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Overview: LSU Genomics Facility


• GF 2021 Survey – Our Past & Future?

• Visual Tour of Facility.

• Who has access to the website?

• Who has access to the facility?

• How can I begin using the facility?

• Instruments & selected Services.

• Selected Web pages.

• Common Room resources for Biological Sciences.



Covid-19 Policy (Fall 2022): Clients are encouraged to wear a mask if planning to be in the facility for more than a few minutes. A mask is not needed if you are simply depositing your samples in the A628 Mini-fridge (by sink).

Suspension of Self-Service: Due to a lack of Service Agreements to cover instrument repairs, only facility staff may operate the instruments in the facility. For complete details, please see Operations during Self-Service Suspension.


GF 2021 Survey – Our Past & Future?

Since 2001, under the auspices of Dr. Mark Batzer, the LSU Genomics Facility has provided services to the LSU Baton Rouge campus under a very generous operational model in which instrumentation, service contracts, and staff were provided without charge. In essence, clients reimbursed the facility solely for the actual costs of reagents or consumables used to provide their services.

With shifting funding sources and aging instrumentation, that generous operational model is being reconsidered along with an assessment of what services and instrumentation might be provided in the future. Thus, during Fall 2021, we submitted a survey to our clients in order to assess the facility's performance and future client needs.

View survey results at GF 2021 Survey – Our Past & Future?

Visual Tour of Facility

For a visual introduction to our offerings, view this Slide show (*.pdf) or this 90-second silent video. The video is best viewed in "full screen" mode; it is not downloadable.


Who has access to the website?

Earth viewed by Apollo 17, courtesy of NASA Open access is provided to protocols, FAQs, links, and most documents on our website. The "Science Aid Center" provides extensive guidance, especially for DNA sequencing. Experimental protocols, documents, software, and informational sites are available through "Links".

Who has access to the facility?

Courtesy of U.S. Department of Energy Genomics: GTL Program Members of the College of Science (LSU—B.R.) are our primary clients; other local campus labs may have access if their Cores lack similar capabilities. Some equipment is available for use directly by researchers; other equipment is managed solely by facility staff — see listings below. People lacking a Genomics Facility Login ID can view the online request options available to authorized users by visiting the "View Only" version of the Request Form Options page.

How can I begin using the facility?

How can you begin using the facility? New Login IDs can be obtained through Request a Login ID. However, if the lab's PI has never used the Genomics Facility before, prior to issuance of the Login ID, you (and your PI) must first meet with Scott to discuss the facility’s regulations and how to access restricted portions of the Website. Use of the 'self-serve' equipment requires an Advance Reservation, made through the Biosci-Booked (Genomics) instrument reservation system. All other requests for supplies, services, or sequencing require submission of an online Request Form.

Login ID's are not transferable because they:
  • tag your submissions to a specific PI;
  • identify for the PI who submitted the request;
  • provide access to your online data; and,
  • supply your email address for automated notifications
    regarding processing and completion of requests.

  • You must Request a Login ID if you:
  • do not currently have a personal Login ID;
  • shift to the laboratory of a different PI;
  • begin working for a second PI; or,
  • need to upgrade from a Biosci-Booked (Genomics) Login ID.

  • Exceptions: Requests may be submitted under another person's Login ID under two circumstances:

    1) Transient researchers who are visiting the laboratory for a limited time; and,
    2) Undergraduates temporarily working under the specific direction of the person to whom the Login ID was issued.

    Note:  Existing Login ID's are deactivated when a client no longer works for the original PI.

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    Instruments, Services, & Links

    Staff-run Instruments

  • Ion Torrent S5 (NGS, Next Generation Sequencing)
  • ABI 3130xl Genetic Analyzers (Sanger-Sequencing, etc.)
  • Agilent Bioanalyzer (QC for DNA, RNA, & proteins)
  • BluePippin (DNA Size Selection for Next-Gen Sequencing)
  • Reservations required — Biosci-Booked (Genomics)

  • Client PC Workstation (on LSU network)
  • SmartCheck (rapid pipette validation)
  • ABI ViiA·7 & QuantStudio·6 (qPCR, protein melt-curves, etc.)
  • ABI Veriti (standard PCR thermal cycler)
  • Qubit 4.0 (Nucleic Acid & Protein quantitation; RNA Integrity)
  • Diagenode Bioruptor NGS (DNA fragmentation)
  • SPD1010 SpeedVac (sample concentration)
  • Typhoon 8600 Variable Mode Imager (Phosphor screens, etc.)
  • Other Instruments & selected Services

  • E-gel (DNA Size-Selection for NGS libraries, etc.)
  • Eppendorf Centrifuge 5810R (96-well plates; 15/50 ml tubes)
  • Victor·3 Multilabel Counter (fluorescence, luminescence, etc.) 
  • DNA Columns by Zymo Research (purification & Size-Selection)
  • Selected Web pages

  • BioSci Thrift Store
  • Self-Service instruments
  • Reagents & Supplies
  • Software, qPCR, Technical info, and Training
  • Documents for Equipment & Protocols
  • Common Room (A624, Life Science Annex)

    Next door to the Genomics Facility (A628), there is a Common Room (A624) which houses additional equipment maintained by the Department of Biological Sciences. Please note that the Genomics Facility has no information regarding Common Room equipment... aside from the following:

  • Only members of Biological Sciences are authorized users.
  • Equipment oversight is provided by specific Faculty members.
  • Report equipment problems to overseeing Faculty member; if unavailable, submit a Work Request to the department.
  • Finally, some equipment in A624 belongs to specific Faculty members and is not available for common use.
    • Common Equipment (partial listing):
    • Ice Machine (granular ice).
    • Milli-Q Synergy UV (ultrapure, type 1 water).
    • Thermo NanoDrop 2000 (micro-volume spectrophotometer).
    • ChemiDoc XRS (photo documentation, uv-gels).
    • Beckman centrifuges (high-speed centrifugation).
    • Hood, standard (e.g., organic extractions).
    • Jouan MSC 12 (biosafety cabinet).

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    Ion Torrent S5

    Ion_Torrent_S5 The S5 provides options for both high and low-to-moderate NGS throughput. The 540 chip can generate modal read lengths of up to 200-bp (maximum size is ~250-bp), while the 520 and 530 chips can generate modal read lengths of up to 400-bp (with emulsion PCR by the OneTouch·2) and 500-bp ( with Isothermal amplification).

    Typical post-filtering yields by chip type:

  • 520 chip, ~5-8 million FINAL Library reads;
  • 530 chip, ~20 million FINAL Library reads;
  • 540 chip ~60-80 million FINAL Library reads.

  • Read output can be higher for very high quality NGS libraries that result in low levels of polyclonal ISPs and minimal filtering for low-quality reads.

    Sequencing is based on pH changes associated with the incorporation of native nucleotides; data accuracy is improved by incorporating flow-space information (i.e., which nucleotide was being flowed across the chip at the time of incorporation) into basecalling... as well as in downstream mapping with Ion-optimized software, TMAP. Prior to developing libraries for sequencing on this platform, please contact us to discuss your project.

  • Related Documents
  • Services for the ABI Ion Torrent S5
  • Back to List of Instruments & selected Services

    ABI 3130xl Genetic Analyzers

    ABI Prism 3130xl The 3130xl Genetic Analyzers (Applied Biosystems) can run a wide variety of sequencing and fragment analysis applications. As of January 2020 (when security updates to Windows 7 ceased), we converted the computers for our instruments to Windows 10 (64-bit); for details on this process, please see my LinkedIn post, Converting an ABI 3130xl computer to Windows 10. Typically, our three 3130xl’s are set up for standard DNA Sanger-Sequencing (≤900 bp) with POP7 polymer and 50-cm arrays, a combination which also performs well for fragment analysis; upon special request, we can install 80-cm arrays (≥1000 bp reads) or 36-cm arrays (rapid sequencing and fragment analysis). Requests for sample processing and data retrieval are both handled online through the Genomics Facility website.

  • Standard DNA Sanger-Sequencing options:
    Electrophoresis-Only: Client performs the BigDye sequencing reaction, cleans the products, and resuspends them in (preferably) ABI Hi-Di formamide such that the samples are ready for electrophoresis on the 3130xl. Guidelines and requirements for DNA sequencing are outlined in Sequencing_Instructions.docx; additional assistance can be found in the Science Aid Center and Documents & Protocols (under the heading of "ABI 3130xl Genetic Analyzers").
    DNA Templates: Client submits cleaned-&-quantitated DNA templates (see Full-Service DNA Sequencing Instructions.docx), with the Genomics Facility performing the BigDye sequencing reactions and cleanup procedures, followed by sample electrophoresis on the 3130xl. (Note: If the DNA Templates need to be cleaned by the Genomics Facility prior to sequencing, see Physical Submission of Samples).

  • Fragment Analysis options:
    Electrophoresis-Only: Samples must be submitted as completed reactions, including the addition of any necessary size standards.
    Sample Denaturation: Upon request, FA samples will be heated and snap-cooled immediately prior to loading them on the 3130xl.

  • 'Tube' Requirements:
    Sequencing or Fragment Analysis: All samples must be submitted in either strip-tubes (with detachable caps) or 96-well plates.
    DNA template purification: In some cases, users might request that the Genomics Facility purify their DNA templates prior to sequencing. For processing with our EDTA-Ethanol precipitation protocol, samples must be submitted in either strip-tubes (with detachable caps) or 96-well plates. However, for processing with the Zymo DNA Clean & Concentrator-5 Kit, standard 0.5-ml or 1.5-ml tubes are preferred.

  • Data analysis: The following software packages (see descriptions) are installed on our 3130xl computers and may be used upon request by our clients:
      – GeneMapper Software v5
      – SeqScape Software v3
      – Variant Reporter v2
      – Sequencing Analysis v6

  • Related Documents
  • Services for the ABI 3130xl
  • Back to List of Instruments & selected Services

    Agilent Bioanalyzer

    Agilent_Bioanalyzer The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA, RNA, proteins and cells on a single platform, providing high quality digital data. The Genomics Facility currently stocks the DNA High Sensitivity kit; however, other kits can be ordered. The DNA-HS chip provides critical Library QC data (quantitation AND fragment size distribution) for NGS experiments... regardless of which NGS platform is used. For additional information on this platform and available kits, see Bioanalyzer options.

  • Related Documents
  • Services for the Agilent Bioanalyzer
  • Back to List of Instruments & selected Services

    BluePippin (DNA Size Selection for NGS)

    BluePippin instrument The BluePippin.jpg has the capabilities of the Pippin Prep, plus pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination. Gel cassettes for DNA selections are available in 4 agarose concentrations to provide a full range of size selection options from 100bp up to 50kb. Run times range from ~30 minutes (small fragments) to several hours (pulsed-field runs for very large DNA fragments).

    Cassette Kits

  • 10 disposable pre-cast gel cassettes.
  • All necessary standards and reagents included.

  • Gel Cassette Types and Target Ranges
  • 3% agarose, 100-250bp
  • 2% agarose, 100-600bp
  • 1.5% agarose, 250bp – 1.5kb
  • 0.75% agarose, 1-50kb

  • Downstream Technologies
  • miRNA isolation
  • DNA sequencing, RNA-seq, genotyping
  • DNA sequencing, ChIP-seq
  • Mate-pair, single molecule

  • Related Documents
  • Back to List of Instruments & selected Services

    Client PC Workstation

    Client computer station Advance Reservations, made through the Biosci-Booked (Genomics), are required for use of this computational resource (Computer-Workstation.jpg) in the Genomics Facility. The computer has a variety of genomics-related software (see List) with associated User Guides, as well as standard Microsoft Office software. For descriptions of some of the ABI software, please see Data Analysis on the 'Services' page for the ABI 3130xl platform. Suggestions for additional 'genomics' software are welcome.

    The Client PC Workstation is on LSU's network, and remote access to this resource will be granted on a case-by-case basis. Clients must adhere strictly to the schedule in Biosci-Booked (Genomics); otherwise, analyses might be lost when they log in while someone else is already using the computer. When accessing this resource from off-campus, your computer must have the LSU-approved VPN (gp.vpn.lsu.edu) installed and connected. Finally, clients must log on to the computer with their LSU credentials; however, such logins do not count against their allotment of "5 LSU PC registrations".

    Back to List of Instruments & selected Services

    SmartCheck

    SmartCheck [Entry in Progress - 11Aug21] Advance Reservations, made through the Biosci-Booked (Genomics) [in progress], are required for use of this instrument (SmartCheck.jpg) in the Genomics Facility. The SmartCheck provides a fast, practical way to verify that a pipette is dispensing accurately (±5% at 10 µl, 20 µl, 50 µl, 100 µl, 200 µl, 300 µl and 1000 µl). Simply dispense distilled water into the opening and the test volume will be automatically detected. Repeat this three times to obtain a Pass/Fail result.

    Thus, you can both quickly verify your pipette's performance immediately prior to 'volume-critical' experiments and know when you really need to have your pipettes re-calibrated. The SmartCheck can also be used to train (or re-train!) personnel in the proper operation of pipettes.

  • Related Documents
  • Self-Service, SmartCheck [in progress]
  • GF Services, SmartCheck [in progress]
  • Back to List of Instruments & selected Services

    ABI ViiA·7 and QuantStudio·6 (qPCR)

    ABI ViiA7, qPCR ABI QuantStudio-6, qPCR

     

     

     

     

     


    Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of these instruments. A great feature of these two platforms is that, although they have different outside 'shells', they use exactly the same internal components, calibration standards, and software; thus, users can safely swap back-and-forth between the platforms even within the same experiment. In the rare instance in which an assay uses an unusual combination of dyes, the ViiA·7 does offer additional flexibility by virture of its six decoupled excitation and emission filter channels (which allow for additional dye combinations and maximum multiplexing capabilities).

  • Related Documents
  • Self-Service, qPCR platforms
  • Freeware (v1.3) to analyze *.eds files on your PC
    Warning: v1.7 is not compatible with our platforms.

  • Back to List of Instruments & selected Services

    ABI Veriti (standard PCR thermal cycler)

    Veriti Thermal Cycler Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of the ABI Veriti thermal cycler.jpg. This instrument performs standard PCR, including temperature gradients with 6 individualized sub-blocks, and it is protected from brief power outages by an APC backup power supply. Normally, all other standard thermocyclers in the Genomics Facility are reserved solely for use by the Facility or members of the Batzer lab; however, you may request permission to use the other standard thermocyclers if you can plead extenuating circumstances.

  • Self-Service, Veriti thermal cycler

  • Back to List of Instruments & selected Services

    Qubit 4.0

    Qubit_small
    The Qubit-4.0 (jpg) can quantify DNA, RNA, & proteins. In addition, with the Qubit RNA IQ assay, the Qubit 4.0 distinguishes intact from degraded RNA by using two unique dyes: one binds to large, intact RNA; the other binds to small, degraded RNA.

    There are many Qubit assays available from ThermoFisher. Assays require 1-20 ul of sample, resulting in the quantitation ranges shown with each kit. Samples are analyzed using Axygen 0.5-ml tubes (PCR-05-C, thin-wall, clear).

  • RNA IQ assay (integrity & quality)
  • dsDNA HS Assay Kit (0.2-100 ng)
  • dsDNA BR Assay Kit (2-1000 ng)
  • ssDNA Assay Kit (1-200 ng)
  • RNA HS Assay Kit (5-100 ng)
  • RNA BR Assay Kit (20–1,000 ng)
  • RNA XR Assay Kit (0.02-8 µg)
  • microRNA Assay Kit (1-1000 ng)
  • Protein Assay Kit (0.25-5 µg)
  • If using your own kits, this instrument is available for use directly by you through the Biosci-Booked (Genomics) instrument reservation system; otherwise, samples are processed by the Genomics Facility.

  • Related Documents
  • Services using Qubit 4.0

  • Back to List of Instruments & selected Services

    Diagenode Bioruptor NGS

    Diagenode_Bioruptor_NGS Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of this instrument. Further, prior to each use of this 'self-service' instrument, clients must ask the Genomics Facility staff to prepare the system for operation.

    To retain the integrity of DNA, Diagenode’s Bioruptor® NGS uses a gentle method of sonication and a chilled water bath to generate indirect sonication waves. As a result, the Bioruptor® produces better and more consistent results than are achieved with harsher sonication methods. Up to 12 closed tubes can be sonicated in parallel and the continuous rotation of tubes allows even distribution of the energy for efficient sonication.

  • Related Documents
  • Self-Service, Bioruptor NGS

  • Back to List of Instruments & selected Services

    SpeedVac SPD1010

    SpeedVac SPD1010 Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of this instrument. This ThermoFisher instrument (SPD1010 SpeedVac.jpg) efficiently processes large batches of DNA or RNA samples. Currently, we have rotors for microtubes (1.5-ml, or 0.2-ml with inserts) and for 96-well plates. Typical applications include concentrating DNA extractions and removing low concentrations of non-agressive organic solvents (methanol, ethanol, acetonitrile) from samples. Most samples can be processed by simply pressing the "Start" button; however, users may also adjust settings for vacuum pressure, temperature, and run time.

  • Related Documents
  • Self-Service, SpeedVac SPD1010

  • Back to List of Instruments & selected Services

    Typhoon 8600 Variable Mode Imager

    Typhoon Variable Mode Imager Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of this instrument. The Typhoon™ 8600 Variable Mode Imager is primarily used for storage phosphor experiments, but it is also capable of fluorescence detection of gels and blots. The Typhoon can scan storage phosphor screens (mounted or unmounted), gels and blots (≤ 35 × 43 cm). Images can be manipulated with ImageQuant™ Image Analysis Software; alternatively, users can change the file extension (i.e., *.gel) to "*.tif" and import the image into other software such as Adobe Photoshop.

  • Related Documents
  • Self-Service, Typhoon

  • Back to List of Instruments & selected Services

    E-gel (DNA Size-selection)

    E-gel_small The E-Gel® SizeSelect™ Gels are a convenient method for the purification of DNA libraries for Next Generation Sequencing applications. DNA is size-selected in three easy steps: Load; Run; and, Retrieve. The E-Gel® SizeSelect gel features two rows of wells. To extract a DNA region of interest without conventional gel purification, simply load samples into the top row and electrophorese until the band (or smear of the desired size range) moves into the bottom row of wells. Then, simply use a pipette to remove your purified DNA (for smears, fragment sizes will have an ~50-bp range).

    Use of the E-gel can be either self-service (with permission) or staff-run. The Genomics Facility usually stocks the 2% E-Gel® SizeSelect™ Gels; however, other E-gel product options include:

    • E-Gel EX agarose gels
    • E-Gel NGS agarose gels
    • E-Gel Clonewell agarose gels
    • E-Gel 48/96 sample agarose gels

  • Related Documents
  • Back to List of Instruments & selected Services

    Eppendorf Centrifuge 5810R

    Eppendorf Centrifuge 5810R At this time, we do not require reservations for this instrument. The Eppendorf 5810R Centrifuge is a refrigerated unit (-9 to 40°C), capable of handling both large tubes and microtiter plates. Maximum speed is ~2800 rcf, and a soft acceleration-deceleration option is available. The Genomics Facility has the A-4-62 rotor, which sports two types of adaptors: (A) microtiter plates or 96-well PCR plates; and, (B) 15-ml or 50-ml tubes (with correct inserts). Other rotors could be obtained if there is sufficient interest.

  • Related Documents
  • Self-Service, Eppendorf Centrifuge 5810R

  • Back to List of Instruments & selected Services

    Victor·3 Multilabel Counter

    MultiLable Counter This instrument is owned by Dr. Stephen Hand; thus, prior to your first use of the Victor·3, you must contact members of his lab (Rm. A627 & A629) for authorization and training. The Victor·3 Multilabel Counter (model 1420-011) includes fluorescence intensity (both top and bottom reading), luminescence, and absorbance (VIS) technologies as well as scanning, shaking and kinetics features. The instrument accepts all types of microtitration plates (from 1 to 1536 wells), as well as Petri dishes, slides, filters and Terasaki plates. Not all features described in the associated Victor·3 documents are applicable to this model. To learn how to operate the Victor·3, you can burn a CD of the software (available from the Genomics Facility)and install it in “Demo Mode” on your personal computer.

  • Related Documents
  • Self-Service, Victor·3 Plate Reader

  • Back to List of Instruments & selected Services

    DNA Column Purification & Size Selection

    Zymo Research The Genomics Facility stocks DNA columns by Zymo Research. Predominantly, we use two particular kits for 'column' Services, but Zymo kits designed for other applications can be ordered. For product specifications of all available kits, visit either the distributor's website (Genesee Scientific) or the manufacturer's website (Zymo Research).

    DNA Clean & Concentrator-5 Kit — (Cat #: 11-303):

  • Clean and concentrate up to 5 µg DNA in as little as 6-µl elution with 0-µl wash residue carryover.
  • Eluted DNA is well suited for use in applications such as PCR, DNA sequencing, DNA ligation, endonuclease digestion, RNA transcription, radiolabeling, and arrays.
  • DNA Size Limits: 50 bp to 23 kb.

  • Select-A-Size DNA Clean & Concentrator Kit — (Cat #D4080):
  • Size-Select DNA with retention points of ≥50-bp, ≥100-bp, ≥150-bp, ≥200-bp, ≥300-bp (other cutoffs between 50-300 bp can be attempted by titration).
  • Clean and concentrate up to 3 µg DNA in as little as 10-µl elution with 0-µl wash residue carryover.
  • Eluted DNA is of high quality and well suited for NGS, ligations, restriction endonuclease digestions, and library preparation cleanup.
  • DNA Size Limits: 50 bp to 23 kb.

  • Other Zymo Kits (currently carried by Genomics Facility):
  • Quick-gDNA MicroPrep (Cat. #D3020)
  • Quick-DNA Universal Kit (Cat. #D4068)
  • ZR Genomic DNA-Tissue MicroPrep (Cat. #D3040)
  • Back to List of Instruments & selected Services