Abi 3130 how does it work

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Learn More - opens in a new window or tab Any international shipping and import charges are paid in part to Pitney Bowes Inc. Learn More - opens in a new window or tab Any international shipping is paid in part to Pitney Bowes Inc. Instead, do it manually, so that you won't introduce bubbles into the supply tube.

Select Buffer valve and Close — Send Command , to limit backflushing from the interconnect tube. Select Polymer delivery pump , Move piston up , and counts — Send Command ; submit command repeatedly until the chamber is nearly full. Caution : If necessary, temporarily halt this process and add polymer to the supply bottle. Dry the wedge with a Kimwipe; reinstall anode buffer jar filled with fresh buffer. Check for bubbles in the array port; to determine if it is advisable to remove bubbles from this area, see How to remove bubbles from array port?

Flush array with fresh polymer How to fill an array? If there is sufficient polymer in the supply bottle, continue refilling the pump chamber by selecting Polymer delivery pump , Move piston up , and counts — Send Command ; submit command repeatedly until the chamber is nearly full. Finally, select Polymer delivery pump and Initialize polymer delivery pump — Send Command — to completely fill the chamber and open the buffer valve.

First, verify that there is sufficient polymer in the pump chamber to complete this action. If uncertain regarding this point, see How many runs possible with existing polymer in chamber? If the volume is insufficient, check the supply bottle to see if there is enough polymer available to fill the pump chamber either partially or completely, as desired.

If not, add the desired amount of polymer to the supply bottle see How to add POP-7 with a modified supply bottle? Once there is sufficient polymer volume in the pump chamber, use the manual controls to fill the array. For a cm array, select Polymer delivery pump and Fill 50 cm capillary array — Send Command. Submitting this command will close the buffer valve and fill the array with fresh polymer. Should you become distracted by other events and never start the run, the oven will shut down automatically.

Select Oven , Set oven temperature , and 60 — Send Command. Click on Instrument Status , and verify that the oven has actually turned on bar turns red. Others have said that POP-7 lasts for many weeks at room temperature. The truth lies somewhere in between these two extremes. It is true that one can continue to use POP-7 that has been on the instrument for over a month. However, polymer deposits will gradually build up on the capillary walls, slowing the rate of DNA migration leading to increased peak spacing and resulting in decreased read length.

At some point, data quality will suffer along with read length. Aside from examining each sequence that comes off the xl, the progression of this process can be monitored by tracking the EP current during each pre-run and the peak spacing from each plate see When do you need to replace your POP-7? By that time, we begin to see substantial rises in the EP current as well as in the peak spacing.

Although data quality is still quite good, using the POP-7 for longer than 14 days reduces the capillary array's regeneration interval for further information, see How to keep Capillary Arrays 'fresh' longer? To avoid having to waste POP-7, we have modified the supply bottle so that we can easily add polymer on an as-needed basis for further information, see How to add POP-7 with a modified supply bottle? Although data quality is still quite good, using the POP-7 for longer than 14 days reduces the capillary array's regeneration interval for further information, see How to clean 'nitric acid' Capillary Arrays?

There are two factors that you can monitor to determine if your POP-7 has been on the instrument too long: EP current; and, Peak spacing. Note : According to ABI, each xl has its own 'unique' values for these parameters. Thus, although typical values are given below for our instruments, actual values need to be determined empirically for each xl.

Thus, we keep track of the maximum EP current achieved during the pre-run for the first set of 16 samples of each well plate run on the sequencer. As the polymer ages, it migrates more slowly — resulting in wider peak spacing and shorter read lengths.

Thus, we keep track of the average peak spacing Use Excel template to calculate 'Average Peak Spacing'. Thus, you must keep those issues in mind when evaluating these variables. Clearly, this is primarily an issue of laboratories which do not have sufficient sample throughput to keep their xl's running nearly all the time. For those who do, the polymer will be used up long before a week has passed.

For the rest of us, the following concepts may help. Temperature is an important factor in maintaining the longevity of POP-7; thus, you should keep POP-7 in the refrigerator until it is needed; however, until ABI designs a cooling chamber into the xl, the only efficient way to keep the polymer cool while in use is to keep the room cool.

With energy costs what they are, it isn't cost-effective to maintain air conditioning at 4 o C; nevertheless, the cooler the better as far as POP-7's longevity. Get used to wearing a jacket! Because it inevitably results in bubbles that must be removed leading to some wasted polymer and lots of wasted time , it is not practical to remove the supply bottle and store it in the refrigerator whenever the xl will be idle.

However, if you are going to leave the instrument idle for long enough, you can use the manual controls for further information, see How to minimize POP-7 usage during bubble-removals?

If done properly, you will not introduce bubbles into the polymer supply tube, and you can return the polymer to the supply bottle when it is needed see final paragraph. Another important factor is 'evaporation'. As water evaporates from the polymer, it becomes more viscous.

Thus, ensure that polymer bottles are not left open any longer than necessary. Further, it may help to initialize the polymer pump whenever the xl will not be running so as to trap more of it where the water cannot evaporate. Ideally, if you have the resources, you should design a new supply 'bottle' that would minimize the head space above the level of the polymer — which would greatly minimize evaporation. The best way to increase POP-7 longevity is to use it on an 'as-needed' basis rather than putting on an entire bottle each time.

This topic is covered in How to add POP-7 with a modified supply bottle? Normally, the first two digits of a lot number for an ABI product represent the year in which that lot was manufactured; the second two digits indicate the month of manufacture. However, on POP-7, lot numbers represent the date of bottling. Here's how it works. ABI generates a very large batch of POP-7, which is then stored in large containers under refrigerated conditions.

Periodically, those containers are tapped for filling the small bottles of polymer that ABI sells to customers. This is the date referred to by the lot number on POP-7, not the actual manufacture date. Why is this an issue? Normally, when you suspect that a particular lot of some reagent was incorrectly manufactured or handled, you obtain a fresh batch of that reagent which bears a different lot number. With POP-7, every bottling of the original large batch of polymer bears a different lot number, even though the polymer was all made at the same time.

In fact, when ABI bottles both 3. Yet, unless there was an unrecognized problem with the storage conditions of that batch of polymer or unless something odd happened while bottling the polymer, each successive bottling from the original large batch should behave the same — despite the different lot numbers.

Thus, for POP-7, the only way that you can ensure you are testing the system with a truly different batch is to note the expiration date on the bottle. Fortunately, this is based on the original date of manufacture of the large batch, rather than on when the small bottles were filled. Note: ABI products that lack expiration dates on the product are usually guaranteed for one year from the date you receive them.

There are no moving parts inside a capillary array and the array is made of glass tubes coated on the outside with metal. Thus, in principle, an array ought to last nearly forever — even though ABI guarantees them only for runs. Unfortunately, accretion of polymer and proteins contaminants from processed samples on the capillary lumens ultimately limits the useful life of an array. Typically, these accretions can be flushed away by repeated washing of the array with water.

If water-washing is not sufficient, filling the array with nitric acid 1 N will hydrolyse the proteins into peptides; this reduces the adhesion of such contaminants to the capillary lumen, enabling subsequent high pressure water to flush them away. The array can be regenerated in conjunction with washing the polymer block, or by itself. Regenerating the array only requires the least polymer; thus, it is the preferred method unless the array regeneration cycle happens to coincide with the need to wash the block.

For further information, see How to rinse water Capillary Arrays? There are three factors that you can monitor to determine if your capillary array needs to be regenerated: Sequence read length; EP current; and, Peak spacing. As polymer and proteins accrete to the capillary lumens, the migration rate of the DNA through the polymer slows — resulting in a reduced read length for the time allotted by the run module.

Surprisingly, even such 'clogged' arrays still deliver good quality data; nevertheless, the read lengths are clearly shorter than normal. Peak spacing : On our instruments, a 'fresh' capillary array typically achieves peak spacings as shown in Sequencing Analysis 5. As polymer and proteins accrete, the migration rate of the DNA through the polymer slows — resulting in wider peak spacing and shorter read lengths. Always remember to don protective clothing and eyewear before opening the stock bottle; be especially careful when pressurizing the nitric acid wash system.

Among other possibilities, nitric acid splashed or squirted into the eyes will be more than just painful. ON-Instrument vs. Array Degradation : Nitric acid has the capacity to etch the glass walls of the capillaries; although minor etching will be invisible once recoated with fresh polymer. However, over time, we would expect that excessive use of nitric acid in terms of the length or number of soak times might substantially degrade an array. Minor degradation is expected to take the form of 'cloudiness' at the detection cell reducing signal intensity ; major degradation might include sloughing of glass fragments inside the capillaries — potentially clogging them.

As a point of reference, we used to regenerate cm capillary arrays — without any apparent undesirable effects — at least 8 times. Further, for some 'regenerations', we even left the nitric acid in the array for hours rather than only minutes as recommended — so, the eventual expected array degradation may be a long time coming We now perform a nitric acid wash only as a last resort to restore an array; usually, once an array has clogged that badly, even the nitric acid wash does not restore it.

Otherwise, at some point, nitric acid will burn your face as it sprays from the top of the array-fill syringe. Polymer Reserve Syringe 5. Not only are the syringes expensive, but breakage will also discharge nitric acid, potentially burning some portion of your anatomy.

You need the following parts from either an ABI sequencer or from the original ABI polymer delivery setup: Upper polymer block; Polymer-reserve syringe 5. Seal off outlet for the interconnect tube. Ideally, use a solid bolt made of a material that is impervious to 1 N nitric acid; however, a special thread type is required. Alternatively, remove the interconnect tube from the 'bolt' noted in "iv"; then, use a red-hot screw to soften the plastic enough to seal the hole in the bolt. After covering the threads with teflon tape, screw the bolt into the outlet — carefully tightening with a pliers.

If you choose to use a 'sealant' to plug the outlet, ensure that the sealant is impervious to 1 N nitric acid; otherwise, sealant components might be leached and then deposited on the lumens of the capillary array. Screw the 5. Attach the 'clogged' capillary array to the block with the array knob and plastic ferrule. Ensure that the capillary tips are securely held inside a buffer reservoir used to store arrays; has a rubber gasket.

Set the 'wash block' on top of a ml stryofoam tube rack to create a stable surface the bolt projects out of the block. Attach the array to the 'array wash' system as described in How to create a manual 'array wash' system? Fill the 5. With one hand over the array-fill syringe, apply a steady, slow pressure to the polymer-reserve syringe so as to force fluid into the array-fill syringe.

If the plunger on the array-fill syringe does not rise on its own, give it a slight assist. Nevertheless, be patient! Just be patient! Choose whether to store or reinstall the array: Reinstallation : After disconnecting the array from the wash block, follow the instructions at How to reinstall a 'regenerated' array?

Storage : Nanopure water is an aggressive solvent; thus, it probably isn't a good solution for long-term storage. Press the tray button to bring the autosampler forward. Remove the buffer tray and the two water trays; place an empty tray in the buffer tray slot. Remove the polymer supply bottle and the anode buffer jar. Recovering polymer already on the instrument is not recommended and should be done only if absolutely necessary; even under the best of circumstances, you are likely to introduce contaminates present in the interconnect tube into your supply bottle and pump However, if you insist, then at least follow these instructions to minimize the chance of collecting contaminated polymer: Using the manual controls, discharge the 'dirty' polymer in the interconnect tube, and then dry the wedge as discussed in How to recapture POP-7 during Bubble Removals?

Place the supply bottle under the wedge. Caution : When action is complete, tap the valve pin to verify that the buffer valve is open, as the next command would burst the interconnect tube if the valve were closed. Select Move piston down and 38, counts — Send Command. Repeat this pair of commands see above until essentially all of the polymer has been discharged into the supply bottle Cap the supply bottle, spin down the polymer, and place the bottle in the refrigerator for storage.

Open the oven door and the detection cell block; then, carefully remove the array tip from the array port. If the array tip is stuck, it might be necessary to hold the array tip with a needle-nose pliers while unscrewing the capillary array knob; otherwise, the array tip might twist too far and snap one or more of the capillaries. With the tip removed from the pump block, clean any polymer from the array port, the array tip, the double-tapered ferrule, and the capillary array knob.

A Kimwipe wetted with nanopure water is ideal for this purpose. Reinstall the array and close the oven door. Water and old polymer will discharge into the removable tray below. When the operation is complete, dump the accumulated liquid into the appropriate hazardous waste container. Resubmit the commands to prewarm the oven, as the oven is just about to turn itself off or, already has.

Open instrument doors, and refill beaker with hot water; close the doors to return the autosampler to its operating position. Either wash the array manually or with a mouse-driven macro. If performing a manual wash: Open the 'Manual Control' window, and select Polymer delivery pump and Initialize polymer delivery pump — Send Command.

Select Fill cm capillary array — Send Command. Repeat 2X. This will move the piston to near the bottom of the chamber. For a mouse-driven macro, open the 'Manual Control' window, and set the command boxes to match the manner in which your macro was designed. Then, open the mouse-driven macro program. Start the macro for flushing the capillary array, with repeats. Note: Exceeding 65 repetitions may overfill the 'buffer' tray collecting the waste discharged by the capillaries.

This process will sometimes trigger a 'Leak Detected' error message; the message can be ignored until the wash is complete. At that time, it is necessary to restart the software, as clearing the error will not fully resolve the problem. Remove the buffer tray and discard the contents. Choose whether to refill the array with polymer or to dismount it for cleaning with nitric acid: Refill with polymer : Clean and refill the water and buffer trays, as well as the anode buffer jar.

Perform other maintenance as necessary. Use the wizard to 'Replenish Polymer', taking care to ensure that the supply bottle contains at least 2. Ideally, the fresh polymer will not have exceeded its expiration date; however, some leeway in this regard is possible as long as the polymer has been properly stored and the expiration date is not too far in the past!

To move polymer into the array, either manually fill the array see How to fill an array? Given that a spatial is needed at this point anyway, I prefer the latter option. Dismount array : manually, or by the Wizard. Wizard : Open the Wizard, and choose to 'store' the array. This will allow you to reinstall the array on that xl with the Wizard.

If you choose 'discard', the Oracle database will not allow reinstallion of the array with its correct serial number; however, it will allow you to install it as a 'new' array under a false serial number. Manually : Open the detection cell block, pull the pump block forward, and completely unscrew the capillary array knob. Snap the protective cover over the detection cell.

Pull out the array combs, unclip the cathode bar, and slip the array tip out of the array port. Seal the block with the amber screw plug, so as to minimize the introduction of bubbles into the system and to prevent the polymer from drying out. Cover the capillary pins with a gasketed buffer reservoir, and set the capillary array down in a safe place.

However, this Wizard was dropped from the XL and the xl sequencers; further, it is unclear whether nitric acid might damage the polymer delivery pump on the xl.

Further, note that a nitric acid wash is not listed as an approved ABI protocol for the xl; thus, the company might cite an "on-instrument" acid wash as the cause of any pump failure — regardless of whether or not nitric acid actually has the capacity to damage the pump.

Thus, we do not perform the nitric acid wash directly on the instrument; for further comments, see notes at end of this section. Finally, before embarking on a nitric acid wash, please note that we no longer routinely wash our arrays with nitric acid. Thus, we now perform a nitric acid wash only as a last resort to restore an array; usually, once an array has clogged that badly, even the nitric acid wash does not restore it.

Instructions : Second, it is best to perform the off-line array wash only after first flushing the array of polymer by a few water-washes on the instrument; otherwise, it is extremely easy to snap the glass syringe by applying too much pressure while trying to flush out the polymer manually.

Once the polymer has been removed, it is relatively easy to move either water or nitric acid through the array by hand. Now, if not already done, dismount the capillary array either with the Wizard or manually — see 'Dismount Array' in above section.

As described previously, the protective cover should be attached to the detection cell, the 'pins' should be secured inside the gasketed buffer reservoir, and the polymer block should be sealed with the amber plug. Then, attach the array to the nitric acid 'wash block' How to create a manual 'array wash' system?

Repeat this process as many times as desired. We usually flush the array with 5. Then, we immediately rinse the array with 5. However, for particularly dirty arrays, we may wait minutes before flushing the array with water — or, we may perform a second nitric acid wash and then immediately flush the array with another 5. Further Notes regarding On-Instrument Acid Washes : In response to periodic queries, I emphasize that I have never performed the nitric acid wash directly on the instrument because of the possibility that the acid might damage other parts of the instrument block, seals, etc.

My primary concern would be for the integrity of the two o-ring seals at the top of the pump; I do not know how that material would hold up to acids. As for the other parts of the system, I think that they would safely withstand a nitric acid wash assuming no leaks and if the nitric acid wash were immediately followed by water washes Frankly, for the most part, I no longer perform nitric acid washes at all.

For normal maintenance of the capillaries, I perform the on-instrument water washes. I perform a nitric acid wash ONLY as a last resort in an effort to recover an array that has not responded well to a water wash treatment. It takes time and patience, but it can be effective. The biggest issue aside, perhaps, from finding a source of the block or syringes is that one has to apply the pressure completely in line with the syringe no wobbling, twisting, or tilting and not force the plunger too hard Of course, you should wear glasses, gloves, and a lab coat while performing the nitric acid wash.

Overall, if I had to guess, I suspect that with certain precautions it would be safe to perform the acid wash directly on the instrument It would probably be necessary to still use 1 N nitric acid, as lower concentrations might eliminate the benefits of the nitric acid wash while not necessarily eliminating the potential detriments.

Of course, immediately after doing a nitric acid wash, the Entire system should be Thoroughly washed with purified water. In addition to the on-instrument water washes, remove the pump and thoroughly flush it manually with purified water; further, rinse the outside of the tubing and any other parts that might have contacted the acid. Nevertheless, to be perfectly clear, I would not recommend on-instrument acid washing of the capillary arrays; instead, I would perform only water-washes on the instrument and take the capillary array off the instrument to perform manual nitric acid washes.

Accretion of polymer and proteins is the slowest when the xl is processing samples constantly. By contrast, it occurs very rapidly when the instrument is idle for a few days in a row. Thus, if you have no samples to run, you should at least run a Spatial with fill to help slow the process. Ideally, you should also prewarm the oven to normal operating temperature prior to doing the spatial. Any savings in polymer that you might achieve by consolidating samples from successive days will be negated by reductions in the array's regeneration cycle.

Further, if you perform the recommended Spatial with fill instead of running the 'short' set of samples, there won't be any polymer savings either. Finally, proteins cannot accrete on the capillary lumens unless they are present as contaminants in the samples you are processing. To the extent it's practical, ensure that all users are taking appropriate steps to fully clean their samples, both with respect to DNA templates especially for cloned DNA and the final sequencing product.

The method of remounting a 'regenerated' array depends on: a how it was dismounted; and, b whether you are putting it back on the same xl or a different instrument. The "Install Array" option will lead you through the entire process; nevertheless, it will use a substantial amount of polymer in the process. With care, you may conserve some polymer by using the "Update Cap Array Info" option instead. Although the title implies that this Wizard applies only to updating information on the current array e.

Remounting requires that you use the Wizard. However, to remount it on the same xl, you must use a fake serial number, as the Oracle database has locked down the real serial number. The correct serial number should be used if you mount the regernated array on a different xl; further, you should manually input the actual 'Array Usage' value from the previous instrument so that the age of the array remains accurate.

Of course, there really is no reason to 'discard' the array in the first place, if you are planning to regenerate it. To remount it on the same xl, you input the the correct serial number, which will restore the previous 'Array Usage' value. If you mount the regernated array on a different xl; you should manually input the actual 'Array Usage' value from the previous instrument so that the age of the array remains accurate. If you mount the array on a different xl, you must use the Wizard and you should manually input the actual 'Array Usage' value from the previous instrument so that the age of the array remains accurate.

However, a manual dismount does not alter the Oracle database with respect to the serial number of the array 'on record' for the original instrument. Thus, the regenerated array can be remounted on the same xl without any need to use either Wizard. This process is detailed below: With the oven and instrument doors closed, press the Tray button.

Once the tray has stopped moving in its forward position , open both sets of doors. Snap the cathode bar of the array into position. Separate the array combs and put them into the holders on the oven panel except for the position closest to the detection cell block.

Move the pump block forward to ease access to the array port for the next step. Unclip the protective cover on the detection cell on the array; insert the array tip into the array port on the pump block; and, insert the final array comb in its holder. Move the pump block to its operating position; then, while holding the array tip firmly in place, tighten the array knob thoroughly.

Caution 1 : Take care to ensure that the detection cell ends up fitting flat against the detection cell block — without having to be forced to stay in the proper position and without being jammed against the left edge of the cell block. Caution 2 : It is critical that the knob be truly tight; if you undertighten the array knob, the high pressure of future capillary array fill operations might shove the array tip out of its normal position — deforming the array tip such that it is difficult or impossible to fully insert the tip into the array port.

Clear bubbles from the interconnect tube see How to remove bubbles from interconnect tube? Fill the capillary array with fresh polymer see How to fill an array? Typically, the pattern and approximate peak heights should resemble the spatials for the array prior to its being regenerated.

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