Overview: LSU Genomics Core
GC 2021 Survey – Our Past & Future?
Since 2001, under the auspices of Dr. Mark Batzer, the LSU Genomics Core 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 Core 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 Core's performance and future client needs.
View survey results at GC 2021 Survey – Our Past & Future?
Visual Tour of Core
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.
Request Instrument Acquisition
Are you interested in having a new platform available "in your backyard"... the LSU Genomics Core? If so, please email the Genomics Core, outlining why you would like to see that platform physically available here. Some helpful issues to include are:
Who has access to the website?
Open access is provided to protocols, FAQs, links, and most documents on our website.
The "Science Aid Center" provides extensive guidance, especially for DNA Sanger-Sequencing.
Experimental protocols, documents, software, and
informational sites are available through "Links". When practical, we will even respond to email requests by non-affiliated researchers for assistance with instruments or protocols.
Who has access to the Core's services?
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 Core staff — see listings below. People lacking a Genomics Core 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 Core?
New Login IDs can be obtained through Request a Login ID. However, if the lab's PI has never used the Genomics Core before, prior to issuance of the Login ID, you (and your PI) must first
meet with Scott to
discuss the Core’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.
regarding processing and completion of requests.
You must Request a Login ID if you:
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.
Instruments, Services, & Links
Common Room (A624, Life Science Annex)
Next door to the Genomics Core (A628), there is a Common Room (A624) which houses additional equipment maintained by the Department of Biological Sciences. Please note that the Genomics Core has no information regarding Common Room equipment... aside from the following:
- LSA-624 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).
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:
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.
— 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 Core 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 Core prior to sequencing, see Physical Submission of Samples).
— Electrophoresis-Only: Samples must be submitted as completed reactions, including the addition of any necessary size standards.
— Partially prepared samples: Clients may submit raw PCR products (i.e., FA products) and request that the Core dilute/aliquot the FA products and add the size-standard to all wells... prior to performing electrophoresis on the ABI 3130xl.
— Sample Denaturation: Upon request, FA samples will be heated and snap-cooled immediately prior to loading them on the 3130xl.
— 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 Core 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.
– GeneMapper Software v5
– SeqScape Software v3
– Variant Reporter v2
– Sequencing Analysis v6
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 Core
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
BluePippin (DNA Size Selection for NGS)
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).
Gel Cassette Types and Target Ranges
Client PC Workstation
Advance Reservations, made through the Biosci-Booked (Genomics), are required for use of this computational resource (Computer-Workstation.jpg) in the Genomics Core. 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".
[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 Core. 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.
Advance Reservations, made through the Biosci-Booked (Genomics) instrument reservation system, are required for use of this instrument.
– Warning: v1.7 is
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 Core are reserved solely for use by the Core or members of the Batzer lab; however, you may request permission to use the other standard thermocyclers if you can plead extenuating circumstances.
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).
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 Core.
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 Core 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.
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.
Typhoon 8600 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.
E-gel (DNA Size-selection)
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 Core 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
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 Core 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.
Victor·3 Multilabel 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 Core)and install it in “Demo Mode” on your personal computer.
DNA Column Purification & Size Selection
The Genomics Core 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):
Select-A-Size DNA Clean & Concentrator Kit — (Cat #D4080):
Other Zymo Kits (currently carried by Genomics Core):