The Genomics, Biostatistics, and Bioinformatics Core at the Tulane Center for Aging provides the following services:
Other equipment available for use:
The core can also help project investigators with:
Investigators can discuss applications and obtain information about the time-frame for services.
Next-generation sequencing (NGS) is a technology for high throughput and high depth sequencing. There are several applications involved: whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome analysis (RNA-Seq or AmpliSeq) and others.
The Ion S5 XL (Fig. 1) next-generation sequencing system, funded by COBRE project, utilizes semiconductor technology based on direct real-time measurements of hydrogen ions (protons) liberated as a result of phosphodiester bond formation during DNA replication.
Fig. 1. Ion S5 XL system
Recently paired with Ion S5 XL, the Ion Chef (Fig. 2) and AB Library Builder (Fig. 3) significantly simplify the next-generation sequencing workflow with automating library preparation, template generation, and chip loading. This modification increased the volume of our experiments (RNA-Seq, AmpliSeq, miRNA-Seq and whole-exome sequencing).
RNA - Seq
RNA - Seq
miRNA - Seq
130 - 160X
60 - 75X
Depends on source
Data from exome sequencing are generated in BAM format. Data from RNA-Seq are generated in FASTQ format. NGS files are saved on an external drive and provided by the core to investigators. Other results will be provided as Excel or pdf files or other readily accessible formats and sent via e-mail to investigators with source files available on request.
The Applied Biosystems 3130xl Genetic Analyzer (Fig. 4) is a 16-capillary electrophoresis instrument for Sanger sequencing with read lengths up to 900 bps. This system is useful for a wide variety of sequencing applications: SNP validation, SNP screening, mutational profiling, cell line authentication with the AmpFLSTR Identifiler Plus PCR Kit, etc.
Fig. 4. 3130xl Genetic Analyzer
Misidentification and cross-contamination of cell lines is a recurrent problem in life sciences research. In response, various scientific journals and funding agencies are enforcing strict usage of well-identified cell lines for research purposes and that cell line authentication must be performed prior to grant approval and/or publication. We offer comprehensive Human Cell Line Authentication Services using Short Tandem Repeat Profiling (STR) technology with AmpFLSTR Identifiler Plus PCR Kit (Life Technologies). This kit uses 16 markers in the human genome (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, Amelogenin, D5S818, and FGA) to ensure the correct identity of your cells, avoiding the risk of misidentified or contaminated cell lines in your research.
The Agilent 2100 Bioanalyzer (Fig. 5) provides highly reproducible on-chip electrophoresis that allows sizing, quantitation and quality control of DNA and RNA. It is used extensively in the NGS workflow for quality control and provides quality determination of RNA samples prior to RNA-seq.
Fig. 5. Agilent 2100 Bioanalyzer
The Applied Biosystems™ QuantStudio™ 7 Flex Real-Time PCR System (Fig. 6) delivers the proven reliability, sensitivity, and accuracy of the data in a new industrial design. The QuantStudio 7 Flex System has been optimized to enable the broadest range of quantitative PCR applications, with additional dyes, formats, and automation options. This systems allows researchers to use TaqMan Array cards, running up to 384 simultaneous real-time PCR reactions by simply loading the card with your sample and centrifuging, producing consistent results with less pipetting error.
Fig. 6. QuantStudio 7 Flex Real-Time PCR System
This system is very sensitive: the luminescence channel is separated and positioned directly above the sample well, maximizing light capture for the best possible sensitivity. The Modulus™ Microplate Luminometer (Fig. 7) is between 10 and 1000 times more sensitive than other luminometers, simultaneously measuring samples of varying brightness. It is also designed to reduce crosstalk to achieve this extra-large reading range.
Fig. 7. Modulus™ Microplate Luminometer
The Attune Acoustic Focusing Flow Cytometer (Fig. 8) is the first cytometer that uses ultrasonic waves (similar to those used in medical imaging), rather than hydrodynamic forces, to position cells into a single, focused line along the central axis of a capillary. This cytometer is used for immunophenotyping, cell cycle analysis, cell proliferation, apoptosis, GFP & RFP detection, microbiological projects, and a broad range of other cell biology applications. Data obtained with and acoustic flow cytometer are more precise (narrower fluorescence peaks) than data obtained with traditional hydrodynamic focusing instruments, resulting in greater separation and easier data interpretation. The instrument has a violet/blue laser configuration: 405 nm (50 mW) and 488 nm (20 mW) lasers, with three emission channels per laser.
Fig. 8. Attune Acoustic Focusing Flow Cytometer
Genomics, Biostatistics, and Bioinformatics Core
School of Medicine
1430 Tulane Avenue
New Orleans, LA 70112
The COBRE Genomics, Biostatistics, and Bioinformatics Core at the Tulane Center for Aging, Tulane School of Medicine is supported by NIH: NIGSM COBRE grant No. P20GM103629 to Dr. S. Michal Jazwinski.
The Ion Chef was funded in 2016 by Core Lab Equipment Award from the Tulane School of Medicine.