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Deven See Lab

Western Regional Small Grain Genotyping Laboratory (WRSGGL)

Lab Forms:

Plate-Layout-Submission-Document-1
Job Request Form (doc)
Tissue collection and DNA submission instructions
Genotyping Job Status

Due to COVID-19, we are asking that users of the lab sign up with the following links for any equipment they need to use so we can ensure proper social distancing in the lab. Thank you.

Sign Up remotely for the Zeto/ABI machine (HOW TO USE ABI SIGN UP SHEET)

Sign Up sheet for the Plate Reader

Sign Up sheet for the Oktopure

Sign Up sheet for the Qiagility

Data:

42K SNP Consensus map with Physical Position

Known Informative Markers (GMS)

Graduate Students

Elliott Marston

Ph.D. Student, Plant Pathology

Interests: Genetics, discovering of genetic markers for marker assisted selection (MAS), biotic and abiotic stressors of wheat. Main project is focused on the identification of QTL’s and markers for MAS relating to late maturity alpha-amylase.

Jessica Schallon

M.S. Student, Plant Pathology

Interests: Rusts of cereal crops, particularly stripe rust of wheat, in the Pacific Northwest.

 

 


Staff

K. Marlowe (“Marlowe”)

USDA Research Technician

Education: Ph.D., Botany, Washington State University; B.S., Biology, Communications, University of Colorado
Expertise: Next-Generation sequencing, DNA extraction, PCR, Exome Capture, FHB Screening

Email: marlowe@wsu.edu

Travis Ruff

USDA Research Technician

Education: M.S., Crop and Soil Sciences, Washington State University, B.S., Biotechnology and Microbiology, Washington State University
Expertise: Next-Generation sequencing, PCR, Sanger sequencing

Email: truff@wsu.edu

Yan Liu

Research Technician

Education: Ph.D., Crop Genetics and Breeding, Northwest A&F University, Yangling, China; M.S., Crop Genetics and Breeding, Northwest A&F University, Yangling, China; B.S., Engineering, Central South University, Changsha, China
Expertise: Molecular genetics, Host-resistance, Next-Generation sequencing, PCR

Email: y.liu@wsu.edu

Marcus Hooker

Research Technician

Education: Ph.D., Botany, Washington State University; B.S., Biology, Colorado Mesa University
Expertise: Bioinformatics, Data Analysis, Genomics

Email: marcus.hooker@wsu.edu


Computational Capacity

The See Lab as its computational capabilities required to handle large data sets generated by the in-house NGS platforms. We have a 32 core, 512GB RAM system for running the various computational jobs in the lab. In addition, there is a 96 core, 1TB RAM high performance computing cluster for massive parallel computation.

Servers

  • Supercomputer: WRSGGL01
    32 cores, 512GB RAM total memory
  • High Performance Computing Cluster: WRSGGLcluster
    4 compute nodes, 24 cores per node, 256 GB RAM per node, 1TB RAM memory

Storage

  • Supercomputer
  • HPC
  • Independent RAID storage

Technologies, Equipment & Capabilities

Next-Gen Sequencing

  • Illumina NextSeq®500
    -400 million reads/12hours
    -Exome Sequencing
    -Targeted Gene Sequencing (amplicon, gene panel)
    -Whole-Transcriptome Sequencing
    -Cytogenomic Arrays

Sanger Sequencing

  • ABI 3730

Fragment Analysis

  • SSR
  • STS
  • CAP

DNA Extraction

  • Bead Shaker
  • Oktopure
  • Synergy Microplate Reader (Quantification)
  • QiAgility

SNP Analysis

  • KASP
  • Synergy Microplate Reader
  • Genotype by Multiplex Sequencing (GMS)
  • Exome Capture

Software

  • GeneMarker (v1.5,v1.9) [Soft Genetics]
  • Gen5 2.0 [BioTek/Synergy Plate reader]
  • [QiAgility]
  • JMP Genomics
  • Multipoint
  • MultiQTL
  • TASSEL

Undergraduates

Alana Toren

Major: Environmental Engineering

 

 

 

 

 

 

Northern Lilacs

Major: Biochemistry

 

 

 

 

 

 

 


Former Members

  • Dolores Covarrubias, Research Technician
  • Amandeep Dhaliwal, Research Technician
  • Esraa Alwan, Ph.D. Crop and Soil Sciences
  • Kanokporn Triwitayakorn, Fulbright Visiting Scientist
  • Taras Nazarov, Ph.D. Plant Pathology
  • Jennifer Logan, Research Technician
  • Jinita Sthapit, Ph.D. Plant Pathology
  • Vandhana Krishnan, Associate in Research, Bioinformatician
  • Derick Jiwan, Post-Doctoral Researcher, Crop Sciences
  • Jonathan Eagle, M.S. Plant Pathology
  • Sajal Sthapit, Ph.D. Plant Pathology