Biological E Limited is a Hyderabad-based biopharmaceutical company supporting molecular workflows across viral and cell culture research. The lab processes viral and bacterial samples for downstream applications including qPCR, whole genome amplification, and next-generation sequencing.

In these workflows, extraction quality is critical. Poor yields, degraded nucleic acids, or contamination can directly impact downstream results and compromise sequencing and molecular analysis. As the complexity of their research programs grew, maintaining consistent extraction quality became increasingly important.

Lab snapshot

The challenge with manual spin-column extraction

Before adopting Manta, the laboratory relied on QIAGEN spin-column-based manual extraction. While widely used, manual spin-column workflows introduce variability that becomes difficult to manage consistently, particularly for sample types as sensitive as viral cell culture material.

The team encountered recurring challenges across their extraction workflows: inconsistent yields, RNA integrity issues, and occasional contamination events. For whole genome amplification, input quality is especially critical. Poor RNA integrity or yield variability upstream can make results unreliable downstream.

“For whole‑genome amplification, you really need RNA of very high quality and integrity. With QIAGEN’s manual extraction, we used to face some issues in this regard.”, says the team

Recognizing that manual extraction was becoming a limiting factor, the team began evaluating automated solutions.

Evaluating automation: the case for an open platform

The laboratory assessed several commercial automated extraction platforms, including high-throughput systems like KingFisher. While these instruments offered automation, they came with a significant constraint: they operated as closed platforms, restricting users to manufacturer-specific reagent kits.

For a biopharma lab working with specialized viral cell culture samples, this was a fundamental limitation. Existing commercial extraction kits are typically designed for standard clinical sample types not the complex, variable matrices encountered in bioprocessing workflows.

When the Cambrian team approached the laboratory with Manta, the open-platform architecture immediately stood out. Unlike the closed systems evaluated previously, Manta was designed to run any commercial magnetic bead-based kit giving the lab the flexibility to adapt its extraction chemistry to match its sample types.

“When it comes to the Manta, it’s completely different. It’s an open platform. And the engineering is very small - compact footprint, you can install it anywhere in the lab.”, says the team

The compact bench footprint was equally relevant. The laboratory operates a full suite of instruments, making space efficiency a practical requirement for any new addition.

Standardizing a kit for viral cell culture extraction

One challenge the team identified early was the absence of an off-the-shelf extraction kit specifically validated for viral cell culture samples on Manta. Rather than treating this as a barrier, the Cambrian applications team worked directly with the laboratory to solve it.

The team selected the MagMAX Viral kit, a commercial magnetic bead-based kit and collaborated with Cambrian to adapt and write the extraction protocol within the Manta system. The Cambrian team supported the laboratory through the full validation and optimization process until consistent, reproducible results were confirmed.

“There was no suitable kit for cell culture viral sample extraction on Manta. The Cambrian team and the Sheffield application team really helped us in the standardizing of commercial bead-based kits on Manta. They wrote the protocol in the system and helped us with validation and optimization.”

This collaborative approach allowed the lab to run a commercially established chemistry on an automated platform, without being constrained to a closed reagent ecosystem.

Consistent, reproducible results across every run

The laboratory has now been running Manta for over a year, extracting approximately 40-50 viral and bacterial cell culture samples per month. Weekly extraction batches of up to 10 samples feed directly into NGS and qPCR workflows, with whole genome amplification and TaqMan-based custom assay panels among the primary downstream applications.

The most meaningful improvement has been in result consistency. Across every extraction run, the team reports reproducible quality - without the yield losses, RNA integrity issues, or contamination events that were recurring challenges under the previous manual workflow.

“We are getting very good, consistent, reproducible results. We are seeing it run by run, in every run.”

For qPCR workflows, the impact has been particularly clear. Cross-contamination events that previously affected assay reliability have been eliminated since moving to Manta.

“Before, when we used to do manual extraction, somewhere there were handling issues and we used to get NTC cross-contamination results. Once we started using Manta, we are not observing anything like cross-contamination.”

Looking ahead: expanding into long-read sequencing

With extraction quality now stabilized on Manta, Biological E is planning to expand its sequencing capabilities with the addition of an Oxford Nanopore Technologies (ONT) platform. Long-read sequencing places even greater demands on nucleic acid integrity, making consistent, high-quality extraction upstream an essential foundation for the technology.

The reliability the team has built into their extraction workflow with Manta positions them to move into ONT sequencing without reintroducing the variability that challenged their previous manual approach.