--- title: 3500 Genetic Analyzer Troubleshooting Guide | ELIS.AL url: https://elis.al/guides/3500-troubleshooting/ language: en updated: 2026-10-26 source: ELIS.AL (Euro Lab Instrument Services) --- # 3500 genetic analyzer troubleshooting guide Find the likely cause of common data and instrument problems on the 3500 and 3500xL, and what to try before you call service. Updated 26 October 2026Written by the ELIS.AL technical team ## Start here - Check the basics first: polymer and buffers within their on-instrument limits, no bubbles in the pump, the oven preheated for at least 30 minutes, and a green status light before you start a run. - Run a sequencing standard or size standard. If the standard looks good, the problem is in the samples; if it looks bad, look at the instrument and consumables. ## Data quality problems ### Spikes in the electropherogram #### Likely causes - Air bubbles or particles passing the detection window. - Dried polymer or crystals around the array port or in the pump block. - Electrical noise from arcing. #### What to try - Run the bubble removal wizard. - Install a fresh polymer pouch that has reached room temperature. - Clean the pump block and check the array port for dried polymer. - Make sure the top of the cathode buffer container is dry. ### Low signal or no signal #### Likely causes - Too little template or a failed PCR or sequencing reaction. - Salt or leftover dye terminators competing during electrokinetic injection. - Degraded formamide. - An air bubble at the bottom of the well. - A blocked capillary. #### What to try - Run a standard to separate sample problems from instrument problems. - Review the reaction and the cleanup step. - Use fresh formamide from a frozen aliquot. - Spin the plate briefly to remove bubbles. - Check the injection voltage and time in the run module. ### Broad peaks or poor resolution #### Likely causes - Polymer past its on-instrument life. - A capillary array near the end of its life. - Overloaded or salty samples. - Oven not preheated, or the wrong run temperature. #### What to try - Install fresh polymer and check the array’s injection count. - Dilute the samples or shorten the injection. - Preheat the oven for at least 30 minutes. - If a standard shows broad peaks in all four colours too, replace the array. ### Pull-up peaks (colour bleed-through) #### Likely causes - A spectral calibration that is out of date or was made with another array or polymer. - Signal above the detector’s range because the sample is overloaded. #### What to try - Reduce the amount of sample or the injection time. - Run a new spectral calibration for the dye set. - Recalibrate after every array change and every change of polymer type. ### Dye blobs in sequencing data #### Likely causes - Unincorporated dye terminators left after an incomplete cleanup. - A run module that does not match the cleanup chemistry. #### What to try - Improve the cleanup after cycle sequencing. - Use the run module that matches your cleanup method. ### Migration shifts between runs #### Likely causes - The first run of the day started before the oven was stable. - Aging buffer or polymer. - Large temperature changes in the room. #### What to try - Preheat the oven for at least 30 minutes. - Replace buffer containers and polymer within their limits. - Keep the room temperature stable, and use a size standard in every fragment analysis sample. ## Instrument errors ### Unstable current error #### Likely causes - Air bubbles in the pump block or polymer path, which often cause spikes as well. - A leak in the polymer path. - Expired or aged polymer. - Running buffer on the instrument for more than two weeks. - Arcing, missed maintenance or a hardware fault. #### What to try - Run the bubble removal wizard. - Check the pump block and array port for leaks. - Run the wash wizard, then install fresh polymer and both new buffer containers. - Dry the top of the cathode buffer container. - Call service if the error continues. ### Arcing or a run that stops #### Likely causes - Moisture or salt on top of the cathode buffer container or on the septa. - Dried polymer or salt on the electrodes. #### What to try - Dry the top of the container completely before fitting the septa. - Wipe the electrodes with a lint-free tissue. ### Leaks at the pump or array port #### Likely causes - An array that is not fully seated. - Worn seals or damaged pump block parts. #### What to try - Reseat the array and inspect the pump block. - Do not overtighten fittings. - Call service if the leak continues. ### An array that will not move or release #### Likely causes - Dried polymer around the array head. #### What to try - Squirt deionized water around the array head and try again. - Never use force or tools. If it still does not move, request a service visit. ### Spatial or spectral calibration fails #### Likely causes - An array that is not seated, or capillaries not completely filled with polymer. - A dirty detection window. - Bubbles in the wells of the calibration plate, or an expired standard. #### What to try - Reseat the array and refill it with polymer. - Spin the calibration plate to remove bubbles and check the standard’s expiry date. - Repeat the calibration. ### Yellow or red status light #### What it means - Steady yellow: the computer and the instrument are not communicating. - Steady red: the instrument cannot initialize. #### What to try - Restart the computer and the instrument in the start-up order given in the user guide. - Wait for a green light before starting a run. - If the red light returns, contact service. ## Preventing problems Most of the problems above are prevented by routine care: polymer and buffers replaced within their limits, a monthly pump flush, and calibrations after every array change. The [3500 maintenance checklist](https://elis.al/guides/maintenance-checklist/) puts these tasks on one printable page. ## Frequently asked questions ### How do I know if a problem comes from the samples or the instrument? Run a sequencing standard or size standard on the same array. If the standard is good, look at sample preparation and cleanup. If the standard shows the same problem, the cause is in the instrument or the consumables. ### When should I replace the capillary array? When a standard shows broad peaks, shorter reads or poor resolution in all four colours, or when the array has reached its injection limit or expiry date. ### What should I send when I ask for help? The instrument model and serial number, the software version, the kit and lot numbers, the number of runs on the array, the polymer, buffer and formamide lots, and a few sample data files that show the problem. ### Do these fixes also apply to the 3130 and 3730? Many causes are the same, such as bubbles, old polymer or buffer, leaks and arcing, but the error messages and maintenance intervals differ. See the [3130](https://elis.al/3130-genetic-analyzer/) and [3730](https://elis.al/3730-dna-analyzer/) pages. ### My 3500 rejects an array that still gives good data. What can I do? The array has probably reached the injection limit or expiry date stored in its RFID tag. A regenerated array or online regeneration with a new RFID tag lets you keep working. See [regenerated arrays](https://elis.al/regenerated-capillary-arrays/). ## Related pages - ### [Maintenance checklist](https://elis.al/guides/maintenance-checklist/) A printable schedule of daily, 14-day, monthly and yearly tasks for the 3500 and 3500xL. - ### [Genetic analyzer service](https://elis.al/genetic-analyzer-service/) Preventive maintenance, calibration and repair for the 3500 series, 3130, 3730 and SeqStudio, on site or remotely. - ### [Regenerated arrays](https://elis.al/regenerated-capillary-arrays/) Regenerated arrays for the 3500, 3500xL, 3130 and 3130xl, and online regeneration with a kit and remote support. - ### [POP polymers](https://elis.al/pop-polymer/) POP-7, POP-6 and POP-4 pouches in 96, 384 and 960 samples, and how to choose between them. ## Still stuck? Send the error message and a screenshot of the data. We tell you what to check next. [Ask an engineer](https://elis.al/contact/?product=genetic-analyzer-service#quote)