Our lab is experiencing a major issue with PCR results. We switched to a new lot of 96-well plates and suddenly started seeing rampant false signals causing QC failures.

The specific product in question is the Agilent brand: Storage/reaction microplate, 96-well, polypropylene, 1 mL/round well, round bottoms, 32 mm height, irradiated. Part Number: 204357-100.

Looking to see if any other lab out there is or has experienced a similar problem, especially specifically with this equipment.

Edited January 6, 20223 yr by Stack344
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55 minutes ago, Stack344 said:

Our lab is experiencing a major issue with PCR results. We switched to a new lot of 96-well plates and suddenly started seeing rampant false signals causing QC failures.

The specific product in question is the Agilent brand: Storage/reaction microplate, 96-well, polypropylene, 1 mL/round well, round bottoms, 32 mm height, irradiated. Part Number: 204357-100.

Looking to see if any other lab out there is or has experienced a similar problem, especially specifically with this equipment.

Are you using it for qpcr or pcr? Not using those plates but they do not seem be made for either application based on well shape and lack of wall thickness info.

13 hours ago, CharonY said:

Are you using it for qpcr or pcr? Not using those plates but they do not seem be made for either application based on well shape and lack of wall thickness info.

We don't use them for the qPCR reaction itself. We use them for RNA extraction and various reagent storage purposes. The plates as a whole have never been an issue, just a particular lot.

We've actually run into a nearly identical situation a few months back, same product line, different lot. In our case, the issues started showing up during RNA extraction, particularly when using magnetic bead protocols. The only change had been the microplate lot (also Agilent, polypropylene 1 mL, round-bottom), and we started seeing unexplained signal fluctuations and elevated background levels that hadn’t been present with previous lots. After a frustrating round of troubleshooting, we confirmed that well geometry and possible inconsistencies in irradiation or surface treatment were likely contributing factors.

It might be worth checking with Agilent for a lot-specific QC report if you haven’t already. Meanwhile, as a reference point for layout consistency and cross-checking experimental setups, we found this 96 well plate template to be quite useful, especially when trying to rule out plate orientation or setup errors during high-throughput runs.

Curious to know if anyone else has heard back from Agilent or had similar QC discrepancies tied to specific lots. Would be great to get more data points on this.

The original post is a few years old and around that time we started to have couple of issues which we assumed was due to supply chain issues (it was a weird time for many things). But if there are recent issues that is concerning. We had some trouble with RNA extractions recently, but we have been using Eppendorf plate. But I attributed that to personnel changes for now. Potentially need to run some additional quality checks...