricing.
      • The ACE Core also partners with the uAlberta Molecular Biology Services Unit to pass medium capacity sequencing needs over to run on their NextSeq500 system. We coordinate this service and billing on projects being processed at the ACE Core to ensure a seamless experience for our users who wish to keep their sequencing on campus.
      • The ACE Core acts as one of several hundred Drop Boxes that ship samples to Plasmidsaurus weekly. They provide very affordable long read (Oxford Nanopore Technologies) sequencing for plasmids, linear amplicons, bacterial genomes and other specific products starting at $15 USD. See their website for more information and pricing. Our Dropbox is located in the main Flow Cytometry Core (HMRC 667) with a weekly cutoff of Wednesdays at 1:00PM. All samples for uAlberta are currently aggregated and shipped Thursday morning at 11am from MBSU in CCIS. Please ensure all proper packaging steps are followed as improperly packaged samples will not be shipped.
        
        
2. Nucleic acid  QC and Analysis
   1. Invitrogen Qubit Flex
      • DNA High Sensitivity (0.1-120 ng/ug quantification range)
      • RNA High Sensitivity (0.2-200 ng/ug quantification range)
   2. Agilent Bioanalyzer 2100
      • High Sensitivity (Range: 5-500pg/uL, 50-7000np Sizing Range)
      • RNA Nano 6000 (Range: 25-500ng/uL; Used to report RNA Integrity Numbers (RIN))
   3. Qiagen Qiaxcel
      • High Sensitivity DNA
      • DNA Screen
   4. qPCR
      • Biorad CFX96 Real Time System 

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Single Cell Technologies: Single Cell Profiling

1. Single Cell Transcriptomics
   1. 10X Genomics 3’ v3.1 gene expression kits are stocked and are available for purchase per sample from the core as part of a library preparation service.
   2. Other single cell kits compatible with our infrastructure can be ordered on a cost recovery basis and processed at our standard rate of $50 per hour for labour. These include other 10X Genomics assays compatible with the Chromium Controller including single cell ATAC (Assay for Transposase Accessible Chromatin, Chromatin availability), 5’ Immune profiling or multiome and Parse Bioscience Evercode combinatorial single cell barcoding kits. Speak to ACE Core staff for more information. 
2. Spatial Instruments
   1. Vizgen MERSCOPE
      

      The MERSCOPE uses Multiplexed Error-Robust In-Situ Hybridization (MER-FISH) to directly detect hundreds of gene transcript targets in a single tissue slice. It’s equipped with a 60x Objective lens to achieve 100nm optical resolution to allow subcellular localization of detected transcripts. Alongside it’s MERSCOPE capabilities, it is also equipped with a number of protein channels which can be used for cell boundary stains in addition to primary antibodies against a target of interest using Vizgen’s secondaries (anti-Mouse, Rabbit, Goat, Rat, Human, Chicken). 

      Gene panels are currently available in 140, 300 and 500 genes and come standard as customizable against any species that has an annotated genome and are targeted to 20-50 sites across the target transcript for improved detection of degraded mRNAs. This platform is compatible with fresh frozen (FF), fixed frozen, cell culture (CC), and FFPE samples with an available surface area of 1cm2 per run.  

      This platform will become fully online in Fall 2023 once core training has been completed and when service structure and pricing has been set. Users of the ACE Core will receive update announcements and other interested parties can contact mewong@ualberta.ca to be added to core announcement email lists.
      

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Screening Libraries: Genetic and Chemical Screening Libraries

Screening libraries are portioned and diluted using the Janus fluid handler to maintain quality of the plates and prevent cross-contamination. Pricing for screening activities (except for shRNAs) is based on labour ($50 per hour) and plastics on a cost recovery basis.

1. Chemical Screens
   1. LOPAC 1280 Library of Pharmacologically Active Compounds
      • Collection of 1,280 Pharmacologically-Active Sigma Compounds 
      • Stocks are stored in 96 or 384 well plate configuration at 10mM dissolved in DMSO
   2. Myriascreen II Diversity Collection 10 000 
      • Pre-selected pool of over 300,000 TimTec and Sigma-Aldrich compounds on the basis of diversity and structural relevance for general screening. Additional filters were set to consider physical-chemical properties including MW, cLogP, H-acceptor, H-donors, and rotatable bonds. Molecular weight range is from about 120 to 500. The collection is largely drug-like according to Lipinski Rule of 5 and also includes lead like material being suitable for more targets and leaving greater room for molecular optimization.
      • Stocks are stored in 96 or 384 well plate configuration at 10mM dissolved in DMSO
2. siRNA Screens
   1. Ambion Silencer and Dharmacon siRNA libraries available. Please inquire with the core about availability.
3. shRNAs
   1. The RNA Consortium (TRC) shRNA Library Sigma-Aldrich version 1.0-1.5.

      • The shRNA sequences are encoded on pLKO.1 Vectors expressed in E. coli. Stocks of bacteria are grown up in LB-Amp broth and given to researchers to propagate and extract plasmids from for downstream use. We also have empty vector and GFP targeting controls available. Please note that this library does not contain all the variants listed in the most current version 3 libraries.

      • Pricing per stock: 1-5 $20.00; 6-10 $15.00; 11+ $10.00

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Auxiliary Platforms

1. Nucleofector electroporator
2. Agilent Seahorse XFe96 Metabolic Analyzer
   1. This analyzer measures Oxygen Consumption Rate (OCR) and  ExtraCellular Acidification Rate (ECAR, pH) of live cell culture media in a 96-well plate format. These measures are indicators of glycolysis and mitochondrial respiration which allow insights into the metabolic activity of the in-vitro and ex-vivo samples.
   2. One time use FluxPak Sensor plates that are used for all assay types can be purchased from the core at a cost recovery basis ($103 each). A broad range of assay reagent kits are available from Agilent.