UAMS, Genomics Core

University of Arkansas for Medical Sciences

Facility Contact Form orDr. Donald J. Johann (email)

Overview of Services

Salient services provided for molecular profiling include the complete NGS service, which consists of:

  1. sample preparation with QA/QC validation,
  2. running the sample on the NGS instrument,
  3. bioinformatics pipeline processing, specifically, QA/QC analysis of NGS data, sequencing data alignment, molecular characterization of mutational findings, report generation (annotated Excel file) delivered to the customer.

Examples of NGS approaches

  1. for DNA include:
    • whole-exome
    • whole genome
    • targeted cancer panels.
  2. RNA approaches include:
    • mRNA,
    • total RNA for gene expression,
    • isoform expression,
    • expressed mutations,
    • fusion analysis.
  3. Methylation approaches currently utilize the Infinium EPIC array.  RRBS to be offered soon.

Additional Services Offered

Illumina Bead Array

  • MethylationEPIC array for standard or FFPE DNA
  • Tecan Freedom EVO for high-throughput array staining
  • iScan and Autoloader for high-throughput array scanning

Nucleic Acid extraction

  • DNA & RNA from cells, solid tissues, & FFPE
  • cfDNA from plasma & urine

NGS Library Preparation

  • Whole Genome including low-pass or ultra-low-pass (0.1 – 0.3x)
  • Targeted DNA panels
  • RNA-seq with Truseq Stranded Total RNA
  • RNA-seq with Truseq Stranded mRNA
  • RNA-seq with Takara SMARTer Stranded Total RNA
  • single-cell RNA-seq with 10X Genomics

QC for Nucleic Acids and NGS Libraries

  • Qubit fluorometer
  • NanoDrop spectrophotometer
  • Agilent Fragment Analyzer capillary elctrophoresis system
  • Library functional assessment with QuantStudio5 qPCR system

Droplet Digital PCR (ddPCR)

  • BioRad QX200 system

DNA Fragment Size Selection

  • Sage Science PippinHT

Technology and Instrumentation

NGS Instrumentation

  • Illumina HiSeq 3000
  • Illumina NextSeq 500
  • Illumina miniSeq

Other Molecular Profiling

  • Illumina iScan Microarray System with autoloader
  • BioRad ddPCR QX200
  • 10x Chromium System

Support Equipment

  • Advanced Analytical Fragment Analyzer
  • Tecan Freedom Evo Robot
  • QuantStudio 5 Real Time PCR System
  • Sage Science PippinHT

If you would like to contact this core facility, please fill out the "Facility Contact Form" on the right of this page. This contact method helps ARA measure the success of the CFE in connecting potential collaborators and will flow directly to the core director’s email inbox.