STLCC_CPLS Morrison 9/4/2015 Page 1

Genetic Analyzer: ABI

Maintenance,

Calibration, and Supplies

Prepared by: Bob Morrison

STLCC-CPLS, Instrumentation Specialist

Initiated: Sep 10, Last Update Sept 2015 (BAE)

ABI 3500 Genetic Analyzer

ABI @BRDG, R126B

Link to ABI 3500 User Manual…pdf (18mb)

Supplies

Jump to Spatial Cal: Maps array to camera

Jump to Spectral Cal: Dye/polymer/array changes

Jump to Performance Cal: Instrument vs. standards

Genetic Analyzer: ABI, Service Info

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Dear Valued Customer,

Thank you for your recent service request on your model 3500, serial number 22117-071. The reference number for your

service call is 404199796. If this is for an on-site service visit, please expect a call from your Field Engineer within 4 business

hours to schedule an appointment.

On your next call, "Ask for TAC first!".

Request TAC (Technical Assistance Center) for immediate advanced phone support from Life Technologies Certified Service

Engineers.

If the problem requires on-site support, a TAC specialist will work with your field service engineer to get you back on line.

To reach TAC, contact Instrument Services at 1-800-955-6288 Option 3 then option 1 or email

InstrumentServices@Lifetech.com with your Serial number, Contact information and the problem you are experiencing.

For your reference, your current Contract is valid from 10-27-2012 thru 10-26-2013. Please note that this only reflects current

coverage and does not include future contracts already purchased. If you have any Service Contract questions you may reach

Service Sales by email at Service.Sales@Lifetech.com or by phone at 800-955-6288 option 3 then Option 2 If you have already

purchased a future contract please disregard this notice.

Experience the new no-cost, no-hassle Instruments & Services Portal today at www.lifetechnologies.com/ISportal or ask your

Local Field Service Engineer about this exciting new tool for your lab.

Please contact us with any questions or concerns,

Thank you for doing business with Life Technologies,

Remote Services

phone: 1-800-955-6288 option 3 then option 1

fax: 760-930-2300

email: InstrumentServices@Lifetech.com

Genetic Analyzer: ABI: Maintenance, Daily/Before Each Use

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Genetic Analyzer: ABI: Maintenance, Weekly

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Genetic Analyzer: ABI: Maintenance, Monthly

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Genetic Analyzer: ABI: Maintenance, Quarterly, Annually

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Genetic Analyzer: Calibration Runs, Checklist

• From Dashboard, go to Maintenance Wizards

– Wash pump and channels

• Install Conditioning pouch, Wash 25 minutes

• Remove Conditioning pouch, seal with parafilm and return to Cold room

• Mount Polymer pouch, select “validate”

• Select Fill Array with Polymer, then Finish

• Proceed to Calibration Options (Spatial, Spectral) on next slides

• After Calibration, If ABI is not to be used immediately remove the polymer

pouch, store in Cold room, and install a Conditioning pouch.

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Genetic Analyzer: Spatial Calibration

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Do not open door

Spatial Calibration determines the position of the image from each capillary on the CCD array. (pg 99)

Spatial required

when:

1.Move or replace

cap array.

2. Open detector

door or move cell

3. Move or shake

instrument

Genetic Analyzer: Evaluate Spatial Calibration Results

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May Reject for

another try, Seeking

even peaks around

6K

Genetic Analyzer: Spectral Calibration, When required?

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Spectral calibration generates matrix for each capillary to compensate for dye overlap. Also used to

convert the 20 color data into 4,5,6 data.

Genetic Analyzer: Spectral Cal Notes

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• 09/04/2015, BAE – spectral calibration failed due to >1 bad capillary (#s 1/A & 5/E), but all

other caps passed criteria (#s 2-4, 6-8) – report saved in “D:\RUNS\MAINT

DOCUMENTATION\Spectral Report 20150730 good but failed due to more than 1 bad cap.pdf”

(note 7/30/15 datestamp – system date changed to allow expired buffers)

Genetic Analyzer: ABI, BigDye Spectral Cal Kit, PN 4404314

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1. Set 1.5ml block heater to 95C

2. Retrieve DS-33 Matrix Stand Std from Cold room, spin 15 sec at 3-6K RPMs in microcentrifuge

3. Resuspend 3uL of the Sequencing Install Standard (PN 4401459) with 297 uL of H-Di

Formamide (PN 4440753 or 4311320 from Cold Room)

4. Vortex thoroughly (max setting 15 sec), then Microcentrifuge 15 sec at 3-6K RPMs

5. Heat Standard at 95C for 5 minutes to denature, then chill on ice

6. Dispense 10 uL of denatured Standard mixture into 96-well ABI plate, wells A1-H1

7. Centrifuge plate with balance plate 1 minute at 3000 RPMs

8. Assemble plate and place on autosampler in ABI

Genetic Analyzer: Spectral Cal; Prepare Standard

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We are using “Z”

June 2011 per BB

Note: In Spectral Cal run, You do NOT have to define plate or link the plate to an Assay as in normal

runs. The plate definition is known and the layout of Standards is As shown here.

Capillary Number/Configuration: 8 7 6 5 4 3 2 1

Genetic Analyzer: Spectral Cal (only) Setup

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2. Select # Wells

3. Select Chemistry

4. Allow borrowing

5. Start-Run

Reads polymer RFID

3. Chemistry

Standard

-Select Sequencing

5. START RUN

4. Check Allow Borrowing,

one cap results and be

used for another

2. Select 96

Select A

Select “Z” dye set

Genetic Analyzer: Performance Check with Spectral Cal

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4. Check this box to Keep/save

Sequenced and Calibration Data

2. Select General Sequencing

1. Under Performance, Select Seq Install Standard

3. Select 96, and A position

Genetic Analyzer: ABI, History View at end of Cal Run

Observe Pass/Fail status of all rows

Genetic Analyzer: Spectral Cal; Evaluation Quality Value, Cond

Number

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Genetic Analyzer: Spectral Cal; Acceptance Criteria

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Genetic Analyzer: Spectral Cal; Evaluate Results

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Genetic Analyzer: ABI, Performance/Cal Sequence Results

Genetic Analyzer: ABI, Maintenance, Shutdown Procedures

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Remove polymer and put

on Conditioning Pouch

for shutdown

Genetic Analyzer: ABI; Reagents, Supplies, PNs

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BigDye® Terminator v3.1 Cycle Sequencing Kit

Part Number 4337455 Quantity/Package 100 rxn

Kit Contents :

800uL Tube of BigDye® Terminator v3.1 Ready Reaction Mix

Tube M13 (-21) Primer

Tube pGEM Control DNA

Two 1mL Tubes of 5x Sequencing Buffer. (PN 4336697)

BigDye XTerminator® Purification Kit - 2 mL (~100 - 20 µL

reactions) Part Number 4376486

BigDye XTerminator® Purification Kit is a DNA sequencing

reaction purification method that removes unincorporated

BigDye® terminators and salts that, if not removed, interfere with

sample injection and basecalling

Contents:

SAM solution: 9ml, PN 4376495

X Terminator Solution: 2ml, PN 4376492

Genetic Analyzer: ABI, Cap Array, Polymers, Polymer Cap

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Analyzer Capillary Array, 36 cm, PN 4404683 (Forensics)

Analyzer Capillary Array, 50 cm, PN 4404685 (Sequence and Fragment)

POP-7 (384 samples) Short to Long Read

Sequencing and Fragments

Performance Optimized Polymer

PN: 4393708

Pouch Cap for 3500

PN: 4412619

Cap Array

PN 4404685

Genetic Analyzer: ABI, Retainer, Base Set, Septas

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96-Well Septa for 3500/3500xL Genetic Analyzers PN 4412614 20 each

Septa Cathode Buffer Container, 3500 series PN 4410715 10 each

Standard Base PN 4410228 4 sets

96 ABI Prism Well Optical Reaction Plate with Barcode (code 128) PN 4306737 20 per pkg

Genetic Analyzer: ABI, Sequence Analysis Reagents

(pg 258 ABI 3500 user manual)

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Genetic Analyzer: ABI, Sequencing Standards

(pg 258 ABI 3500 user manual)

Genetic Analyzer: ABI, Fragment and HID Reagents

(pg 259 ABI 3500 user manual)

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Genetic Analyze: ABI, DS-33 Matrix Standard Kit

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Genetic Analazer: ABI, Pump Cleaning Kit, PN4414007

STLCC_CPLS_Morrison 9/4/2015 Page 29Hotlink to ABI Pump Cleaner Kit Protocol…. Pdf

If/when the Water Wash Wizard is ineffective in

cleaning the pump assembly, use this kit to clean the

entire system via several ports.

Genetic Analyzer: ABI 3500 Consumables