Key facts
- The 3500 uses an 8-capillary array; the 3500xL uses a 24-capillary array.
- Both come in 36 cm and 50 cm. The length must match the run modules you use.
- OEM references: 4404683 (8 capillaries, 36 cm), 4404685 (8, 50 cm), 4404687 (24, 36 cm), 4404689 (24, 50 cm).
- The OEM rates its 8-capillary 3500 arrays for 160 injections or until the expiry date, whichever comes first.
Available arrays
| Product | Instrument | Capillaries | Array length | OEM part no. (reference) | Price |
|---|---|---|---|---|---|
| 8-capillary array, 36 cm | 3500 | 8 | 36 cm | 4404683 | Ask for price |
| 8-capillary array, 50 cm | 3500 | 8 | 50 cm | 4404685 | Ask for price |
| 24-capillary array, 36 cm | 3500xL | 24 | 36 cm | 4404687 | Ask for price |
| 24-capillary array, 50 cm | 3500xL | 24 | 50 cm | 4404689 | Ask for price |
Swipe sideways to see all columns.
OEM part numbers are shown for cross-reference only, so you can match what your instrument uses today.
36 cm or 50 cm: choosing the array length
Choose 36 cm when throughput matters: fragment analysis and short sequencing reads finish in 30 to 60 minutes. Choose 50 cm for long sequencing reads, about 700 bases with POP-7 in roughly two hours.
Run modules in the Data Collection Software are written for one array length and one polymer type, so the array you install has to match the modules your lab has validated.
| Run module | Array | Polymer | Run time | Read length |
|---|---|---|---|---|
| RapidSeq36_POP7 | 36 cm | POP-7 | ≤ 30 min | ≥ 500 bases |
| FastSeq36_POP7 | 36 cm | POP-7 | ≤ 60 min | ≥ 600 bases |
| RapidSeq50_POP7 | 50 cm | POP-7 | ≤ 40 min | ≥ 550 bases |
| StdSeq50_POP7 | 50 cm | POP-7 | ≤ 125 min | ≥ 700 bases |
| StdSeq50_POP6 | 50 cm | POP-6 | ≤ 135 min | ≥ 600 bases |
Values from the manufacturer’s 3500/3500xL specification sheet. Real results depend on the chemistry, cleanup and sample quality.
How long does a capillary array last?
The OEM rates its 8-capillary 3500 arrays for 160 injections or until the expiry date on the label, whichever comes first. The instrument counts injections through the array’s RFID tag and warns you when the limit is reached and the array is due for replacement. With good maintenance, laboratories often see useful life beyond that figure; one forensic laboratory procedure describes typical array life as 150 to 250 injections.
Plan a replacement array when a sequencing or size standard shows any of these signs:
- Broader peaks and loss of resolution in all four colours.
- Shorter read lengths than your reference data.
- Spatial calibrations that fail even after reseating and refilling the array.
- One capillary that no longer injects or shows no signal.
Installing a new array
- Start the Install Capillary Array wizard in the Data Collection Software and follow its prompts.
- Keep the loading end protected until it goes into the instrument. Never touch the capillary tips or the detection window.
- Check that the array is fully seated in the polymer block and that the detection cell is closed before the wizard fills the capillaries with polymer.
- Run a spatial calibration, then a spectral calibration for every dye set you use.
- Run a sequencing or size standard before the first customer samples.
The loading end has small, blunt capillary tips that can cause piercing injuries. Wear gloves and eye protection when handling an array.
Storing an array off the instrument
Store arrays at room temperature. If you remove an array, keep the loading end in deionized water so the polymer inside the capillaries does not dry out. Before leaving the instrument unused for more than two weeks, run the shutdown wizard, which flushes the system with conditioning reagent.
Regenerated 3500 and 3500xL arrays
For much less than a new array, we also supply original 3500 and 3500xL arrays that we have cleaned, regenerated and fitted with a reprogrammed RFID tag. If your own arrays have reached their RFID limit, we can regenerate them online. See regenerated capillary arrays.
Frequently asked questions
Can I use a 36 cm array with 50 cm run modules?
No. Run modules are defined for one array length and polymer type, so the array has to match the modules you run. If you change length, use or create modules for the new length and validate them.
Do I need a new spectral calibration after changing the array?
Yes. Run a spatial calibration after installing the array, then a spectral calibration for each dye set and polymer combination you use.
Why does a new array fail spatial calibration?
Usually the array is not fully seated, the detection window is dirty, or the capillaries are not completely filled with polymer. Reseat the array, check the detection cell, refill with fresh polymer and repeat the calibration.
Is the array the same for the 3500 and the 3500 Dx?
The OEM sells separate part numbers for Dx instruments, for example 4404682 (36 cm) and 4404684 (50 cm) for the 3500 Dx. Tell us if your instrument runs in Dx mode so we quote the right item.
Can a used 3500 array be regenerated?
Yes. We clean and regenerate the array and reprogram its RFID tag, or we send you a kit to regenerate it in your lab with our engineer online. See regenerated capillary arrays.
Do SeqStudio Flex arrays fit the 3500?
No. SeqStudio Flex arrays (A49104 to A49107) are not interchangeable with 3500 arrays, even though both instruments share the same polymer pouches and buffer containers.
Related pages
Regenerated arrays
Regenerated arrays for the 3500, 3500xL, 3130 and 3130xl, and online regeneration with a kit and remote support.
POP polymers
POP-7, POP-6 and POP-4 pouches in 96, 384 and 960 samples, and how to choose between them.
Buffers and reagents
Anode and cathode buffer containers and the conditioning reagent pouch, with installation and storage tips.
Compatibility chart
Arrays, polymers and buffers for each Applied Biosystems genetic analyzer, with OEM part numbers.