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Protein Array

Dec 21, 2019 | Scale Up

In order to develop a protein array, client needed to automate the process of cloning 1000 genes amplified from genomic DNA of a plant pathogen. GenoFAB helped with process scale up by automating the design of sequencing and PCR primers, the analysis of data, and the standardization of laboratory workflows.

Protein array of a plant pathogen effector proteins

Problem

Goal: Characterize the biological function of 1,000 candidate effector proteins of a plant pathogen by developing a protein microarray to share with the scientific community.

Problem: While the client had standard molecular biology skills, they quickly realized that scaling their current process to 1,000 clones was unrealistic.  Client was under intense pressure to meet project deadlines as or run the risk of becoming the bottleneck in a major collaboration.

They needed help with planning and executing the process scale up.

Solution

GenoFAB worked with the client to:

  • Design primers
    • 2000 PCR primers with similar Tm and common overhangs to eliminate the need for multiple protocols using GenoCAM
    • 2000 primers for Sanger sequencing using GenoCAM
  • Optimize and standardize workflows
    • Workflow for stability and reproducibility to minimize the cost of failed experiments.
    • Workflow to allow technicians with little prior molecular biology experience to complete the work.
  • Automate data analysis
    • Analysis of all 2000 sequencing reads.
    • Analysis of PCR profiles exported from the TapeStation software.
  • Manage workflows
    • Data by developing a model to capture all project samples in GenoFAB’s LIMS. Client was able to automate the generation of barcode label and upload of data in Excel spreadsheets.
    • Results by developing a solution to identify genes that did not complete the process successfully in order to re-run them.
    • Project by developing a custom dashboard pulling data out of the LIMS to keep track of the project progress.

Results

Client delivered a collection of 900 plasmids with more than 90% of the target genes in under 4 months. The plasmid collection was used to allow Client’s collaborators to make the protein array.

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