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Magnetic bead nucleic acid extraction & NGS library prep: Why automated pipetting improves results
Lab Academy
- Molecular Biology
- Liquid Handling
- Automation
- Liquid Handling Workstations
- Essay
Handling magnetic beads is a critical step within NGS library preparation or nucleic acid purification. There is a lot to be considered that this process does not mutate into a strenuous and error-prone tightrope act. Wouldn't it be nice if there was some relief – topped with an improved precision, accuracy and reproducibility? Read why automated pipetting makes your bead-based cleanup become a walk in the park!
The benefits of an automated bead clean-up
Pipetting robots take all those considerations off your shoulders. What an enormous relief! Magnetic bead-based protocols like NGS library preparation, magnetic bead nucleic acid extraction, or NAP become a walk in the park:1. Reduced hands-on time. Complex pipetting-intensive protocols become ready-to-run with minimal interventions. For example: Preparing an NGS library prep out of total RNA requires 2 days manual work of repetitive pipetting and outstandingly high concentration. With an automated liquid handler, you can reduce your hands-on time to something between 30 min and 2 h and as little as 10 to 50 pipetting steps (depending on your sample number and used protocol). For NAP you can reduce your hands-on time down to 10-15 minutes and reduce the manual pipetting steps to a bare minimum for a 2 h run. Imagine what you could do with the time you gained!
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Overview of genomic workflows with pipetting steps and hands on time.
2. No more loss of beads or carryover. Concentrated manual “Sisyphus Work” with invisible pellets in tiny wells belongs to the past. Honestly, the pipetting robot can do it better and never gets tired! And you have practically no bead carryover as beads are transferred safely and precisely, improving overall beads purification performance.
3. Perfect bead handling for NGS-library prep. Your pipetting robot is perfectly equipped and educated for the recovery of a reproducible DNA fragment size. The volume ratio of bead-to-DNA will be kept, beads will be thoroughly resuspended, a strong magnet will recover beads without loss, the proper consumable-to-magnet fit during separation ensures a high-quality cleanup. Ethanol will remove optimally so you avoid inhibitory downstream effects. Beads in PEG-solutions will be pipetted precisely.
4. Pre-optimized bead-based protocols for NGS library prep and NAP. Modern liquid handlers support automated library prep workflows. For customization, you can break down complex workflows into single steps with simple commands which you can easily align in the software.
5. Consistent precision and accuracy. No person-to-person and day-to-day variability and no errors associated with manual pipetting keep precision and accuracy and pave the way for reproducible results.
6. Scale your throughput up. Process up to 96 samples with ease and without nervous breakdowns.
7. Improved user safety. Less manual pipetting, less strain on muscles and joints.
3. Perfect bead handling for NGS-library prep. Your pipetting robot is perfectly equipped and educated for the recovery of a reproducible DNA fragment size. The volume ratio of bead-to-DNA will be kept, beads will be thoroughly resuspended, a strong magnet will recover beads without loss, the proper consumable-to-magnet fit during separation ensures a high-quality cleanup. Ethanol will remove optimally so you avoid inhibitory downstream effects. Beads in PEG-solutions will be pipetted precisely.
4. Pre-optimized bead-based protocols for NGS library prep and NAP. Modern liquid handlers support automated library prep workflows. For customization, you can break down complex workflows into single steps with simple commands which you can easily align in the software.
5. Consistent precision and accuracy. No person-to-person and day-to-day variability and no errors associated with manual pipetting keep precision and accuracy and pave the way for reproducible results.
6. Scale your throughput up. Process up to 96 samples with ease and without nervous breakdowns.
7. Improved user safety. Less manual pipetting, less strain on muscles and joints.
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Which pipetting robot should you choose for your bead-based cleanup?
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Several pipetting robot models are available. You can choose from smart benchtop versions up to large high-throughput machines depending on your sample numbers, workflow complexity, and future automation plans.
For labs performing routine magnetic bead-based nucleic acid extraction, NGS library prep, or other sample preparation NGS workflows, a compact liquid handler is often an ideal starting point. Systems such as the Eppendorf epMotion® 5073 are designed for applications including NGS library preparation, magnetic nucleic acid extraction, PCR setup, dilution series, and normalization while requiring only a small laboratory footprint.
If your lab processes larger batches of samples, the Eppendorf epMotion® 5075 offers increased deck capacity and can automate workflows ranging from NGS library preparation and nucleic acid extraction to solid-phase extraction and magnetic bead cleanups for up to 96 samples. epMotion 5075 is also ideal for automated protein purification workflows.
For plate-based workflows, the Eppendorf epMotion® 96 Flex provides fast 96-channel liquid handling for 96- and 384-well plates. Its design is particularly well suited to repetitive bead cleanup steps, where precision, and reproducibility are essential.
The good news is that bead-based workflows are among the most automation-friendly laboratory processes. Whether you are looking to streamline a few weekly NGS cleanups or fully implement library prep automation, there is an automated liquid handling solution that can help reduce hands-on time, improve reproducibility, and minimize the risk of bead loss or carryover.
For labs performing routine magnetic bead-based nucleic acid extraction, NGS library prep, or other sample preparation NGS workflows, a compact liquid handler is often an ideal starting point. Systems such as the Eppendorf epMotion® 5073 are designed for applications including NGS library preparation, magnetic nucleic acid extraction, PCR setup, dilution series, and normalization while requiring only a small laboratory footprint.
If your lab processes larger batches of samples, the Eppendorf epMotion® 5075 offers increased deck capacity and can automate workflows ranging from NGS library preparation and nucleic acid extraction to solid-phase extraction and magnetic bead cleanups for up to 96 samples. epMotion 5075 is also ideal for automated protein purification workflows.
For plate-based workflows, the Eppendorf epMotion® 96 Flex provides fast 96-channel liquid handling for 96- and 384-well plates. Its design is particularly well suited to repetitive bead cleanup steps, where precision, and reproducibility are essential.
The good news is that bead-based workflows are among the most automation-friendly laboratory processes. Whether you are looking to streamline a few weekly NGS cleanups or fully implement library prep automation, there is an automated liquid handling solution that can help reduce hands-on time, improve reproducibility, and minimize the risk of bead loss or carryover.
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Excellent work needs excellent equipment
The best painter cannot paint with a bad brush! And so, does a pipetting robot. Stability comes first! Warping microtiter plates after heating is an absolute no-go. A perfect fit between vessel and magnet is crucial for NGS to have an optimal purification. Otherwise, the plate has to be exchanged after heating, which means sample loss. Microtiter plates with smallest dead volume minimize liquid loss. Take care that your consumables are clean and leachable-free.
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