ion pi ic 200 kit - thermo fisher scientific

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Ion PI IC 200 Kit Catalog Number 4488377 Pub. No. MAN0010079 Rev. C.0 Note: For safety and biohazard guidelines, refer to the “Safety” appendix in the Ion PI IC 200 Kit User Guide (Pub. no. MAN0010078). Read the Safety Data Sheets (SDSs) and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves. Workflow ...................................... 1 Interior hardware and consumables .................. 1 Create a Planned Run ............................. 1 Dilute the libraries ............................... 2 Prepare the libraries and consumables ................ 2 Prepare the chip for loading ....................... 2 Load the Ion Chef System ......................... 3 Start the run .................................... 5 Clean and initialize the Ion Proton Sequencer ......... 6 Unload and prepare the chips for sequencing .......... 6 Sequence the chip on the Ion Proton Sequencer ........ 7 Clean the instrument ............................. 8 Kit consumables and accessories .................... 9 Workflow Create a Planned Run within the Torrent Suite Software. q Dilute the library samples, prepare the Ion chips, and thaw the reagents. q Load the Ion Chef Instrument. q Start the Ion Chef Instrument. q Clean and initialize the Ion Proton Sequencer. q Unload the Ion Chef Instrument. q Sequence the Ion Chips. Interior hardware and consumables 2 4 1 8 7 3 6 5 9 1 New pipette tips 2 Automated heated cover 3 Thermal cycler sample block 4 Waste pipette tips 5 Reagents station 6 Solutions station 7 Chip-loading Centrifuge (buckets not shown) 8 Enrichment station 9 Recovery Centrifuges Create a Planned Run 1. Open the Torrent Browser for the Torrent Server connected to your Ion Chef System. 2. Select the Plan tab, click Templates, locate the application that you want to run (such as Whole Genome) then select either Plan New Run or Plan Run from the drop-down-list of the Settings tab to the right of an existing template you select from the template list. 3. In the Planned Run wizard, review each screen and edit as needed. In the Kits tab, select Ion Chef, select the Ion PI IC 200 Kit from the Template Kit drop-down list, select Ion PI IC 200 Seq Kit from the Sequencing Kit drop-down list, then enter or scan the barcodes of the Ion Chef Library Sample Tubes into the appropriate Sample Tube Label fields. 4. When you have completed your selections, click Plan Run at the bottom right of the Plan tab screen to save the run. The run is listed on the Planned Runs page under the name that you specified and is automatically used by the Ion Chef System when the associated sample is loaded and scanned. QUICK REFERENCE For Research Use Only. Not for use in diagnostic procedures.

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Ion PI™ IC 200 KitCatalog Number 4488377Pub. No. MAN0010079 Rev. C.0

Note: For safety and biohazard guidelines, refer to the “Safety”appendix in the Ion PI™ IC 200 Kit User Guide(Pub. no. MAN0010078). Read the Safety Data Sheets (SDSs) andfollow the handling instructions. Wear appropriate protectiveeyewear, clothing, and gloves.

■ Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

■ Interior hardware and consumables . . . . . . . . . . . . . . . . . . 1

■ Create a Planned Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

■ Dilute the libraries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

■ Prepare the libraries and consumables . . . . . . . . . . . . . . . . 2

■ Prepare the chip for loading . . . . . . . . . . . . . . . . . . . . . . . 2

■ Load the Ion Chef™ System . . . . . . . . . . . . . . . . . . . . . . . . . 3

■ Start the run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

■ Clean and initialize the Ion Proton™ Sequencer . . . . . . . . . 6

■ Unload and prepare the chips for sequencing . . . . . . . . . . 6

■ Sequence the chip on the Ion Proton™ Sequencer . . . . . . . . 7

■ Clean the instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

■ Kit consumables and accessories . . . . . . . . . . . . . . . . . . . . 9

Workflow

Create a Planned Run within the Torrent Suite™ Software.

q

Dilute the library samples, prepare the Ion chips, and thaw thereagents.

q

Load the Ion Chef™ Instrument.

q

Start the Ion Chef™ Instrument.

q

Clean and initialize the Ion Proton™ Sequencer.

q

Unload the Ion Chef™ Instrument.

q

Sequence the Ion Chips.

Interior hardware and consumables

2 41

87

3

6

5

9

1 New pipette tips2 Automated heated cover3 Thermal cycler sample block4 Waste pipette tips5 Reagents station6 Solutions station7 Chip-loading Centrifuge (buckets not shown)8 Enrichment station9 Recovery Centrifuges

Create a Planned Run

1. Open the Torrent Browser for the Torrent Server connectedto your Ion Chef™ System.

2. Select the Plan tab, click Templates, locate the applicationthat you want to run (such as Whole Genome) then selecteither Plan New Run or Plan Run from the drop-down-listof the Settings tab to the right of an existing template youselect from the template list.

3. In the Planned Run wizard, review each screen and edit asneeded. In the Kits tab, select Ion Chef, select the Ion PI™ IC200 Kit from the Template Kit drop-down list, select Ion PI™

IC 200 Seq Kit from the Sequencing Kit drop-down list,then enter or scan the barcodes of the Ion Chef™ LibrarySample Tubes into the appropriate Sample Tube Label fields.

4. When you have completed your selections, click Plan Run atthe bottom right of the Plan tab screen to save the run. Therun is listed on the Planned Runs page under the name thatyou specified and is automatically used by the Ion Chef™

System when the associated sample is loaded and scanned.

QUICK REFERENCE

For Research Use Only. Not for use in diagnostic procedures.

Dilute the libraries

Dilute the two (2) stock libraries with Nuclease-free Wateraccording to the following table. Prepare a fresh dilution of eachlibrary before use with the Ion Chef™ System, and use the librarydilutions within 48 hours.

Library Recommendedconcentration [1]

RNA-Seq 100 pM

TargetSeq™ Exome 50 pM

Ion AmpliSeq™ Exome 50 pM

Ion AmpliSeq™ Exome RDY 50–100 pM

Ion AmpliSeq™ ComprehensiveCancer Panel

70 pM

Human CEPH Control 200 library[2] Dilute 2 µL into 68 µLNuclease-free Water

[1] Recommendations are based on qPCR quantification. If libraries are quantified with a 2100 Bioanalyzer® instrument, a higher calculated concentration may need to be used for equivalent input.

[2] Obtained from the Ion PI™ Controls 200 Kit (Cat. no. 4488985).

Prepare the libraries and consumables

1. At least 45 minutes prior to use, unbox the Ion PI™ ICReagents 200 Cartridge and allow it to thaw at roomtemperature.

IMPORTANT! The IC Reagents 200 Cartridge must warm toroom temperature for at least 45 minutes before use.

2. Pipet 70 µL of each diluted library to the bottom of theappropriate Ion Chef™ Library Sample Tube (flagged tubes).

Note: If running the Human CEPH Control 200 Library fromthe Ion PI™ Controls Kit v2 (Cat. no. 4482414), prepare thecontrol library for use by diluting 2 µL of stock library into68 µL Nuclease-free Water.

3. Cap and store the two diluted DNA libraries on ice until youare ready to load them onto the Ion Chef™ Instrument.

4. Remove all cartridges and consumables from theirwrappings and boxes, then place them on the bench next tothe Ion Chef™ Instrument.

IMPORTANT! Prior to use, gently tap the IC Reagents 200and the IC Solutions 200 Cartridges on the bench to force thereagents to the bottoms of the tubes.

Prepare the chip for loading

IMPORTANT! Wear gloves for the following steps. The Ion PI™

Chip Preparation Solution is a skin irritant.

1. Label a new Ion PI™ v2 BC Chip to identify the experiment,then place the chip on a stable surface such as a benchtop.

Note: The shipped Ion Chip Priming Solution is concentratedand must be diluted 1:10 using Chip Priming Dilution Bufferbefore use.

Note: If the chip was not used to initialize the Ion Proton™

Sequencer, skip the next step.

2. If the chip was used to initialize the Ion Proton™ Sequencer,inject 100 µL isopropanol into the chip loading port, theninject 100 µL of Nuclease-free Water into the loading portand remove the expelled liquid from the opposite port.Repeat the water flush one more time and remove theexpelled liquid.

3. Attach an Ion Proton™ Chip Adapter to the chip exit well(located on the side of the chip with the notched corner,opposite the loading port; see figure below). Press firmly toensure the adapter is tightly engaged around the well.

4. Perform the chip wash:

a. Inject 200 µL of 100% isopropanol into the chip loadingport, then remove the expelled liquid from the exit wellfitted with the adapter.

b. Attach a P200 pipette tip to a vacuum line, insert thepipette tip into the chip loading port, and aspirate theisopropanol from the chip flow cell for 5–10 seconds.Inspect the chip to make sure it is dry.

Note: Make sure that the Ion PI™ Chip PreparationSolution has completely equilibrated to roomtemperature before proceeding to the next step.Immediately re-cap the solution tube after use toprevent evaporation and exposure to air.

c. Inject 100 µL of Ion PI™ Chip Preparation Solution intothe chip loading port, then remove the expelled liquidfrom the exit well.

Note: Be careful not to introduce bubbles in the chip. Ifbubbles appear, repeat this wash step.

d. Place the chip on the flat surface of an aluminum heatblock pre-heated to 50°C and incubate for 2 minutes.

e. Remove the chip from the heat block and place it on astable surface such as a benchtop.

f. Inject 200 µL of 100% isopropanol into the chip loadingport, then remove the expelled liquid from the exit well.Repeat the isopropanol flush one more time.

g. Inject 200 µL of Nuclease-free Water into the chiploading port, then remove the expelled liquid from theexit well.

h. Inject 200 µL of 0.1 M NaOH into the chip loading port,then remove the expelled liquid from the exit well.

2 Ion PI™ IC 200 Kit Quick Reference

i. Wait 1 minute, then inject 200 µL of Nuclease-freeWater into the chip loading port and remove theexpelled liquid from the exit well.

5. Repeat step 4 twice more, for a total of three chip washes.

6. Inject 200 µL of 1X Ion Chip Priming Solution into the chiploading port, then remove the expelled liquid from the exitwell.

7. Attach a P200 pipette tip to a vacuum line, insert the pipettetip into the chip loading port, and aspirate the remainingfluid from the chip flow cell for 5-10 seconds. Inspect thechip to make sure it is dry.

8. Remove the Ion Proton™ Chip Adapter from the chip.

(Optional) Store the prepared chip

The prepared chip can be stored for up to 24 hours before use. Tostore the chip:

Place the dry chip in its original anti-static blister pack and store itat room temperature in the dark (for example, in the box that thechip came in).

Load the Ion Chef™ System

IMPORTANT! Rated centrifuge speeds are only intended foroperation with provided buckets and approved consumable chips,tubes, and sample preparation reagents.

IMPORTANT! The Chip-loading Centrifuge is rated to operate atthe listed rotational frequencies with the chip buckets, chips, andadapters. The centrifuge must be load balanced. Proper care mustbe taken to load the bucket properly. If excessive vibrations arise,check to ensure that items are installed properly and rotors areequally balanced on each side.

Follow the procedure below to load the Ion Chef™ Instrument,where each step corresponds to a numbered area in the followingdiagram.

23

89

4

6

5

7

1. Open the instrument door:

a. In the instrument touchscreen, touch (Open Door)then wait for the latch to open.

b. Lift the instrument door to the top of the travel until thelatch mechanism engages.

2. Load an empty pipette tip rack to the Used (Waste) PipetteTip Position, then change gloves.

IMPORTANT! To prevent contamination, change glovesimmediately after moving the empty pipette tip rack to theUsed (Waste) Pipette Tip Position.

3. Load a Ion PI™ IC 200 Tip Cartridge to the New Pipette TipPosition:

a. Unwrap the Ion PI™ IC 200 Tip Cartridge and removethe cover to expose the pipette tips. Load two new IonChef™ IC Piercing Tips into tip positions G7 and H7 onthe Ion PI™ IC 200 Tip Cartridge (numbering thepositions from left to right and lettering from top tobottom).

Tip positions G7 and H7 Piercing tip

1

A

2 3 4 5 6 7 8 9 10 11 12

BCDEFGH

b. Pull the catch forward, then pivot the locking bracketupwards. Load the assembled Ion PI™ IC 200 TipCartridge into the New Pipette Tip Position, then pullthe bracket downwards to lock the cartridge in place.

3

New tip cartridge

Bracket

Catch

4. Load a new PCR plate into the thermal cycler sample block,then slide a new PCR Plate Seal underneath the automatedheated cover.

IMPORTANT! When the PCR Plate Seal is positionedcorrectly, its tabs project upward and contact the heatedcover.

Well A1

Cover

Keyed corner4

Ion PI™ IC 200 Kit Quick Reference 3

5. Load the Ion PI™ IC Reagents 200 Cartridge and dilutedlibraries into the Reagents station:

IMPORTANT! Thaw the IC Reagents 200 Cartridge at roomtemperature for 45 minutes prior to use.

a. Gently tap the Ion PI™ IC Reagents 200 Cartridge on thebench to force the reagents to the bottoms of the tubes.

b. Load the cartridge into the Reagents station so that itsnaps into place and is level on the deck.

IMPORTANT! Do not force the Ion Chef™ cartridgesinto place. Each cartridge fits only one location on thedeck and in one orientation. If a cartridge does not fit,confirm that you are loading the correct cartridge in thecorrect orientation.

5

IC Reagents Cartridge

c. Uncap and load the two Library Sample Tubes, eachcontaining 70 µL of diluted library, into Positions A andB on the IC Reagents 200 Cartridge.

IMPORTANT! Make sure to orient the sample tubes sothat the barcodes are visible and oriented to the right(see below).

IMPORTANT! Make sure to remove the caps to theLibrary Sample Tubes before proceeding.

d. Uncap both the tube of NaOH in Position C and theempty tube in Position D on the IC Reagents 200Cartridge.

D

A

B

C

00012647

00012216 Position A (DNA Library)

Position B (DNA Library)

Position C (NaOH)

Position D (Empty tube)

6. Load the Ion PI™ IC Solutions 200 Cartridge to the Solutionsstation:

a. Gently tap the Ion PI™ IC Solutions 200 Cartridge on thebench to force the reagents to the bottoms of the tubes.

b. Load the IC Solutions 200 Cartridge into the Solutionsstation until it snaps into place and is level on the deck.

6IC Solutions Cartridge

7. Load the consumables into the Recovery centrifuges:

a. Load six Recovery Tubes into each RecoveryCentrifuge.

IMPORTANT! Confirm that the Recovery Tubes areseated correctly within the centrifuge buckets. Thebuckets are keyed to ensure that the tubes fit in aspecific orientation.

7

Keyed position Tube

b. Place a Recovery Station Lid over each centrifuge.Orient the lids so that the ports are located as shown inthe figure below.

c. Close the lid of the Recovery Centrifuges. Confirm thatno ports are located in the positions facing the front ofthe instrument.

7a 7b 7c

No port

IMPORTANT! Do not obstruct or place any object ontop of the lid.

8. Load the Enrichment Cartridge, then press down on thecartridge to ensure that it is level with the instrument deck.

IMPORTANT! Confirm that the Enrichment Cartridge isloaded so that the lettering on the cartridge is right-side-up.

EnrichmentCartridge

Lettering

8

4 Ion PI™ IC 200 Kit Quick Reference

9. Load the Chip-loading Centrifuge:

a. Load each prepared chip into a centrifuge bucket, thenattach a Chip Adapter to the assembly.

Ports (align with chip)

Tabs

Slots

Keyed corner (align with bucket)

Chip adapter

Bucket

Ion chip

b. Load the adapter/chip/bucket assemblies into the Chip-loading Centrifuge.

Mounting grooves

Chip-loading centrifuge

9

c. Close the lid of the Chip-loading Centrifuge.

10. Confirm that all cartridges and reagents are installedcorrectly before continuing:

• Confirm that each cartridge is at the correct location andin the correct orientation.

• Press down on all cartridges to confirm that they arefirmly locked in place.

• Confirm that all tubes on the Ion PI™ IC Reagents 200Cartridge are uncapped and firmly locked in place.

• Confirm that the centrifuge lids are installed correctly sothat the ports are oriented toward the rear of theinstrument.

• Confirm that the tube and chip buckets are seatedsecurely within the rotor arms of the Chip-loading andRecovery Centrifuges, and that the consumables theycontain are correctly installed.

CAUTION! To ensure correct and safe instrumentoperation, you must confirm that all consumables areinstalled correctly to the deck before you start a run.The Ion Chef™ Instrument does not verify all aspectsof the consumable setup prior to beginning each run.

Start the run

1. Confirm that you have loaded the instrument with all kitsand consumables.

2. On the Ion Chef™ Instrument home touchscreen, touch Setup run.

3. Touch Step by Step to have the instrument lead you throughthe instrument setup, or touch Quick Start to skip theinstrument setup screens.

4. Follow the on-screen instructions. When prompted, close theinstrument door by first lifting it slightly to disengage thelocking mechanism, then push down on the door until thelocks engage. After the door closes, the instrument visionsystem activates.

IMPORTANT! Do not close the door by pulling it straightdown from the open position. You must lift the door slightlybefore you can close it. Confirm that both sides of the doorare locked after closing it.

Lift Lower Press down

5. When prompted, touch Start check to begin Deck Scan. Waitwhile the instrument scans the barcodes of all consumablesand reagents to confirm their presence and compatibility.

IMPORTANT! The Deck Scan function is not a substitute formanual inspection of the reagents and consumables on theIon Chef™ Instrument prior to starting a run. To ensureproper and safe instrument operation, confirm that allconsumables are installed correctly before you continue.

6. When Deck Scan is complete, touch Next to display the DataDestination screen.

7. Confirm that the instrument displays the correct kit name,chip types, chip barcodes, and Planned Run. If the correctPlanned Runs do not display, touch the drop-down menu to select the Planned Run for each chip, then touch Next.

IMPORTANT! If the kit name and chip type are incorrect,confirm that you are using the correct kit and chip. If you areusing the correct kit and chip, contact Technical Support.

8. On the Run Options screen, touch the appropriate option tocomplete the run and enter the desired time of runcompletion, if necessary.

9. On the Run Options screen, touch Start run to begin the run.

Ion PI™ IC 200 Kit Quick Reference 5

10. Clean and initialize the Ion Proton™ Sequencerapproximately 1.5 hours before the Ion Chef™ System finisheschip loading.

11. If you chose to pause the run to analyze the templatingefficiency, remove the samples for testing when prompted todo so by the Ion Chef™ Instrument (approximately 12.2 hoursafter the start of the run).

a. When prompted to remove the QC sample, open theinstrument door.

b. Transfer the unenriched QC samples (entire volume)from Positions A and B of the Ion PI™ IC Reagents 200Cartridge on the instrument deck to two new labeledmicrocentrifuge tubes.

c. Analyze the QC samples.

d. Close the instrument door, then touch Continue tocomplete the run.

12. When the run is complete, unload the Ion Chef™ Instrumentand sequence the chips immediately.

Note: If you are performing quality assessment of enrichedsamples, transfer QC samples from positions A and E of theEnrichment Cartridge to two new labeled microcentrifugetubes. Refer to Appendix B, "Supplementary procedures", ofthe Ion PI™ IC 200 Kit User Guide (Pub. no. MAN0010078) formore information.

Clean and initialize the Ion Proton™ SequencerAt least one hour before the completion of the Ion Chef™

Instrument run, clean, and initialize the Ion Proton™ Sequencer asdescribed in the Ion PI™ IC 200 Kit User Guide (Pub. no.MAN0010078).

IMPORTANT! Use only the specified materials and follow theprotocols found in this document. The Ion Proton™ Sequencercleaning and initialization procedures described here are similar tothat of other Ion sequencing kits, but the materials and protocolsare not identical. Do not substitute reagents from other kits.

Unload and prepare the chips for sequencing

1. Open the instrument door:

a. In the instrument touchscreen, touch (Open Door)then wait for the latch to open.

b. Lift the instrument door to the top of the travel until thelatch mechanism engages.

2. Open the lid of the Chip-loading Centrifuge, then unloadboth chip/bucket assemblies from the Ion Chef™ Instrument.

Remove

To unload each chip:

a. Remove the chip/bucket assembly from the Chip-loading Centrifuge.

b. Apply pressure to both ends of the Chip Adapter, thenremove and discard it.

c. Grasp the chip by its edges, carefully lift the chip out ofthe bucket and set it aside on a clean, static-free surface,then return the bucket to the Chip-loading Centrifuge.

Press and remove adapter

Remove carefully

Chip adapter

Bucket

Ion chip

3. Close the instrument door by first lifting it slightly todisengage the locking mechanism, then push down on thedoor until the locks engage.

IMPORTANT! Do not close the door by pulling it straightdown from the open position. You must lift the door slightlybefore you can close it. Confirm that both sides of the doorare locked after closing it.

4. Load one or both chips into Ion Proton™ Sequencers andpromptly begin the sequencing runs.

If you cannot sequence a loaded chip immediately, place thechip into a separate chip storage container and store at +4°Cuntil you are ready to sequence it (up to 6 hours maximum).

IMPORTANT! If you choose to store a loaded chip, removethe chip from the container and place it on a clean surface inthe dark to warm to room temperature at least 20 minutesbefore you intend to run it.

6 Ion PI™ IC 200 Kit Quick Reference

Sequence the chip on the Ion Proton™ Sequencer

IMPORTANT! Observe the following when sequencing the chips:

· The Ion Proton™ Sequencer must be cleaned and initializedbefore sequencing the chips.

· Empty the waste container before you begin the sequencing run.· Do not use reagents from other sequencing kits for sequencing

chips prepared by the Ion Chef™ System.· To avoid damage due to electrostatic discharge (ESD), do not

place the chip directly on the bench or any other surface.Always place the chip either on the Ion Proton™ Sequencergrounding plate or in the custom Ion centrifuge adapter/rotorbucket.

· To avoid ESD damage, do not wear gloves when transferringchips to and from the instrument.

Sequence the loaded chips on the Ion Proton™ Sequencer as soonas possible after unloading the Ion Chef™ Instrument. If not, storethem under the recommended conditions.

IMPORTANT! Do not start the sequencing run with the loadedchip. Use a used chip for the line cleaning at the start of the run.

1. With the used chip from initialization still in the chip clamp,press Run on the Main Menu, then touch Next and confirmthat "Cleaning fluid lines" displays on the instrumenttouchscreen. Observe the chip for leaks. The Run Setupscreen automatically populates the fields when the IonProton™ Sequencer connects to the server.

2. Follow the on-screen instructions to empty the waste bottle,load the cleaning chip, and clean the fluid lines of the IonProton™ Sequencer. After line cleaning, touch Next.

3. When prompted, enter or scan the barcode of the chip thatyou intend to sequence, then touch Next.

4. Confirm that the pre-populated settings are correct or makechanges using the buttons and drop-down lists if necessary.

5. Load the chip as follows:

a. Pull the metal tab forward to release the chip clamp.

IMPORTANT! Do not wear gloves when transferringthe chips on and off the instrument.

b. Remove the chip currently in the clamp.

c. Place the chip to be sequenced in the chip clamp withthe chip notch in the bottom-front corner.

IMPORTANT! Do not force the chip into the clamp. Ifthe chip does not fit easily in the clamp, confirm thatthe notch is oriented as shown below.

d. Push the metal tab back until it clicks to engage theclamp.

e. Touch Next to perform the calibration.

The system calibrates the chip (~1 minute), then begins thesequencing run.

IMPORTANT! During a run, do not open the chipcompartment lid or reagent compartment door, and avoidtouching the instrument. Touching the instrument during thesequencing run may reduce the quality of the measurements.

6. If you will be sequencing a loaded chip that you have stored,remove the stored chip from the chip container in therefrigerator twenty (20) minutes before the end of the firstrun, and place it on a clean surface in the dark to warm toroom temperature.

Ion PI™ IC 200 Kit Quick Reference 7

7. When the first run is complete, empty the waste container,then sequence the remaining chip as soon as possible.

IMPORTANT! After the first sequencing run is complete:

· Empty the waste container before you begin the nextsequencing run.

· Leave the first chip in the instrument while you initiatethe second run. Load the second chip when prompted.

When the run is complete, the touchscreen returns to the MainMenu. Use the Torrent Suite Browser to review the results.

Clean the instrument

IMPORTANT! Clean the Ion Chef™ Instrument as described belowafter every run. To prevent contamination, do not operate theinstrument unless it has been recently cleaned.

1. Open the instrument door:

a. In the instrument touchscreen, touch (Open Door)then wait for the latch to open.

b. Lift the instrument door to the top of the travel until thelatch mechanism engages.

2. Remove and dispose of any used consumables from theinstrument.

bc

gf

a

e

d

h

a. Remove and discard the PCR plate from the PCRsample block.

b. Remove and discard the box of used pipette tips fromthe waste tip position.

IMPORTANT! Do not reuse the waste pipette tip rack.Always move the empty Tip Cartridge from the new tipposition to the waste tip position.

c. Move the empty Tip Cartridge to the waste tip position.

IMPORTANT! Do not discard the empty Tip Cartridge.

d. Remove and discard the Ion PI™ IC Reagents 200Cartridge.

IMPORTANT! Make sure to transfer the QC samplesbefore you remove and discard the IC Reagents 200Cartridge.

e. Remove and discard the Ion PI™ IC Solutions 200Cartridge.

f. Close the lid of the Chip-loading Centrifuge.

g. Remove and discard the Enrichment Cartridge.

h. Remove and discard the consumables from theRecovery Centrifuges, including the:

• Recovery Station Lids

• Recovery Tubes

3. Inspect the Recovery Centrifuge for residue. If excessiveliquid is present, clean the centrifuge bowl and buckets asdescribed in the Ion PI™ IC 200 Kit User Guide(Pub. no. MAN0010078). Close the Recovery Centrifuge lid.

IMPORTANT! Clean the Recovery Centrifuge occasionally,only when excess liquid is noticeable in the bowl and/orbuckets. You do not need to clean the centrifuge after everyrun.

4. Close the instrument door by first lifting it slightly todisengage the locking mechanism, then pushing down on thedoor until the locks engage.

5. From the Ion Chef™ Instrument touchscreen, begin thecleaning:

a. On the screen that appears after run completion, touchNext.

Note: You may also clean the instrument at any timestarting from the home touchscreen. Touch Settings,then touch Clean Ion Chef.

b. Confirm that you have removed all consumables fromthe Ion Chef™ Instrument, except for the empty TipCartridge in the waste tip position, then touch Next.

c. With the door closed, touch Start. The instrumentperforms a load check before starting the cleaningroutine. The Ion Chef™ Instrument stops ventilation andilluminates the ultraviolet (UV) light within theinstrument.

CAUTION! The Ion Chef™ Instrument emitsUV light at 254 nm. Wear appropriate eye wear,protective clothing, and gloves when workingnear the instrument. Do not look directly at theUV light while it is illuminated during thecleaning routine.

8 Ion PI™ IC 200 Kit Quick Reference

Kit consumables and accessories

Description Catalog orPart no.

Ion PI™ IC 200 Kit, 8-reactions 4488377

Ion Chef™ Installation Kit 4488374

Ion PI™ Controls 200 Kit 4488985

Ion PI™ Chip Kit v2 BC, 8-pack 4484270

The information in this guide is subject to change without notice.

DISCLAIMER

TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, ORCONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

©2015 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Bioanalyzer istrademark of Agilent Technologies, Inc.

For support visit lifetechnologies.com/support or email [email protected]

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6 April 2015