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Integrated Genomics

Genomic Technologies Workshop

June 6th - 9th, 2022; 8:30am to 5:20pm, TH 1506


Four-days lecture / laboratory / computer laboratory course on the modern techniques to study genes and genomes with a major focus in gene expression analysis using next-generation (NG) sequneicng approach. Students will prepare the RNA-seq libraries, sequence them with Illumina Sequencing System, and analyze NG sequence data.


  • Alina Akhunova, Research Professor, Dept. of Plant Pathology
  • Sanzhen Liu, Associate Professor, Dept. of Plant Pathology
  • Eduard Akhunov, University Distinguished Professor, Dept. of Plant Pathology
  • David Cook, Associate Professor, Dept. of Plant Pathology
  • Katherine Jordan, Research Geneticist, USDA-ARS


  • Next Generation Sequencing Technologies and Their Applications. Illumina DNA Sequencing Technology: DNA-seq, RNA-seq, Single Cell Gene Expression, Metagenomics, eDNA-seq.
  • RNA-seq 101.
  • RNA-seq: Differential Gene Expression Experimental Design. Interpretation of RNA-seq Results.
  • Third Generation Sequencing Technologies. PacBio and Oxford Nanopore DNA Sequencing Technologies.
  • Multi-Omics Approach to Study Genome Biology.
  • CRISPR Gene Editing.
  • Overview of Real Time PCR Technology.
  • Quantitative Real Time PCR: from RNA to Data Analysis.


  • The students will prepare the RNA-seq libraries using Tru-Seq Stranded mRNA Illumina reagents and sequence them with the MiSeq Illumina sequencing system.
  • The students will perform SYBR Green based gene expression analysis on provided samples using the Bio-Rad OPUS CFX Real-Time PCR system.

Computer Laboratory

  • Does my sequencing run look good? Illumina Base Space Cloud Computing.
  • RNA-Seq Data analysis using GALAXY.
  • RNA-Seq Data analysis using Beocat super computer.

Course Credit Option (Tuition Fee)

PLPTH 885 (Course number 12071) Genomic Technologies Workshop.

A 2-credit course with credit/no-credit grading.

Recommended prerequisites. One of the following courses: PLPTH610, AGRON610, BIOCH521, BIOCH522, BIOL580, BIOL676.

Enrollment limit: 20

Instructor permission is not required. No textbooks. All materials will be provided.