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Integrated Genomics

Integrated Genomics Facility (IGF)

Lab # 4511, 4732, 4411, 4716 Throckmorton
Plant Sciences Center
Department of Plant Pathology
Kansas State University
Manhattan, KS 66506

phone: (785) 532-1393

Wheat CAP RNA-Seq Workshop, July 9th - 13th, 2018

 

Workshop materials:

Workshop Instructors

Workshop Schedule

Illumina Lab protocol (short)

Illumina Lab protocol (detailed)

RNA-Seq 101 Akhunova

MolBio_NGS_protocols_Akhunova

Gene Expression_Ed_1

Gene Expression_Ed_2

RNA-Seq Data Analysis_Ed

Networks_Fei_He

Data Distribution_Fei He

Galaxy

Intro to R_ Yuanwen Guo

Wheat NAM resource_Katie Jordan

RNA-Seq in wheat_Stephen Pearce

  


One-week lecture / laboratory / computer laboratory course on Gene Expression Analysis using next generation (NG) sequencing approaches. Students will prepare the RNA-seq libraries, sequence them with Illumina Sequencing System, and analyze NG sequence data. The workshop is specifically designed for Wheat CAP graduate students.

Lectures:

  • RNA-Seq 101
  • Gene Expression and Its Regulation
  • RNA-Seq Data Analysis Overview
  • Network-Based Gene Expression Data Analysis
  • New Trait Mapping Resource - Wheat Nested Association Mapping Panel
  • RNA-Seq and Wheat Functional Genomics

Laboratory:

  • Purify and Fragment mRNA, Synthesize First and Second Strand cDNA
  • Purify ds cDNA. Adenylate 3’ Ends, Ligate Adapters, Perform Reaction Purification, Enrich DNA Fragments.

Computer Lab:

  • RNA-Seq Data Analysis using GALAXY
  • Alignment Visualization Tools (Tablet)
  • Introduction to R Programming Language
  • RNA-Seq data analysis using R
  • Wheat expression data bases