Division of Biotechnology and Molecular Medicine (BIOMMED)

BioMMED is comprised of three service-oriented, centralized core laboratories:

GeneLab: Managed by Division of Biotechnology and Molecular Medicine at LSU School of Veterinary Medicine

Integrated Molecular Biology, Next-Generation Sequencing & Bioinformatics Core

1. Mission & Scope
GeneLab is a full-service core that supports investigators across LSU and beyond with state-of-the-art molecular biology, next-generation sequencing (NGS), and bioinformatics resources. We offer end-to-end project support—from experimental design through data analysis and interpretation—while fostering training and collaboration within the research community.

2. Instrumentation & Core Facilities
Platform | Key Instruments & Upgrades
--------|---------------------------
Sanger Sequencing | 2 × Applied Biosystems 3130xl Genetic Analyzers
Next-Generation Sequencing | NEW Illumina NextSeq 2000, Illumina NextSeq 550, Illumina MiSeq, 10x Genomics Chromium Controller (single-cell & spatial)
Quantification & QC | Agilent 2100 Bioanalyzer, NEW Agilent 4200 TapeStation, AATI Fragment Analyzer
PCR & q/dPCR | Applied Biosystems QuantStudio 12K Flex, 2× ABI QuantStudio 6Pro, Bio-Rad QX200 Droplet Digital PCR
Flow cytometry & Imaging | BD Accuri C6, Olympus Vivaview Live, Zeiss Observer Z1, Leica 4000B Fluorescent Scope, Leica DM-IRB Fluorescent Scope, Olympus IX71 Fluorescent Scope, Olympus MVX Fluorescent Dissecting Scope, Xenogen IVIS-50 In Vivo Imaging
Automation & Robotics | Eppendorf epMotion 5075 Liquid Handler, NEW ThermoFisher KingFisher Flex
Computational Resources | High-performance workstations with CLC Genomics Workbench, Illumina DRAGEN, Galaxy, and custom pipelines

3. Core Services
Sequencing & Genomics:
- Sanger sequencing, primer walking, dye-terminator clean-up
- NGS library prep: genomic DNA, RNA-seq(single cell, small RNA, amplicon, ATAC-seq, ChIP-seq)
- 10x Genomics single-cell 3′/5′, multi-ome (ATAC + GEX) & immune profiling
- Long-read library preparation (PacBio/Oxford Nanopore partner labs)
- Digital PCR & absolute quantification
- Custom target capture & panel sequencing
- Complete data delivery (FASTQ, BAM/CRAM, VCF) and interactive reports

Molecular & Cellular Biology:
- Gene cloning, mutagenesis, plasmid construction
- CRISPR guideRNA design & validation

Imaging & Flow cytometry:
- Confocal, live-cell, and whole-animal imaging
- Automated cell counting and viability
- Flow cytometry analysis & sorting (via FACS Core collaboration)

Bioinformatics & Data Science:
- Project design consultations (no-cost)
- End-to-end analysis pipelines for bulk & single-cell RNA-seq, ATAC-seq, metagenomics, ML-driven multi-omics integration
- Custom scripts, visualization, and figure generation
- Training modules: Introduction to Bioinformatics, Bytes & Molecules, Biomedical Data Analysis in R/Python, Infectious-disease omics, and more

4. Training & Workshops
GeneLab hosts hands-on workshops, webinars, and semester-long courses covering wet-lab techniques, NGS workflows, and advanced bioinformatics. Many modules are cross-listed on the LBRN Training Platform for on-demand access.

5. GeneLab Supply Center
Through our on-site Supply Center (Room 3212, SVM), researchers can purchase Life Technologies/Thermo Fisher reagents and consumables at discounted prices with free shipping to GeneLab. Orders can be:
- Picked up at the lab (no fee)
- Delivered anywhere on campus for a flat $5 internal-transaction charge

6. How to Engage
1. Request Services via iLab (https://lsu.ilab.agilent.com/) (project initiation, quotes, scheduling).
2. Consultation: Email or visit us for experimental design assistance—complimentary for LSU-affiliated investigators.
3. Support Letters: Available for grant submissions upon request.

For pricing, detailed workflows, or to schedule a tour of the new NextSeq 2000 platform,

Contact

Robert Ellis, Lab Coordinator

rellis10@lsu.edu

For registration or login click here LOGIN TO ILAB

GeneLab is committed to delivering high-quality data, rapid turnaround, and comprehensive support to accelerate your research.

Sequencing

GeneLab launched its NGS and bioinformatics support services initially in January 2013 under a developmental stage and officially in July 1, 2013 to assist researchers at all stages of research, from experimental design to data generation and analysis of NGS data. The close alignment of GeneLab’s NGS capabilities and bionformatics provides an integrated approach to experimental design, NGS experimentation and fast analysis of the project data, while creating a unique forum for cross-training biologists and computer scientists in NGS methodologies and bionformatics. GeneLab is equipped with a suite of Life Technologies NGS equipment including:

Ion Torrent PGM
Quant Studio Flex (digital PCR validation).
Ion Proton.

Both the Ion Torrent PGM and Ion Proton have web-based Ion Torrent server with which produced sequencing data access and integrated data analysis pipelines are available. GeneLab-Bioinformatics Unit operates two high-end servers. The visualization server supports windows as well as linux environments, providing memory intensive visualization tasks and tools working on the two OS environments. A different, high-end server is equipped with large memory (128 GB) and large number of cores (32), is networked to the Ion PGM and Ion Proton platforms for dealing with analyses requiring large memory footprint and multi-core performance applications. These two high-end servers are backed with network-connected expandable NAS storage system, resulting in total storage space of 90 Terabytes at this time, which are directly connected to the servers and software tools integrated to the sequencing platforms. NextGen sequencing and bioinformatics analysis services can be scheduled via iLab.

GeneLab, also offers capillary DNA sequencing services for a wide range of templates including plasmid DNA, PCR fragments, cosmid DNA, bacterial genomic DNA, BAC and cDNA. Clients who have large inserts can take advantage of our primer walking service (see below) to get information on their entire clone.

We perform standard sequencing reactions using Applied BioSystems BigDye Terminator version 3.1 or version 1.1 (depending on template) chemistries. Reactions are run on either of our two ABI Prism 3130, a four capillary based DNA sequences.

Sample Submission Requirements

No DNA/Primer premixing
No special sample tubes
Quantitate your DNA
The #1 reason sequencing reactions fail is that researchers do not quantitate their samples. Please quantitate your DNA by OD, agarose gel, or the NanoDrop -1000 available in GeneLab.
Send DNA and Primers separately
The main benefits of NOT premixing include Additional reactions may be performed on a particular DNA template without having to provide more sample AND GeneLab can troubleshoot projects by adjusting DNA-primer concentrations...
You will be redirected to the order page.
You can place the order now, following the ordering instructions beginning with step 2.

Send template sample(s) and primer(s) to GeneLab. Please see Template Concentrations below for appropriate amounts of template to submit. All samples must be submitted through iLab.

Login to your iLab:

*We typically request more DNA than we need to have a sufficient quantity for any repeats that may need to be performed. A general rule of thumb for PCR products is to submit 2 ng/µl per 100 bp.

GeneLab provides standard sequencing primers (see below) at no charge. If using your own primers, please see Primer Concentrations (above) and include with template shipment.
Universal primers provided at no extra cost (see table below)

GeneLab uses the Sequencing Cycle Run Parameters below on a PTC 200 Thermalcycler from MJ Research:

40 cycles of:

96° for 10 seconds
50° for 5 seconds
60° for 4 minutes

In general, a single run should result in at least 500-700 bases of high-quality sequence information. Turn-around time is generally 1-2 days from receipt of the template and primers, depending on the workload at the facility. Investigators will receive the results as a sequence file and a color electropherogram for each template/primer combination. Files will be sent by e-mail to all investigators. For more information regarding automated DNA sequencing, see Applied Biosystems' Sequencing Chemistry Guide for Automated Sequencing. To visualize and print the chromatogram traces, please point your favorite web browser to the following URLs to obtain free software for Windows based computers

Sequence Scanner v1.0

Chromas

CodonCode Aligner (for academic users only)

Sequencing by primer walking

This is an effective strategy for the efficient sequence determination of cloned DNA fragments which range in size from 0.5-8 kb. Initially sequence data is obtained using a standard primer which hybridizes to the vector sequence upstream of the insert DNA. Based on this initial data, GeneLab will design a custom oligonucleotide, have it synthesized, and use it to prime a second sequencing reaction. The data obtained from the second reaction should overlap with the initial data and extend the sequence further downstream of the initial primer. By repeated cycles of custom oligonucleotide synthesis and DNA sequencing, the cloned insert is sequenced completely in one direction. Pricing is dependent upon size of the project.

For DNA sequencing rates, please see the " GeneLab Rates page "

For more info contact:

Robert Ellis
Lab Coordinator
Phone: 225.578.9708
genelab@lsu.edu

Scheduling and Ordering through iLAB

Welcome to iLab Solutions

iLab Solutions provides web-based services designed to streamline research operations. GENELAB uses iLab’s Core Management Platform to support reservations, service requests (including training and purchasing), equipment tracking, project management automated billing, and reporting

Recommended Browser*

Firefox is preferred when using the iLab application. Safari or Chrome are also acceptable browser options. At present Internet Explorer does not behave consistently for some iLab functionality depending on the version. iLab is addressing this.

iLab Account

To register for a new account:

Contact:

Robert Ellis
Core Manager
Office: SVM 3212B
E-mail: rellis10@lsu.edu
Phone: (225) 578-9708

Login to your existing account:

iLab Help Resources:

iLab Chat Tool - click on the chat link or popup Help

Email your questions to: support@ilabsolutions.com

Call iLab Support at :617.297.2805 (Eastern time business hours)

iLab support page: Support

iLab FAQ page: FAQ's

GeneLab Rates:

GeneLab Proposed Schedule of Fees for NGS/ Bioinformatics:

NGS Bioinformatics and Biostatistics Support

Bioinformatics Support Overview

GeneLab offers Next Generation Sequencing (NGS) data analytics with a broad range of programs such as tools of Ion Torrent suite, tools from Life technologies, community-wide recognized bioinformatics tools, and commercial desktop tools for NGS sequencing and downstream analysis. Our data analytics tasks are facilitated by bioinformatics infrastructure that comprises backend computing resources including high-end servers, network storage and HPCs, software tools, and various in-house services provided by DARE-based science gateways and a local blast infrastructure. The right schematic illustrates our bioinformatics infrastructure supporting our service that utilizes available tools.

Data analyses for NGS include

RNA-Seq data analysis using our pipelines
RNA-Seq data analysis using commercial packages including Partek (workflow, genome suite, and pathway)
Various analyses such as alignment, variant calling, de novo assembly, and many from Ion Torrent plug-ins
Analysis using standalone tools for alignment, de novo assembly, RNA-Seq., ChIP-Seq., and others

Bioinformatics Support Team:

Joohyun Kim, PhD
jhkim@cct.lsu.edu

Nayong Kim, PhD
nykim@cct.lsu.edu

Shayan Shams
Graduate Assistant
sshams2@cct.lsu.edu

QPCR/ Digital PCR

Combining flexible throughput capabilities with a streamlined workflow, the QuantStudio™ 12K Flex system takes you from targeted discovery through confirmation and screening, all on a single platform.

Five interchangeable blocks: (OpenArray® plate, TaqMan® Array Card, 384-well, Fast 96-well, and 96-well blocks).
Provides a seamless switch from qPCR to digital PCR using QuantStudio™ Digital PCR kits and DigitalSuite Software with the QuantStudio™ OpenArray® block.
Maximum multiplexing & chemistry options with Enhanced OptiFlex® System.
Comprehensive software analysis tools for gene expression, genotyping, and digital PCR.

GeneLab also maintains four Real-Time PCR instruments: one Roche LightCycler 480 II, two ABI 7900 Sequence Detection Systems. All are in room 3212 of the LSU School of Veterinary Medicine.

The Roche LightCycler 480 Real-Time PCR System is a fully integrated multiwall-plate based real-time PCR platform for highly accurate qualitative and quantitative detection of nucleic acids. Building on the benefits of Roche's capillary-based LightCycler Systems, it goes one step further in offering enhanced throughput, compatibility with automation equipment and maximum flexibility regarding hard- and software. Providing novel ways to combine speed and accuracy without compromises, the LightCycler 480 Real-Time PCR System meets the needs of a broad range of applications in research fields such as gene expression studies, discovery and analysis of genetic variation or array data validation.

Achieve faster and easier assay setup with the new sample editor.
Set up experiments with just a few clicks, with options to refine your results later.
Benefit from enhanced templates and macros for all applications.
Perform genotyping based on endpoint analysis or melting curves.
Use basic and advanced methods for gene expression and genotyping.

The Applied Biosystems 7900HT Fast Real-Time PCR System is the only real-time quantitative PCR system that combines 384-well plate compatibility with fully automated robotic loading and now also offers optional Fast real-time PCR capability.

Fast PCR option reduces run time to about 35 minutes in a standard 96-well format, or about 55 minutes in a 384-well plate.
Continuous wavelength detection from 500-660 nm allows the use of multiple fluorophores in a single reaction.
Measure gene expression levels, detect and quantitate pathogens, perform allelic discrimination (SNP genotyping) assays as well as score the presence of gene sequences.
96- or 384-well plate compatibility (including the TaqMan Low Density Array).
Optional Enterprise edition software provides data analysis tools that support 21 CFR Part 11 guidelines providing data integrity and security.
Hands-free plate-loading and unloading provides true walkaway automation allowing you to increase your lab's productivity.
Proven assay development guidelines save time and money.

Applied Biosystems has developed two types of chemistries to detect PCR products using Sequence Detection Systems (SDS) instruments:

TaqMan chemistry (also known as fluorogenic 5' nuclease chemistry)
SYBR Green, I dye chemistry

FACS and Automated Cell Counting

Viral Vectors Laboratory

The VVL provides custom baculovirus, adenovirus, vaccinia virus, herpes, and other recombinant virus construction for heterologous gene expression, and vaccine and gene therapy studies. For the production of proteins in eukaryotic cells the laboratory uses recombinant baculoviruses-based expression in insect cell cultures.

The VVL is currently supported by a Louisiana Governor's Biotechnology Initiative Program Grant as a support facility for the construction of recombinant adenoviruses and herpes simplex viruses for cancer therapy. In addition, VVL is funded by NIH for the generation of vesicular stomatitis viruses as vaccine vectors for West Nile virus and simian retroviruses in collaboration with the Tulane National Primate Research Center in Covington, Louisiana.

VVL provides technological and scale-up support services via direct contractual arrangements. For further information, contact Dr. Vladimir Chouljenko.

Vladimir Chouljenko

PhD

Associate Professor (Research)

Department of Pathobiological Sciences

DR. CHOULJENKO'S FACULTY PAGE

Protein and Antibody Production and Purification Laboratory

This laboratory concentrates on the production and purification of proteins and antibodies under contractual arrangements with clients. The laboratory produces monospecific antibodies in rabbits and mice using conventional immunization methodologies using purified protein immunogens as well as genetic immunization methods. Antibodies are concentrated and purified using standard methodologies.

The laboratory provides service support on the use of chromatographic methods for the purification of proteins from bacterial or eukaryotic expression systems. One example of a purification procedure involves the purification of histidine-tagged proteins produced in bacteria and insect cells. Purification by FPLC is done using immobilized metal ion adsorption chromatography (IMAC). Additional chromatographic methodologies that can be applied include Ion Exchange chromatography (IEC) and reverse-phase chromatography.

The laboratory has a fully automated chromatographic system AKTAExplorer FPLC system (Amersham/Pharmacia). The entire system is refrigerated and computer controlled using Unicorn software v3.10. HPLC equipment are available for further protein purification in collaboration with the Analytical Chemistry Laboratory of the department of Comparative Medical Sciences at the LSU School of Veterinary Medicine.

Gus Kousoulas

Konstantin"Gus"Kousoulas

PhD

Professor and Head of Department

Department of Pathobiological Sciences

DR. KOUSOULAS'S FACULTY PAGE

Seetharama Jois

SeetharamaJois

Professor

Department of Pathobiological Sciences

Dr. Jois's Faculty Page

Harikrishnan Mohan

PhD

Department of Pathobiological Sciences

email harikrishnan

Welcome to the Division of Biotechnology and Molecular Medicine (BioMMED) at the LSU School of Veterinary Medicine. We are engaged in innovative research to determine the molecular basis of various diseases, as well as to develop novel therapeutics for the treatment of cancer and infectious diseases. BioMMED is a multidisciplinary research, support and development unit that provides centralized access to state-of-the-art equipment and advanced training in molecular and cell biology.

In addition, BioMMED oversees two NIH:NCRR funded research cores: INBRE-funded The Molecular and Cell Biology Core. The functions of these core laboratories are integrated within BioMMED and the Louisiana State University School of Veterinary Medicine facilities and consist of state-of-the-art equipment and support services that are jointly staffed by BioMMED and TNPRC faculty and personnel.

Affiliations

The Louisiana Biomedical Research Network (LBRN) was established in September 2001 with Biomedical Research Infrastructure Networks (BRIN) funding by the National Institutes of Health (NIH), through the National Center for Research Resources (NCRR) and is committed to raising the research competitiveness of Louisiana researchers. IDeA Networks of Biomedical Research Excellence (INBRE) is the second phase of the BRIN Program.