Training options & Documents
Training Requests & Suggestions
Please submit training requests and topic suggestions through the Core's email address (Genomics Core). For training, please indicate how many people from your lab would like to attend and provide some tentative dates/times you would be available. For topic suggestions, please include your rationale for the topic suggestion and your best guess as to how popular training on that topic would be to others at LSU.
Links: Software, qPCR, Technical info, & Training
Documents: Equipment & Protocols
Self-paced online Training?
There are many training opportunities through self-paced online webinars. For instance, some of the course offerings at ThermoFisher Instrument and Applications Training are free, recorded sessions. In particular, you should consider viewing materials at CE Sequencing & Fragment Analysis and at Real-Time PCR. As of February 2019, the following free online sessions were available:
– CE Sanger Analysis Modules on Thermo Fisher (TF) Cloud.
– Genotyping Data Analysis Using GT App on TF Connect.
– Introduction to High-Resolution Melt (HRM).
– High Resolution Melt Analysis Using HRM App on TF Connect.
– Gene Expression Data Analysis Using RQ App on TF Connect.
– Real-Time PCR Video Training Series (22-part series covering qPCR fundamentals, including an in-depth look at gene expression).
– Set up experiment using Design & Analysis App on TF Cloud.
– Standard Curve Analysis Using SC App on TF Connect.
– Presence Absence Test Analysis using PA App on TF Connect.
– Gene Expression Data Analysis Using Expression Suite Software.
– Module 2: Real-Time PCR Assay Design Choices.
– Module 3: Normalization.
– Module 4: Multiplexing.
– Module 5: Real-Time PCR Reagent Choices.
– Module 6: Theory of Real-Time Quantitative PCR Analysis.
The Genomics Core can help labs with training personnel in various molecular biology techniques and software. If your training needs are not listed here, please make a suggestion as described above.
- Project Development
- Sequence Scanner software
- qPCR software (ViiA·7 & QuantStudio·6)
- DNA Quantitation Methods
- DNA Size-Selection Methods
- PCR Basics
- Restriction Digest Basics
- Online GC Submissions & Biosci-Booked (Genomics)
The Genomics Core periodically arranges for vendors to provide local training opportunities... either on its own or at the behest of clients. Training sessions can be virtual or in-person. If there is sufficient interest, vendors are sometimes even willing to put on a workshop rather than just presentations. Listed below are some of the training opportunities available through ThermoFisher.
- Fundamentals of Real-Time PCR
- Assay Design Choices
- Reagent Choices
- Theory of Analysis
- Protein Thermal Shift
- Special Purpose Assays
- GeneMapper software
- Minor Variant Finder software
- SeqScape software
- Cloud Analysis
Project DevelopmentIt can be daunting to flesh out the "path" for achieving the aims of a project, especially for beginning graduate students. For instance, there are often many potential molecular biology approaches, which vary in the level of effort, time and funding required as well as the information they can deliver. Feel free to use the Genomics Core as a sounding board to help you identify what approaches are most suitable for your project's needs in the context of your available resources.
Sanger-SequencingTopics may include the following:
Sequence Scanner softwareMost researchers skip the critical step of QC'ing their Sanger-Sequencing data, often simply trusting the sequence text file without even examining the electrophoretic trace; this practice can lead to erroneous conclusions and lost time/money. Discover how to use Sequence Scanner (freeware!) to properly and quickly QC Sanger-Sequencing data. Of particular importance, this software enables users to examine the raw data behind the pretty electropherogram... and detect when that pretty data might not be especially reliable. For an example, please visit Why Analyze Data with Sequence Scanner? in our Science Aid Center.
qPCR software (QuantStudio·6)Mechanics of starting instrument & computer, setting up the run, creating & saving templates for future runs, when to use Melt Curves, performing basic QC using on-instrument software, & exporting data.
DNA Quantitation MethodsPros & cons of quantifying DNA using Bioanalyzer chips, Gel electrophoresis, Nanodrop, Qubit, or qPCR. Primary emphasis is on applications to NGS work with respect to library construction.
DNA Size-Selection MethodsPros & cons of size-selecting DNA using the Bluepippin, Columns, E-gels, or standard agarose gel electrophoresis. Primary emphasis is on applications to NGS work with respect to library construction.
PCR BasicsProper technique for setting up reactions (e.g., methods to prevent pipetting errors), typical cycling parameters (including what's really needed vs. historically used), and gel electrophoresis of the finished reactions. Additional topics could include best practices for DNA/Primer Resuspension, PCR Cycling Parameters, and PCR/qPCR Plastics Considerations.
Restriction Digest BasicsBasics of single-digests and double-digests, using the NEB Catalog & Technical Reference as a guide.
Online GC Submissions & Biosci-Booked (Genomics)Covers various topics, such as the difference between a 'Standard' & a 'Biosci-Booked (Genomics)' Login ID; the mechanics of applying for a Login ID & submitting or amending online requests (including filling out the Excel templates); options for DNA Sanger-Sequencing (including electrophoresis-only vs. full-service); & available services and supplies.
Fundamentals of Real-Time PCRModule 1 (ThermoFisher): Overview of real-time PCR instrument choices and how real-time PCR differs from endpoint PCR. How can you use real-time PCR in your research? What is the difference between TaqMan® chemistry and SYBR® Green chemistry?
qPCR Assay Design ChoicesModule 2 (ThermoFisher): What should you consider when planning your gene expression assays? What is the impact of multitranscript assays and assay specificity? How do you design custom assays?
qPCR NormalizationModule 3 (ThermoFisher): What is normalization and why is it important? What are the types of normalizers and what are their functions? How does multigene normalization work?
qPCR MultiplexingModule 4 (ThermoFisher): What is multiplexing, and when and how do you use it?
qPCR Reagent ChoicesModule 5 (ThermoFisher): Covers aspects of real-time PCR chemistries, such as hot start, UNG, passive reference dye, Fast vs. standard master mixes and reverse transcription.
qPCR Theory of AnalysisModule 6 (ThermoFisher): Perform dynamic range testing with standard curves, quantify your data using the ΔΔCt method, and gain a better understanding of absolute vs. relative quantification.
Protein Thermal ShiftProtein Thermal Shift (PTS) is a technique to detect changes in protein stability using a real-time PCR instrument. PTS is used to identify optimal buffers for protein storage or crystallization, and to measure the impact of molecules interacting with the protein, such as ligands, nucleic acids or other proteins.
3130xl Special Purpose AssaysSome potential topics are listed below; please visit Sequencing Applications for some additional possibities.
3130xl GeneMapper software
Provides DNA sizing and quality allele calls for microsatellite and SNP genotyping analysis. A typical training sessionwould include Fragment Analysis Fundamentals, covering experimental design, optimizing PCR, optimizing capillary electrophoresis, selecting the appropriate size standard, and troubleshooting analysis issues. For additional potential topics, please see the chapters in the DNA Fragment Analysis by Capillary Electrophoresis User Guide.
The full version of GeneMapper is available at no charge on the Client Computer workstation in the Genomics Core, and the freeware version, PeakScanner, can be accessed at Thermo Fisher Cloud. For a full list of TF Cloud apps, see Connect Data Analysis Apps.
3130xl Minor Variant Finder SoftwareDesigned for accurate detection and reporting of minor variants in Sanger Sequencing traces; available at no charge on the Client Computer workstation in the Genomics Core. Minor Variant Finder removes background noise by comparing test samples with a normal control sample, producing a list of candidate variants and cleaned electropherograms for users to review and confirm candidate variants on both forward and reverse strands. Within the region of strand overlap for test and control .ab1 files, the software can identify 5% minor variants with a sensitivity ≥95% & specificity ≥99%.
3130xl SeqScape SoftwareResequencing package designed for mutation detection & analysis, SNP discovery and validation, pathogen sub-typing, allele identification, and sequence confirmation. SeqScape is available at no charge on the Client Computer workstation in the Genomics Core.
3130xl Cloud analysisThermoFisher: Applied Biosystems Sanger Analysis Modules are cloud-based secondary data analysis tools that bring together multiple data sets in one place, making it easier to view, store, and analyze Sanger sequencing data. These free modules can be accessed at Connect Data Analysis Apps.
Ion NGS Microbial ApplicationsTargeted or whole genome sequencing (WGS) approaches can be employed effectively on the Ion S5 for Microbial Sequencing.
Ion NGS RNA ApplicationsThermoFisher: The Total RNA-Seq Kit v2 is designed as a complete solution with a common workflow, combining optimized reagents and protocols for discovery of small RNAs and isoforms, coding RNA, noncoding RNA, and alternative splice variants. Strand information is preserved, enabling more accurate determination of the structure & expression level of transcripts, and aiding in the discovery of novel transcription regions from both positive & negative genomic strands.
Ion NGS Targeted ApplicationsThermoFisher: Ion AmpliSeq technology delivers a highly muliplexed, PCR-based workflow allowing researchers to:
– sequence low quality samples with minimal input DNA or RNA;
– target one to hundreds of genes in a single run; and,
– go from sample to results in as little as 24 hours.