Thermo Fisher Scientific GeneAmp® In Situ PCR System 1000 Reference guide

Brand
Thermo Fisher Scientific
Model
GeneAmp® In Situ PCR System 1000
Type
Reference guide
GeneAmp® In Situ
PCR System 1000
Quick Reference Guide
© Copyright 2001, Applied Biosystems. All rights reserved. Printed in the United States of America.
Reproduction or publication of this document in any form or format is prohibited without written permission of Applied
Biosystems.
For Research Use Only. Not for use in diagnostic procedures.
APPLIED BIOSYSTEMS MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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GeneAmp is a registered trademark of Roche Molecular Systems, Inc., licensed to Applied Biosystems.
The GeneAmp PCR Process, Taq DNA Polymerase, and AmpliTaq DNA Polymerase are covered by U.S. patents issued and
pending owned by Roche Molecular Systems, Inc.
Registered trademarks, etc. used in this document, even when not specifically marked as such, are protected by law.
Part Number 0993-6007 Rev. B
1
There are three main functions of the software that you can access after you turn
on the GeneAmp In Situ PCR System 1000.
 #EEGUUC&GHCWNV(KNG
Access a default file to customize, store, or run a PCR file and method.
 #EEGUUVJG(KNG&KTGEVQT[
Review a directory of all or some of your PCR files.
 #EEGUUVJG%QPHKIWTCVKQPCPF&KCIPQUVKE(KNGU
Perform two configuration tasks and run six diagnostic tests.
(see pages 2,3)
Press then
press
then
press
SOAK FILE
STEP to edit file #1
(see pages 2,3)
Press then
press
then
press
TIME DELAY FILE
STEP to edit file #2
(see pages 2,4)
Press then
press
then
press
THERMO-CYCLE FILE
STEP to edit file #3
(see pages 2,5)
Press then
press
then
press
STEP-CYCLE FILE
STEP to edit file #4
(see page 6)
Press then
press
File Directory
ALL - BY TYPE
(see page 9)
Press then
press
Select Function
CONFIG-DIAGNOSTIC
2
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Soak File #1 Time Delay File #2
Soak files hold a single temperature until you
abort the run.
Time Delay files hold a single temperature for
a specified period of time.
Thermo-Cycle File #3 Step-Cycle File #4
Thermo-Cycle files contain programmed
thermal transitions and thermal plateaus for
PCR cycling. You can also select the Auto
Segment Extension feature.
Step-Cycle files contain programmed
thermal plateaus for PCR cycling. You can
also select the Auto Segment Extension
feature.
3
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SOAK FILE
STEP to edit file #1
This is the first display in the Soak file.
Press STEP to edit the first parameter.
Enter the desired soak temperature.
•
Press STEP to accept a default value and move to
the next display.
Or, to change a value and move to the next
display, use the numeric keys then press ENTER.
Soak temperature
(-5 to 100) 70°C
End of file
RUN-STORE-PRINT
Press NO to select one of the options, then ENTER.
Press STOP to return to the first display in the file.
TIME DELAY FILE
STEP to edit file #2
This is the first display in the Time Delay file.
Press STEP to edit the first parameter.
Enter the desired delay time and temperature.
•
Press STEP to accept a default value and move to
the next display or parameter.
Or, to change a value and move to the next
display or parameter, use the numeric keys then
press ENTER.
•
Press HELP to move to the previous parameter.
•
Press STOP to move to the last display in the file.
Delay Time
(0-999) 7min 0sec
Delay Temperature
(-5 to 100) 72°C
Beep while Delay
NO-YES
Choose YES to turn on a beeper, which will sound while
the file is running, by pressing NO, then ENTER. Or, press
ENTER to choose NO.
Link to stored file
(0-99,0=SHUT-OFF) 0
Enter the file number of the file you wish to link to in a
method, then ENTER, or press STEP to accept the
default link to shut off.
End of file
RUN-STORE-PRINT
Press NO to select one of the options, then ENTER.
Press STOP to return to the first display in the file.
{
{
4
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THERMO-CYCLE FILE
STEP to edit file #3
This is the first display in the Thermo-Cycle file.
Press STEP to edit the first parameter.
Enter the desired temperatures and times for Segments
#1, 2, 3, 4, 5, and 6. Odd-numbered segments are
thermal transitions and even-numbered segments are
thermal plateaus.
•
Press STEP to accept a default value and move to
the next display or parameter.
Or, to change a value and move to the next display
or parameter, use the numeric keys then press
ENTER.
•
Press HELP to move to the previous parameter.
•
Press STOP to move to the last display in the file.
Seg 1 Target Temp
(-5 to 100) 94°C
Seg 1 Segment Time
(0 to 999) 0min 1sec
Segment #7 is the terminating segment in the file and
must have a time of zero. The terminating segment
marks the end of one cycle.
•
Press STEP to accept a default value and move to
the next display or parameter.
Or, to change a value and move to the next display
or parameter, use the numeric keys then press
ENTER.
•
Press HELP to move to the previous parameter.
Seg 7 Target Temp
(-5 to 100) 0°C
Seg 7 Segment Time
(0 to 999) 0min 0sec
Choose YES to automatically extend any segment by
pressing NO, then ENTER. Then enter the number of the
segment you wish to extend (usually 6) and the
extension time per cycle in seconds.
Or, press ENTER to choose NO.
Auto Seg. Extension
NO-YES
Cycle Count
(1-99) 25
Enter the number of cycles you wish to run. Use the
numeric keys and ENTER to change the value or, press
STEP to accept the default value.
Link to stored file
(0-99,0=SHUT-OFF) 0
Enter the file number of the file you wish to link to in a
method, then ENTER, or press STEP to accept the default
link to shut off.
End of file
RUN-STORE-PRINT
Press NO to select one of the options, then ENTER.
Press STOP to return to the first display in the file.
{
{
5
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STEP-CYCLE FILE
STEP to edit file #4
This is the first display in the Step-Cycle file.
Press STEP to edit the first parameter.
Enter the desired temperatures and times for Segments
#1, 2, and 3, which are thermal plateaus.
•
Press STEP to accept a default value and move to
the next display or parameter.
Or, to change a value and move to the next display
or parameter, use the numeric keys then press
ENTER.
•
Press HELP to move to the previous parameter.
•
Press STOP to move to the last display in the file.
Seg 1 Target Temp
(-5 to 100) 94°C
Seg 1 Segment Time
(0 to 999) 1min 0sec
Segment #4 is the terminating segment in the file and
must have a time of zero. The terminating segment
marks the end of one cycle.
•
Press STEP to accept a default value and move to
the next display or parameter.
Or, to change a value and move to the next display
or parameter, use the numeric keys then press
ENTER.
•
Press HELP to move to the previous parameter.
Seg 4 Target Temp
(-5 to 100) 0°C
Seg 4 Segment Time
(0 to 999) 0min 0sec
Choose YES to automatically extend any segment by
pressing NO, then ENTER. Then enter the number of the
segment you wish to extend, and the extension time
per cycle in seconds. Or, press ENTER to choose NO.
Auto Seg. Extension
NO-YES
Cycle Count
(1-99) 25
Enter the number of cycles you wish to run. Use the
numeric keys and ENTER to change the value or, press
STEP to accept the default value.
Link to stored file
(0-99,0=SHUT-OFF) 0
Enter the file number of the file you wish to link to in a
method, then ENTER, or press STEP to accept the default
link to shut off.
End of file
RUN-STORE-PRINT
Press NO to select one of the options, then ENTER.
Press STOP to return to the first display in the file.
{
{
6
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Use these instructions to store your customized user files.
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Use the File Directory to view all or some of the stored files.
End of file
RUN-STORE-PRINT
When the last display in your customized file appears,
press NO to select the STORE option, then press ENTER.
Assign a one- or two-digit File Number (7 to 99) to your
customized file by using the numeric keys and ENTER.
•
Use this number for direct access to your customized
file anytime in the future. In this example, you would
press FILE, 7, then ENTER.
File Store
Enter File #7
Yes to store
File #7
Press YES to store your file. In this example, we assigned
File #7 to our customized file.
File Directory
ALL-BY TYPE
Press NO to select the kind of directory you wish to view,
then press ENTER.
{
This option lets you view all stored files
in numerical order (by file number).
This option lets you view all files of a specific type.
For example, all Soak files, all Time Delay files, etc.
7
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Use these instructions to run any file. You can run a file even if you haven’t stored it yet.
Run-Time Displays for Cycle Files
While a file is running, a display with information about the run appears. The following example
shows the run-time displays for a Thermo-Cycle and a Step-Cycle file run.
1. Access the desired file by pressing FILE,
the desired file number, then ENTER.
2. Press the START key.
3. If you have configured your instrument
for use with a printer, use the NO key to
select a print mode, then press ENTER.
4. The run begins.
or
1. From the last display in a file, press
ENTER when the cursor is positioned
under the RUN option.
2. If you have configured your instrument
for use with a printer, use the NO key to
select a print mode (OFF, CYCLE, or
SEGMENT), then press ENTER.
3. The run begins.
Smp= 94°C Time 0:15
End= 94°C Cycles=19
Seg# 1 Tot.Cyc.=20
LEN.= :40 File# 7
Current calculated
sample temperature
Time remaining
in current segmen
t
Press
to toggle
between the
two run-time
displays
Number of
Current Segment
Total number of
cycles in the file
Programmed target
temperature for
current segment
Cycles
remaining
Programmed total
hold time of
current segment
Current
file number
8
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A method is a series of files linked together in a specific sequence. To create a method:
*QYVQ4WPC/GVJQF
1. Edit or create the first file in the sequence.
Link this file to the file number of the second file in the sequence, using the “Link to Stored
File” parameter.
2. Store the file. Remember to assign the correct file number.
3. Edit or create the second file in the sequence.
Link this file to the file number of the third file in the sequence.
4. Edit or create the third file in the sequence.
Link the file to shut off (by selecting File 0 as the “Link to Stored File” parameter) if it is the
last file in the method, unless the last file in the method is a Soak file, in which case you will
have to manually abort the run.
5. Store the file. Remember to assign the correct file number.
STEP-CYCLE FILE
STEP to edit file #11
Link to stored file
(0-99,0=SHUT-OFF) 12
STEP-CYCLE FILE
STEP to edit file #12
Link to stored file
(0-99,0=SHUT-OFF) 13
SOAK FILE
STEP to edit file #13
User Abort
The method shown here on the right is typically used
for in situ PCR. In this example, File #11, a single-cycle,
one-temperature Step-Cycle file, is linked to File #12, a
20-cycle, two-temperature Step-Cycle file. This file, in
turn, is linked to File #13, a post-PCR cycle incubation
file. This Soak file will run indefinitely until you abort
it.
1. Run the first file in the method.
2. When that file has been run, the second file
in the method will run automatically.
3. When the second file has been run, the third
file in the method will run automatically.
4. When the last file in the method has been
run, temperature control will end and the
block temperature will drift to ambient.
Or, if the last file is a Soak file, the
temperature will be maintained at the
temperature programmed in the Soak file
until you manually abort the run.
9
6JG%QPHKIWTCVKQP(KNG
This file contains the two configuration parameters.
Select Function
CONFIG-DIAGNOSTIC
Press ENTER to access the Configuration file.
User Configuration
STEP to edit
Press STEP to edit the first configuration parameter.
The pause time-out limit is the time at which a manually
paused run will automatically abort.
•
Press STEP to accept a default value and move to
the next display.
Or, to change a value and move to the next display
or parameter, use the numeric keys then press
ENTER.
•
Press HELP to move to the previous display.
Pause Time-out limit
(9-999) 99sec
Printer Mode
OFF-ON
Press NO to select the ON option, then press ENTER to
configure your instrument for printer output.
Or, press STEP to select the OFF option if you are not
using a printer.
End of config. file
STEP to continue
Press STEP to re-edit the first configuration parameter.
Press STOP to exit the file.
{
10
6JG&KCIPQUVKE(KNG
This file contains six diagnostic tests.
Select Function
CONFIG-DIAGNOSTIC
Press NO to select DIAGNOSTIC, then press ENTER to
access the tests in the Diagnostic file.
Diagnostic Tests
Enter test # (1-6)
Use the numeric keys and ENTER to select the test you
wish to run:
Test #1 - Display/Keypad Test
Test #2 - Delete User Files (This test deletes ALL user files.)
Test #3 - Heater Test
Test #4 - Chiller Test
Test #5 - Overshoot Test
Test #6 - Undershoot Test
11
7UKPIVJG-G[RCF
To Do This Press This Key
Start a run from the first display in the file
View the next display or parameter in a file
Accept a default value or condition and
move to the next parameter in a file
While editing a file, view the previous display parameter
While running a file, toggle between the two
run-time displays
While editing a file, move to the last display in the file
Pause a run in progress
Abort a run in progress
Access a file (for example, File #4)
Access the File Directory
Access the Configuration and Diagnostic Files
Delete an individual file from the first display in that file
Enter numerical values
Erase numerical values not yet entered
Move the screen cursor forward through the
hyphenated list, then return to the first option again.
Accept a selection highlighted by the cursor, or
entered from the keypad.
to
6GEJPKECN5WRRQTVCPF1TFGTKPI+PHQTOCVKQP
PRODUCTS ARE NOT FOR USE IN DIAGNOSTIC PROCEDURES
N804-0001 GeneAmp®
In Situ
PCR System 1000, 120 V, 60 Hz
N804-0002 GeneAmp®
In Situ
PCR System 1000, 220–240 V, 50 Hz
N804-0003 GeneAmp®
In Situ
PCR System 1000, 100 V, 50/60 Hz
N804-0500 AmpliCover® Discs
N804-0501 AmpliCover® Clips
N804-0502
In Situ
PCR Glass Slides
N808-0197
In Situ
PCR Core Kit
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Printed in the USA, 12/2001
Part Number 0993-6007 Rev. B
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Thermo Fisher Scientific GeneAmp® In Situ PCR System 1000 Reference guide

Brand
Thermo Fisher Scientific
Model
GeneAmp® In Situ PCR System 1000
Type
Reference guide
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