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Assay Sample Prep

A critical process, transforming a sample into a compatible format for analytical procedures like PCR, NGS, and cell-based assays.

Assay Sample Prep can involve extraction/purification, concentration/dilution, or modification, depending on the assay requirements. Despite its importance, it poses significant challenges such as maintaining reproducibility, avoiding contamination, and managing labor-intensive workflows – particularly when performed manually. Automated systems can address these issues, offering improved accuracy, enhanced reproducibility, time and labor savings, and reduced contamination risk.

Manual normalization, normalization using a liquid handling system, and normalization using a microplate reader are some methods employed for this process. However, automated systems are increasingly preferred due to their higher accuracy, reproducibility, and efficiency, as well as their reduced risk of contamination.

Workflows For Assay Sample Prep

Assay sample preparation is fundamental to many workflows in molecular biology and proteomics:

  1. PCR and qPCR: Here, sample preparation involves the extraction and purification of DNA or RNA.
  2. Next-Generation Sequencing (NGS): In NGS workflows, sample preparation involves steps like DNA fragmentation, adapter ligation, and amplification.
  3. Protein Assays: For protein-based assays like ELISA or Western blot, sample preparation might involve protein extraction, quantification, and possibly denaturation.
  4. Cell-Based Assays: In these assays, sample preparation could involve culturing cells, treating them with specific compounds, and then possibly lysing the cells to release their contents.

Assay sample prep has never been easier

The OT-2 is a bench-top liquid handler designed to be accessible and flexible enough to automate many common applications.

Top Methods of Assay Sample Prep

  1. Extraction/Purification: This could involve processes like phenol-chloroform extraction for DNA or RNA, or various types of chromatography for protein purification.
  2. Concentration/Dilution: Samples may need to be concentrated using methods such as centrifugal filters, or diluted to an appropriate concentration for the assay.
  3. Modification: Some assays require samples to be chemically or enzymatically modified before analysis. For example, proteins might need to be denatured and reduced before running a SDS-PAGE.

Protocol Spotlights

Opentrons helps you automate assay sample prep with open-source protocols for the OT-2 and Opentrons Flex

Why is Assay Sample Prep so Difficult?

Assay sample preparation is often considered the most challenging part of the experimental process. It requires a high level of precision and accuracy to ensure reproducibility. It is also where the sample is most vulnerable to contamination or degradation, which could lead to inaccurate results. Furthermore, the optimal sample preparation protocol can vary widely depending on the type of sample and the specific assay to be performed.

Key Challenges of Assay Sample Prep with Manual Pipetting

  1. Reproducibility: Even minor variations in pipetting technique can lead to significant differences in results.
  2. Contamination: Samples can easily become contaminated during preparation, especially when manually pipetting.
  3. Time and Labor Intensive: Manually preparing samples for assays can be extremely time-consuming and labor-intensive, especially when handling a large number of samples.

Automating Assay Sample Prep

Automation of assay sample preparation can be achieved with robotic liquid handling systems. These systems can accurately dispense precise volumes, mix reagents, and even perform operations such as heating or cooling. The use of such systems can reduce human error, increase reproducibility, and significantly speed up the sample preparation process.

Benefits of Automation over Manual Pipetting for Assay Sample Prep

  1. Enhanced Reproducibility: Automation ensures consistent conditions and handling across samples, improving reproducibility between experiments.
  2. Time and Labor Saving: Automated systems can handle multiple samples simultaneously, greatly reducing the time and labor required for the process.
  3. Reduced Contamination Risk: Automated systems minimize the amount of human handling, thereby reducing the risk of contamination.

Want to know more?

Our team of experts can help figure out if automation is right for you. Book a virtual demo to discuss your workflow needs with an expert.