--- title: 3500 Maintenance Checklist: Daily to Yearly | ELIS.AL url: https://elis.al/guides/maintenance-checklist/ language: en updated: 2026-10-26 source: ELIS.AL (Euro Lab Instrument Services) --- # 3500 genetic analyzer maintenance checklist A printable schedule of routine tasks for the 3500 and 3500xL, from the daily checks to the yearly service visit. Tick items as you go; your ticks stay in this browser. Updated 26 October 2026Written by the ELIS.AL technical team ## Key facts - Every day the instrument runs: check consumable status, bubbles and leaks. - At least every 14 days: replace the polymer (POP-7 after 7 days above 25 °C) and both buffer containers. - Monthly: flush the polymer delivery pump and water trap with molecular-grade water. - After every array change: spatial and spectral calibration. - Once a year: preventive maintenance and performance verification. ## Daily, before the first run - [ ] Check the dashboard: polymer, buffer containers and array within their limits and expiry dates.The software blocks expired consumables, but checking first avoids a stopped run. - [ ] Look for bubbles in the pump block and polymer path; remove them with the wizard.Bubbles cause spikes and unstable current. - [ ] Inspect the array port, pump block and drip tray for leaks or dried polymer. - [ ] Check that the top of the cathode buffer container and the septa are dry.Moisture on top of the container causes arcing. - [ ] Preheat the oven for at least 30 minutes.This reduces migration differences in the first run of the day. - [ ] Wait for the green status light before starting a run. ## At least every 14 days - [ ] Replace the polymer pouch, or sooner if the injection limit is reached.Above 25 °C, POP-7 lasts 7 days on the instrument. - [ ] Replace the anode and cathode buffer containers.Buffer older than two weeks is a known cause of unstable current. - [ ] Let new consumables reach room temperature before installing them. - [ ] Wipe dried polymer or salt off the electrodes if you see any. ## Monthly - [ ] Flush the polymer delivery pump and water trap with molecular-grade water, using a Luer-lock syringe of 20 mL or larger.Flushing removes diluted polymer and keeps algae out of the water trap. Smaller syringes build too much pressure. - [ ] Run a sequencing or size standard and compare it with your reference data. - [ ] Restart the computer and the instrument, check free disk space and archive old data. - [ ] Back up your run modules, protocols and plate templates. ## After every array change - [ ] Run the Wash Pump and Channels wizard with conditioning reagent warmed to 30–35 °C, never above 40 °C, when changing the array or the polymer type. - [ ] Run a spatial calibration. - [ ] Run a spectral calibration for each dye set and polymer combination. - [ ] Record the array’s serial number and installation date. ## Every year - [ ] Book preventive maintenance and performance verification by a service engineer. - [ ] Review calibration records and error logs with the engineer. ## Before a pause of more than two weeks - [ ] Run the shutdown wizard. It takes about an hour and needs one conditioning reagent pouch. - [ ] Store a removed array at room temperature with the loading end in deionized water. This checklist summarizes common practice for the 3500 series. Your laboratory’s procedures and the instrument user guide take priority. ## Frequently asked questions ### How often should the polymer be changed on a 3500? At least every 14 days at or below 25 °C. Above 25 °C, change POP-7 after 7 days. Change it sooner if the pouch reaches its injection limit. ### How often should the pump be flushed? About once a month, and whenever you see dried polymer or bubbles that the wizard cannot remove. ### Do I need to recalibrate after replacing the polymer? Not after a normal pouch change with the same polymer type. You need a new spectral calibration after an array change, after a change of polymer type, or when pull-up peaks appear across many runs. ### Is there a maintenance schedule for the 3130 or the 3730? Yes. The [3130](https://elis.al/3130-genetic-analyzer/) and [3730](https://elis.al/3730-dna-analyzer/) pages list their intervals: running buffer every 48 hours on both, polymer about once a week on the 3130 and every 7 days on the 3730. ## Related pages - ### [3500 troubleshooting guide](https://elis.al/guides/3500-troubleshooting/) Likely causes and fixes for spikes, weak signal, broad peaks, pull-up, current errors and failed calibrations. - ### [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. - ### [Buffers and reagents](https://elis.al/buffers-reagents/) Anode and cathode buffer containers and the conditioning reagent pouch, with installation and storage tips. ## Yearly service due? Book preventive maintenance and calibration for your 3500. [Book a service visit](https://elis.al/contact/?product=genetic-analyzer-service#quote)