Bio-Rad S1000 Instruction Manual

S1000™ Thermal Cycler

Instruction Manual

Catalog # 184-2000 # 185-2096 # 185-2048 # 185-2384

Windows XP and Windows Vista are trademarks of Microsoft Corporation.

LICENSE NOTICE TO PURCHASER

Purchase of this instrument conveys a limited non-transferable immunity from suit for the purchaser’s own internal research and development and for use in applied fields under one or more of U.S. Patents Nos. 5,656,493, 5,333,675, 5,475,610 (claims 1, 44, 158, 160-163 and 167 only), and 6,703,236 (claims 1-7 only), or corresponding claims in their non-U.S. counterparts, owned by Applera Corporation. No right is conveyed expressly, by implication or by estoppel under any other patent claim, such as claims to apparatus, reagents, kits, or methods such as 5’ nuclease methods. Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.

Bio-Rad’s thermal cyclers and real-time thermal cyclers are covered by one or more of the following U.S. patents or their foreign counterparts owned by Eppendorf AG: U.S. Patent Nos. 6,767,512 and 7,074,367.

Hard-Shell PCR plates are covered by one or more of the following U.S. patents or their foreign counterparts owned by Eppendorf AG: U.S. Patent Nos. 7,347,977, 6,340,589, 6,528,302.

Bio-Rad Laboratories Resources

Table 1 lists Bio-Rad resources and how to locate what you need.

Table 1. Bio-Rad resources

Resource How to Contact

Local Bio-Rad Laboratories representatives

Technical notes and literature Go to the Bio-Rad Laboratories web site (www.bio-

Technical specialists Bio-Rad Laboratories provides quality technical support.

Find local information and contacts on the Bio-Rad Laboratories web site by selecting your country on the home page (www.bio-rad.com). Find the nearest international office listed on the back of this manual

rad.com). Type a term in the Search box and select Literature to find links to technical notes, manuals, and other literature

We staff our Technical Support department with experienced scientists to provide our customers with practical and expert solutions

To find local technical support on the phone, contact your nearest Bio-Rad Laboratories office. For technical support in the United States and Canada, call 1-800-424-6723 (toll-free phone), and select the technical support option

S1000 Thermal Cycler Manual

Warranty

The S1000 thermal cycler and associated accessories are covered by a standard Bio-Rad warranty. Contact your local Bio-Rad Laboratories office for the details of the warranty.

Writing Conventions Used In This Manual

This manual provides instructions on how to safely set up and operate the S1000 thermal cycler and uses the writing conventions shown in Table 2 to quickly provide relevant information.

Table 2. Manual conventions

Convention Meaning

TIP: Provides helpful instructions, including information explained in

further detail elsewhere in this manual

NOTE: Provides important information, including information explained in

further detail elsewhere in this manual

WARNING! Explains crucial information about a topic that may lead to injury

to the user, instrument damage, or data loss

Screen message Indicates the one or more words on the screen the user should

select

iii

Safety and Regulatory Compliance

Table 2. Manual conventions (continued)

Convention Meaning

NAME of control panel

key

Select X Select X using the arrow keys. For example, select NEW means

Select X > Y From menu X, select Y. For example, select MAIN

Press X Press the X key on the control panel. For example, press ENTER

Indicates a key on the thermal cycler control panel. For example, these keys have the following names:

•The ENTER key is

•The right arrow key is

use the arrow keys to select the NEW option on the screen

means select the RUN option in the MAIN menu

means press the ENTER key on the control panel

Safety and Regulatory Compliance

RUN

The S1000 thermal cycler heats and cools very quickly during operation. We strongly recommend that you follow the safety specifications listed in this section and throughout this manual.

Safety Warning Labels

Warning labels posted on the instrument and in this manual warn you about sources of injury or harm. Refer to Table 3 to review the meaning of each safety warning label.

Table 3. Instrument safety warning labels

Icon Meaning

CAUTION: Risk of danger! This symbol identifies components that pose a risk of

personal injury or damage to the instrument if improperly handled. Wherever this symbol appears, consult the manual for further information before proceeding

CAUTION: Risk of electrical shock! This symbol identifies components that pose a risk of electrical shock if improperly handled

CAUTION: Hot surface! This symbol identifies components that pose a risk of personal injury due to excessive heat if improperly handled

S1000 Thermal Cycler Manual

Instrument Safety Warnings

The following warning labels display on the instrument, and refer directly to the safe use of this S1000 thermal cycler (Table 4).

Table 4. Instrument safety warning labels

Icon Meaning

Warning about risk of harm to body or equipment.

Operating the S1000 thermal cycler before reading this manual can constitute a personal injury hazard. Only qualified laboratory personnel should operate this instrument

Warning about risk of harm to body or equipment from electrical shock.

Do not attempt to repair or remove the outer case of this thermal cycler base, power supply, heat pump, or other accessories. If you open these instruments, you put yourself at risk for electrical shock and void your warranty. All repairs must be done by an authorized repair service

Never remove the outer case of a thermal cycler base. This may cause you to receive an electrical shock.

This thermal cycler uses neutral fusing, which means that live power could still be exposed inside the instrument even when the fuse is blown or removed

Warning about risk of burning. A thermal cycler generates enough heat to cause serious burns. Wear safety goggles or other eye protection at all times during operation. Always allow the sample block to return to idle temperature before opening the lid and removing samples. Always allow maximum clearance to avoid accidental skin burns

Warning about risk of explosion. The sample blocks can become hot enough during the course of normal operation to cause liquids to boil and explode

Safety and Regulatory Compliance

This instrument has been tested and found to be in compliance with all applicable requirements of the following safety and electromagnetic standards (Table 5).

Table 5. Safe use specifications

Safe User Requirements Specifications

Input power Rated 100–240 Vac, 50–60 Hz

Fuses 250 V, 10 A

Temperature Indoor use Ambient temperature of 15–31°C. Relative

humidity maximum of 80% (noncondensing)

Altitude Up to 2,000 meters above sea level

Overvoltage Categories

Pollution degree 2

Safety and Regulatory Compliance

SAFETY COMPLIANCE

This instrument has been tested and found to be in compliance with all applicable requirements of the following safety and electromagnetic standards:

• UL Std No. 61010A-1 Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements

• UL Std No. 61010A-2-010 Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements

• CAN/CSA C22.2 No. 1010.1-92 - Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements (includes Amendment 1)

• CAN/CSA C22.2 No. 1010.1B-97 - Amendment 2 CAN/CSA C22.2 No. 1010.1-92

- Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements

• CAN/CSA C22.2 No. 1010.2.010A-97 - Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements for Laboratory Equipment for the Heating of Materials, Amendment No. 1

• IEC 61010-1 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements

• IEC 61010-1 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory use, Part 2: Particular Requirements for Laboratory Equipment for the Heating of Materials

ELECTROMAGNETIC COMPATIBILITY (EMC)

• FCC Title 47 Part 15B as a Class A digital device

• EN61326 Class A Electrical Equipment for measurement, control, and laboratory use

- EMC Requirements

FCC WARNINGS AND NOTES

•Warning. Changes or modifications to this unit, not expressly approved by the party

responsible for compliance, could void the user’s authority to operate the equipment

•Note. This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference, at his own expense

• Note regarding FCC compliance. Although this design of instrument has been tested and found to comply with Part 15, Subpart B of the FCC Rules for a Class A digital device, please note that this compliance is voluntary, for the instrument qualifies as an “exempted device” under 47 CFR 15.103(c), in regard to the cited FCC regulations in effect at the time of manufacture

• Note regarding Canadian EMC compliance: Le present appareil numerique n’emet pas de bruits radioelectrique depassant les limites applicables aux appareils numeriques de class A prescrites dans le reglement sur le brouillage radioelectrique edicte par le Ministere des Communications du Canada

•Cables. Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits

• Use only Bio-Rad USB cable (catalog #184-8000) when using any 1000-series cycler

Bio-Rad Laboratories Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Writing Conventions Used In This Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii

Safety and Regulatory Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv

S1000 Thermal Cycler Manual

Chapter 1. Introduction to the S1000™ Thermal Cycler . . . . . . . . . . . . . . . 1

System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Reaction Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Setting Up the S1000 Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Operating the Reaction Module Lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 2. Creating and Editing Protocols . . . . . . . . . . . . . . . . . . . . . . . . 11

Protocol Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Creating a New Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Parameters for Temperature or Gradient Steps . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Editing an Existing Protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Sample Volume and Lid Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Chapter 3. Running Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Preparing to Run a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Monitoring the Protocol Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Pausing and Resuming a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Skipping a Step During the Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Canceling a Run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Incubating Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Chapter 4. Managing Protocol Files and Folders . . . . . . . . . . . . . . . . . . . 39

Managing Protocol Files and Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

vii

Chapter 5. Optimizing PCR on the S1000 Thermal Cycler . . . . . . . . . . . . 47

Optimizing a Protocol for Faster PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Optimizing Annealing Temperature Steps with a Gradient . . . . . . . . . . . . . . . . . . 49

Optimizing PCR With Small Sample Volumes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Transferring Protocols from Another Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . 50

Troubleshooting PCR Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Selecting Compatible Reaction Vessels and Sealing Options . . . . . . . . . . . . . . . 51

Chapter 6. Advanced Tools and Functions . . . . . . . . . . . . . . . . . . . . . . . . 53

TOOLS Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Controlling S1000 Thermal Cyclers with a C1000 Thermal Cycler . . . . . . . . . . . . 61

Chapter 7. Maintenance and Troubleshooting . . . . . . . . . . . . . . . . . . . . . 63

Cleaning and Maintaining the S1000 Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . 63

Maintaining Sufficient Air Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Troubleshooting Error Messages on the S1000 Cycler . . . . . . . . . . . . . . . . . . . . . 66

Appendix A: Preinstalled Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Standard Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Touchdown Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Optimized Protocol Using iTaq™ Polymerase . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Optimized Protocols Using iProof™ Polymerase . . . . . . . . . . . . . . . . . . . . . . . . . 73

Optimized Protocol Using the iScript™ Reverse Transcriptase . . . . . . . . . . . . . . 74

Nested Primer Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Appendix B: Ordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Components of Bio-Rad’s 1000-Series Thermal Cyclers . . . . . . . . . . . . . . . . . . . 77

Accessories for the 1000-Series Thermal Cyclers. . . . . . . . . . . . . . . . . . . . . . . . . 78

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

viii

S1000 Thermal Cycler Manual

1 Introduction to the S1000™

Thermal Cycler

Read this chapter for information on setting up the S1000 thermal cycler.

• System overview (below)

• Reaction modules (page 3)

• Setting up the S1000 thermal cycler (page 5)

• Operating the reaction module lid (page 7)

System Overview

The S1000 thermal cycler base (Figure 1) includes:

• Reaction module bay – holds the inserted reaction module

• Reaction module locking bar – locks the inserted module in place

• Control panel – provides access to all the functions needed to create and run PCR protocols

• Air vents – allow the thermal cycler to heat and cool quickly

Module locking bar

The back panel of the S1000 thermal cycler includes data ports (Figure 2).

• USB B port — connects the S1000 thermal cycler to a C1000™ thermal cycler

• USB A ports — currently inactive

Reaction module bay

Control panel

Air vents

Figure 1. Frontal view of the S1000 thermal cycler.

System Overview

• Test port — for service testing only

The control panel on the S1000 thermal cycler provides access to all the functions needed to run the thermal cycler and includes the following components:

• Liquid crystal display (LCD) — displays the main menu and other screens

• Command, numeric, and navigation keys — use these keys to enter commands,

The main screen is displayed after booting is complete. Figure 3 shows the components of the control panel.

USB B port

Power switch

Power

input

Fuses

Cooling vents

Figure 2. Back panel of the S1000 thermal cycler.

numbers, or letters, and navigate various screens

Numeric and

LCD

command keys

Test port

USB A ports

Main menu

options

Navigation keys

Screen

key

Figure 3. Components of the control panel on the S1000 thermal cycler.

Function of the Control Panel Keys

The control panel of the S1000 thermal cycler contains five sets of keys with the functions listed in Table 6.

Table 6. Function of keys on control panel

Key Function Additional Notes

Numeric and Command Keys

1 through 9 Enter numbers

0, INCUBATE Inserts a zero or infinity, or starts

instant incubation

S1000 Thermal Cycler Manual

Table 6. Function of keys on control panel (continued)

Key Function Additional Notes

CANCEL (–) Enters a minus sign or cancels a

function

PAUSE (

SCREEN key

Navigation Keys

Right arrow Moves the cursor to the right

Left arrow Moves the cursor to the left

Up arrow Moves the cursor up Press the up arrow key to scroll

Down arrow Moves the cursor down Press the down arrow key to scroll

ENTER Confirms a selection

) Enters a decimal point or pauses

a protocol

Toggles between screens for alternative views

Press this key to delete an entry, cancel a function, stop a protocol, end an incubation, or delete text on the screen

Press this key to view the status of a run

from A to Z on the screen. For example, press the up key three times to select the letter C

from Z to A on the screen. For example, press the down key eight times to select the letter S

Reaction Modules

The S1000 thermal cycler is compatible with any 1000-series reaction module. The reaction modules come in three block sizes: the 96-, dual 48-, or 384-well block. Each block in the reaction module includes a fully adjustable heated lid that is capable of running reliably with a broad range of reaction vessels.

Recommended Sample Volume

When using the S1000 thermal cycler, the maximum sample volume is determined by the type of reaction module used. -well reaction module is used. Table 7 lists the recommended sample volume, as well as the maximum sample volume to be used with different reaction modules.

Table 7. Size and volume limit for the 1000-series reaction modules

Number of Wells

Dual 48/48 2 10–50 µl (50 µl limit)

96 1 10–50 µl (50 µl limit)

384 1 3–30 µl (30 µl limit)

Number of Blocks

Recommended Sample Volume (Upper Limit)

Reaction Modules

Specifications of Reaction Modules

Specifications for each 1000-series reaction module are listed in Table 8.

Table 8. Reaction module specifications

Feature 96-Well Fast Dual 48/48 Fast 384-Well

Sample capacity 96 x 0.2 ml tubes 2 x 48 x 0.2 ml tubes 1 x 384-well PCR

Gradient direction Back (upper

Gradient temperature range

Gradient temperature differential

Gradient accuracy ±0.2°C of

Gradient (end row) uniformity

Gradient calculator accuracy

Heated lid temperature 0–110°C 0–110°C 0–110°C

Average ramp rate 3.3°C/sec 3.0°C/sec 2.0°C/sec

Maximum ramp rate 5.0°C 4.0°C 2.5°C

Temperature range 0–100°C 0–100°C 0–100°C

Temperature accuracy ±0.2°C of

Temperature uniformity ±0.4°C well-to-well

microplate

Back (upper temperature) to front (lower temperature) of block

30–100°C 30–100°C 30–100°C

1–24°C 1–24°C 1–24°C

programmed temperature at end rows

±0.4°C well-to-well (within row) within 10 sec of arrival at target temperature

±0.4°C of the actual well temperature

programmed target at 90°C

within 10 sec of arrival at 90°C

temperature) to front

(lower temperature)

of block

±0.2°C of

programmed

temperature at end

rows

±0.4°C well-to-well

(within row) within 10

sec of arrival at

target temperature

±0.4°C of the actual

well temperature

±0.2°C of

programmed target

at 90°C

±0.4°C well-to-well

within 10 sec of

arrival at 90°C

Back (upper temperature) to front (lower temperature) of block

±0.2°C of programmed temperature at end rows

±0.4°C well-to-well (within row) within 10 sec of arrival at target temperature

±0.4°C of the actual well temperature

±0.2°C of programmed target at 90°C

±0.4°C well-to-well within 10 sec of arrival at 90°C

Each reaction module contains cooling fins for fast heating and cooling and a fully adjustable, heated lid. Figure 4 shows the lid and cooling fins for the 96-well reaction module.

• Heated inner lid — adjusts the lid temperature to prevent condensation and evaporation

• Sample/reaction block — holds reaction vessels, including tubes and microplates

S1000 Thermal Cycler Manual

Lid

Cooling fins

Figure 4. The lid and cooling fins of a 96-well reaction module.

The top of a reaction module lid includes a lid lever, lid force knob, and status LED (Figure 5).

• Lid lever — opens and closes the lid

• Lid force knob — sets lid force and seals the reaction

• Status LED — turns on to indicate that the block is selected or running

Lid force knob

Lid lever

Figure 5. A top view of a reaction module.

Setting Up the S1000 Thermal Cycler

The S1000 thermal cycler package includes:

• S1000 thermal cycler base

• Power cord

• Consumables selection guide

• Instruction manual

• Quick guide for system installation

Reaction modules for use with the S1000 thermal cycler are shipped in separate packaging.

Remove all packaging materials and store them for future use. If any item is missing or damaged, contact your local Bio-Rad office.

Place the S1000 thermal cycler base on a flat, dry surface with sufficient cool airflow to run properly. The instrument can run in two modes: stand-alone or software-controlled. When running the system under software-controlled mode, make sure there is sufficient space for a computer during setup.

Status

LED

Setting Up the S1000 Thermal Cycler

To insert either a 96-, dual 48-, or 384-well reaction module into the reaction module bay of the thermal cycler base, follow these instructions:

1. With the locking bar in the down position and the lid lever of the reaction module pointing to the front, lift the reaction module into the reaction module bay (Figure 6). Leave about 1–2 cm of space in front of the module.

Lid lever (front)

Leave space here

Figure 6. Inserting the reaction module into the bay.

2. Pull the locking bar up to lock the reaction module in place (Figure 7). There is no space at the front of the module when it is locked into the S1000 thermal cycler base.

TIP: Store the reaction module in the base when it is not in use.

Locking bar (down position when unlocked)

No space here

(in the locked position)

Figure 7. Locking the reaction module in place.

3. Plug the supplied power cord into the appropriate electrical outlet.

4. Turn on the thermal cycler using the power switch on the back panel of the thermal cycler base.

NOTE: Before operating the thermal cycler, be sure to read the safety specifications (“Safety and Regulatory Compliance” on page iv) and operating requirements.

5. When the S1000 thermal cycler starts up, it goes through two screens: the black booting and the self-test screens. Once the self-test is run to verify proper functions, the main menu is displayed. Use the main menu to begin operating the thermal cycler.

To remove the reaction module from the thermal cycler base, follow these instructions:

1. Turn off the thermal cycler.

2. Unlock and release the reaction module by pushing the locking bar down.

Locking bar (up position when locked)

3. Carefully lift the reaction module out of the bay (Figure 8).

WARNING! Cooling fins may be hot immediately after running a protocol or incubation. Before lifting the reaction module, make sure that the cooling fins are not hot.

4. After removing the reaction module from the S1000 thermal cycler, store it on a clean, flat surface where it cannot get bumped, scraped, or dropped.

Scraping the cooling fins of the reaction module or dropping the module on the fins could compromise the ability of the module to heat and cool correctly.

Figure 8. Lifting the reaction module out of the bay.

Operating the Reaction Module Lid

S1000 Thermal Cycler Manual

Cooling fins

The inner lid of the reaction module applies heat and force to the reaction vessel lids (caps or tape) to produce consistent and successful reactions. Heating the inner lid prevents condensation, while applying force seals the reaction to prevent evaporation.

WARNING! After a run, the heated inner lid can remain hot. Use caution when opening and closing the lid.

To open the lid, use the following steps:

1. Turn the lid force knob counterclockwise to release the inner lid (Figure 9).

Lid force knob (Turn counterclockwise to release the lid)

Figure 9. Turn the lid force knob counterclockwise to release the inner lid.

Operating the Reaction Module Lid

2. To open the lid, push the lid lever back and then lift it up (Figure 10).

3. Lift the lid lever completely until the reaction module stays open without assistance.

To close the lid, use the following steps:

1. Push the lid lever down (Figure 11), making sure that the front of the lid is secured beneath the housing, and then lock it in place.

Lid lever

Figure 10. Lift the lid lever up to open the lid.

Lid lever

Figure 11. Push the lid lever down.

2. Adjust the lid force by turning the lid force knob (Figure 12).

• Turn the knob 1/4 clockwise (to the right) to increase the lid force

• Turn the knob 1/4 counterclockwise (to the left) to decrease the lid force

Adjust the lid force to a similar setting each time by turning it to the same position.

NOTE: The position marks on the lid indicate 1/4 turns.

Lid force knob (Turn clockwise to secure the lid)

Figure 12. Adjust the lid force by turning the lid lever.

S1000 Thermal Cycler Manual

Loading Sample Vessels into the Reaction Block

To ensure uniform heating and cooling of samples, vessels must be in complete contact with the reaction block. Adequate contact is achieved by:

• Confirming that the block is clean before loading samples

• Firmly pressing the individual tubes or the microplate into the block wells

TIP: When using one or a few tubes, make sure to place them in the center of the block to ensure uniform thermal cycling of all samples. Use the tube frame (catalog #184-9000), or load at least one empty tube in each corner of the block to ensure that the lid exerts even pressure on individual tubes.

Main Menu

The main menu (Figure 13) provides access to all thermal cycler operations and displays the status of the reaction module and the name of the thermal cycler.

Name of

thermal cycler

Options

Status message

Figure 13. The main window of the S1000 thermal cycler.

Select the options in the main menu to start these instrument functions:

• RUN

• NEW

• EDIT — to modify stored protocol files

• FILES

• VIEW

• TOOLS

— to run an existing protocol file

— to create a new protocol file

— to copy, move, rename, delete, or secure protocol files and/or folders

— to review an existing protocol file

— to change thermal cycler settings or to view the last protocol that was run

The File Tree

All protocol files are stored in the file tree. The file tree displays when you need to select a protocol to run, edit, or view.

The file tree (Figure 14) includes these folders:

• MAIN folder — stores the preinstalled protocols and cannot be deleted or renamed. The preinstalled files can be run or copied by any user. Do not store user-created protocols in the MAIN folder

Operating the Reaction Module Lid

• User folders — contain user-created protocol files. User folders and associated files can be secured with a password. The files cannot be edited or deleted without using the password

Selected folder

User folders

Selected file

Figure 14. The file tree of the S1000 thermal cycler.

NOTE: If a folder contains more than six protocols, use the arrow keys to scroll down to see all the protocols. All folder names are displayed with angle brackets (< and >) surrounding the name.

User-created

protocol file

Preinstalled protocols

S1000 Thermal Cycler Manual

2 Creating and Editing Protocols

Read this chapter for information on creating and editing protocols.

• Protocol steps (below)

• Creating a new protocol (page 12)

• Parameters for temperature or gradient steps (page 19)

• Editing an existing protocol (page 22)

• Sample volume and lid temperature (page 27)

Protocol Steps

Table 9 includes a list of steps in a protocol. The table also includes the limits and range of the parameters.

Table 9. Protocol steps and parameters of the S1000 thermal cycler

Step Name Parameters and Ranges Description

TEMP (Temperature)

Temperature in °C: The target

temperature between 0.0 and

100.0°C in tenths of a degree

Hold time: The hold time between 1 sec and 18 hr in the format of hr:min:sec. To enter an infinite hold, press the ∝ (infinite,

0) key

Instructs the thermal cycler to ramp to the target temperature, and hold that temperature for the specified amount of time

Creating a New Protocol

Table 9. Protocol steps and parameters of the S1000 thermal cycler (continued)

Step Name Parameters and Ranges Description

GRAD (Gradient range)

GOTO GOTO step: The step number of

END (No parameters) A protocol step that instructs the

Lower: The lower temperature

in the gradient. Enter a number between 30.0 and 99.0°C in tenths of a degree

Upper: The upper temperature in the gradient. The maximum temperature is 100°C. Enter a temperature within 24.0°C of the lower temperature

Time:The hold time between 1 sec and 18 hr in the format of hr:min:sec. To enter an infinite hold, press the ∝ key (infinite, 0) key

the first step in the repeat.

ADDTNL REPEATS: The number of additional times that the steps repeat.

Instructs the thermal cycler to ramp to the target temperature gradient across the block, and hold that temperature gradient for the specified amount of time

A protocol step that instructs the thermal cycler to repeat a set of steps for the specified number of times. NOTE: The total number of cycles in the protocol is the number of GOTO repeats, plus the first cycle.

thermal cycler to finish the protocol

Creating a New Protocol

NOTE: The internal memory of the S1000 thermal cycler can hold up to 400, 2-step protocols.

To create a protocol:

1. Select NEW from the main menu (Figure 15). Press ENTER to confirm the selection.

Figure 15. Select NEW from the main menu.

2. Use the numeric keys to enter the name of the new protocol file. Enter a letter by pressing the up or down arrow key and a number by pressing the numbered key. For example, to select the letter C, press the up key 3 times. To select the letter S, press the

S1000 Thermal Cycler Manual

down key eight times. Press ENTER to continue to the next space. Press ENTER to continue to the next screen.

NOTE: A protocol file name can contain 1–8 characters and must be unique to the folder. To delete or change a letter, press CANCEL and select a new letter. To delete the entire name, press CANCEL multiple times.

In Figure 16, the characters STD3 are entered, and the cursor is highlighting the next space.

Figure 16. STD3 is entered as the protocol name.

3. (Optional) Enter a new lid temperature, and press ENTER to continue to the next screen.

NOTE: The lid temperature can range from 0 to 110°C. When the block is running an infinite hold at a temperature below the Turn off below parameter, the lid heater maintains 31.0°C. To change the default Turn off below parameter, select TOOLS > DEFAULTS.

4. (Optional) Enter the sample volume in microliters (µl), and press ENTER to continue to the next screen.

NOTE: Entering a sample volume between 1 and 50 selects Calculated Temperature control mode, which is the standard mode. Entering zero (0) in the volume field selects Block mode. Calculated mode is the recommended mode because it most accurately represents the actual sample temperature. For more information about Temperature control modes, see page 27.

5. Using the arrow keys, select TEMP to enter a temperature step or GRAD to enter a gradient temperature step in the protocol file. Press ENTER to continue to the next screen.

In Figure 17, TEMP is selected as the temperature step.

Figure 17. TEMP is selected as the temperature step in this protocol file.

NOTE: The first step in a protocol must be either a TEMP or GRAD step.

6. Enter the target temperature between 0 (zero) and 100.0°C for the temperature step. Press ENTER to continue to enter the next item in the protocol.

Creating a New Protocol

In Figure 18, the target temperature is 95°C.

7. Enter the hold time (TIME) in minutes and seconds using the numeric keys. The hold time (TIME) ranges between 0:01 (one second) and 18:00:00 (18 hours). Entering 0 (zero) adds an infinite hold and holds this step FOREVER. Press ENTER to continue to the next field.

For example, to enter 4 minutes (4:00), type 400. To enter 30 seconds, type 30. In Figure 19, the hold time is four minutes.

Figure 18. Target temperature of 95°C is used in this protocol.

Figure 19. The hold time is 4 minutes in this protocol.

8. Select YES, No, or Option by pressing the right and left arrow keys. Press ENTER to continue to the next screen.

• YES — to confirm the current parameters for this protocol step

• No — to change a parameter in this protocol step

• Option — to add more parameters to this protocol step. For more information

about entering options, see “Adding an Increment to a Temperature Step” (page 19)

9. (Optional) Enter a gradient temperature step by pressing the right arrow key to select GRAD (Figure 20). Press ENTER to continue to the next screen.

NOTE: A temperature gradient is limited to a 24°C spread. The lowest possible “lower” temperature in the gradient is 30°C and the highest “upper” temperature is

S1000 Thermal Cycler Manual

100°C. Therefore the lowest gradient is 30–54°C, and the highest possible gradient is 76–100°C.

Figure 20. GRAD is selected in the gradient temperature step.

TIP: Check the temperature in each row of the block in a gradient by selecting the gradient calculator tool (TOOLS > GRADCALC on page 58).

10.Enter the lower temperature in the gradient. The lower temperature is at the front (row H) of the block.

In Figure 21, the lower temperature is 50°C.

Lower temperature (back row)

Figure 21. The lower temperature is 50°C in this protocol.

11.Enter the upper temperature in the gradient. The upper temperature is at the back (row A) of the block.

NOTE: The range of temperature is limited by the widest available range for gradient, which is 24°C. The highest value that can be entered for the upper temperature is 100°C.

12.Enter a hold time between 0:01 (one second) and 18:00:00 (18 hours).

13.Select YES, No, or Option by pressing the right and left arrow keys, then press ENTER to continue to the next screen:

• YES — to confirm the current parameters for this protocol step

• No — to change a parameter in this protocol step

• Option — to preview the temperature gradient. If Option is selected, select VIEW

on the next screen to view the gradient or EXT to add a hold time extension. Press ENTER again to return to the previous screen

Range of temperatures to be chosen

Creating a New Protocol

In Figure 22, the gradient is formed on a 96-well block with a range from 55–75°C. This screen displays the approximate temperature of each row of the block, and labels the front and back rows.

14.Repeat the instructions in steps 6–9 to continue entering additional temperature steps. In Figure 23, four steps are entered.

Entered steps

Figure 22. The approximate temperature of each row of the block.

Choose new step type

Figure 23. Enter all the temperature steps.

NOTE: A protocol can contain up to 99 protocol steps. The first step must be a temperature (TEMP) step, while the last step must be an END step.

15.(Optional) To enter a GOTO step immediately after the set of steps to be repeated in a cycle, use the arrow keys and select GOTO. Press ENTER to continue to the next screen.

For more information about how the GOTO step creates a cycle, see “Protocol Steps” (page 11).

In Figure 24, step 5 is a GOTO step.

Figure 24. A GOTO step is selected.

NOTE: The GOTO step cannot be the first or the last step in the protocol.

16.Enter the step number for the first step in the GOTO repeats using the numeric keys. Press ENTER to continue to the next screen.

S1000 Thermal Cycler Manual

In Figure 25, the first step is 2. The GOTO step instructs the thermal cycler to return to step 2 and repeat all the steps between steps 2 and 5.

Steps that repeat during GOTO step

First step in

GOTO repeats

Figure 25. Enter the first step in the GOTO repeats.

17.Enter the number between 1 and 9999 for the additional repeats (ADDTNL REPEATS) in the GOTO step. Then press ENTER to continue to the next screen.

NOTE: The GOTO step adds additional cycles to the PCR protocol. The first cycle is not included in the GOTO step. For example, to run a PCR protocol with 31 cycles, enter 30 repeats in the GOTO step.

In Figure 26, the number of repeats is 30, and the total number of cycles is 31.

Steps that repeat in the

GOTO step

Figure 26. Enter the number of repeats in a GOTO step.

18.Select YES to accept the GOTO step parameters (Figure 27), or select No to return to the beginning of this step and change the GOTO step parameters. Then press ENTER to continue to the next screen.

Figure 27. Confirm a GOTO step by selecting YES.

19.Enter the remaining steps by choosing the step type and adding parameters. Then press ENTER to continue to the next screen.

TIP: To instruct the thermal cycler to emit a sound at the end of the protocol, include a BEEP option in the final temperature step (page 21).

Number of additional repeats in a GOTO step

Creating a New Protocol

20.Select END using the arrow keys to instruct the thermal cycler to finish the protocol file. Press ENTER to continue to the next screen. In Figure 28, the END step is selected.

NOTE: The END step must be the last step of a protocol; a protocol can only contain one END step.

21.Select YES (Figure 29) to accept the protocol step parameters or No to return to the beginning and select a different protocol step.

Figure 28. The END step in a protocol.

Figure 29. Select YES to accept the protocol parameters.

22.Use the arrow keys to select the folder where you want the new protocol file to be saved, and press ENTER to save the protocol file.

NOTE: The file tree folder screen does not appear if there are no user-created folders (i.e. the MAIN folder is the only folder on the list). Saving the protocol in the MAIN folder is not recommended. If the protocol is saved in the MAIN folder, we recommend moving it to a user-created folder. (See “Moving a Protocol File” on page 41 for more information.)

In Figure 30, the STD3GRAD file is saved in the GRANT

Figure 30. The STD3GRAD file is to be saved in the GRANT folder.

To run a protocol, follow the instructions in “Preparing to Run a Protocol” on page 29.

folder.

S1000 Thermal Cycler Manual

Parameters for Temperature or Gradient Steps

Table 10 includes a list of options for temperature and gradient steps for the S1000 thermal cycler. The table also includes the limits and range of the parameters.

Table 10. Options and parameters for protocols on the S1000 thermal cycler

Step Name Parameters and Ranges Description

INC (Increment)

EXT (Extend)

RATE (Ramp rate)

Beep (No parameters) Applies only to a temperature step (see

A temperature from –10.0 to

10.0°C per cycle in tenths of a degree

A time from –60 to 60 sec per cycle

A number from 0.1 to 5°C per sec

Applies only to a temperature step (see “Adding an Increment to a Temperature Step” on page 19). Instructs the thermal cycler to increment (change) the target temperature of a step with each cycle, where a positive number increases the temperature and a negative number decreases the temperature

Applies to both temperature and gradient steps (see “Extending the Hold Time in a Temperature Step” on page 20). Instructs the thermal cycler to extend the hold time with each cycle. A positive number increases the hold time and a negative number decreases the hold time

Applies only to a temperature step (see “Changing the Ramp Rate in a Temperature Step” on page 21). Instructs the thermal cycler to ramp to the target temperature at the specified ramp rate in that step

“Adding a Beep to a Temperature Step” on page 21). Instructs the thermal cycler to beep to signal that the thermal cycler has reached the target temperature for that step

Adding an Increment to a Temperature Step

The increment (INC) parameter changes the target temperature of a protocol step. The increment can increase or decrease the target temperature with each cycle in the protocol.

To add an increment:

1. Select OPTION using the arrow keys. Press ENTER to continue to the next screen.

Parameters for Temperature or Gradient Steps

In Figure 31, OPTION is selected to add an increment to a temperature step.

Figure 31. Select OPTION to add an increment to a temperature step.

NOTE: The INC parameter must be added to a step within the GOTO repeats in order to increment with each cycle of the reaction.

2. Select INC using the arrow keys (Figure 32) to add an increment to the protocol step in each cycle. Press ENTER to continue to the next screen.

Figure 32. Select INC to add an increment.

3. Enter the increment temperature using the numeric keys. To decrease the temperature each cycle, enter a negative number by pressing the CANCEL (–) key. Press the PAUSE (

) key to enter a decimal point. Then press ENTER to continue to the next screen.

NOTE: Enter an increment from –10.0 to 10.0°C per cycle in tenths of a degree, and within the limits of a temperature step (0–100°C).

In Figure 33, the increment is +0.5°C. The target temperature for step 3 will increase by

0.5°C each cycle.

Figure 33. Enter the increment temperature.

4. To confirm the parameters of the protocol step, select YES and then press ENTER. To change the parameters, select No and then press ENTER.

Extending the Hold Time in a Temperature Step

The EXT parameter changes the hold time for a temperature or gradient temperature step. The extension increases or decreases the hold time with every cycle.

+ 67 hidden pages

Bio-Rad S1000 Instruction Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Bio-Rad Laboratories Resources

Warranty

Writing Conventions Used In This Manual

Safety and Regulatory Compliance

Table of Contents

System Overview

Reaction Modules

Setting Up the S1000 Thermal Cycler

Operating the Reaction Module Lid

2 Creating and Editing Protocols

Protocol Steps

Creating a New Protocol

Parameters for Temperature or Gradient Steps