Bio-Rad S1000 Thermal Cycler with 96-Deep Well Reaction Module

Bio-Rad S1000 Thermal Cycler with 96-Deep Well Reaction Module

The Bio-Rad S1000 Thermal Cycler with 96-Deep Well Reaction Module is a versatile gradient PCR system designed for conventional DNA amplification, assay optimization, cloning, genotyping, mutagenesis, sequencing workflows, gene-expression research, and other molecular biology applications. Combining Bio-Rad's modular S1000 thermal cycler chassis with a gradient-enabled 96-deep well reaction module, this system provides laboratories with flexible sample compatibility, precise Peltier temperature control, programmable thermal gradients, extensive protocol storage, and reliable performance for routine and research PCR.

The 96-Deep Well module accommodates 96 x 0.2 mL PCR tubes, 48 x 0.5 mL tubes, or one compatible 96-well PCR plate, making it particularly useful for laboratories that need greater vessel flexibility than a standard fast 96-well block. The module provides a 0°C to 100°C temperature range, maximum ramp rate of approximately 2.5°C/sec, temperature accuracy of ±0.2°C at 90°C, and well-to-well temperature uniformity of ±0.4°C within 10 seconds of reaching 90°C.

A programmable thermal gradient from 30°C to 100°C, with a selectable temperature differential of 1°C to 24°C, allows researchers to test multiple annealing temperatures within a single run. This can significantly simplify optimization of new primers and PCR assays.

The S1000 can operate as a standalone thermal cycler or as part of a larger Bio-Rad 1000-Series system controlled by a compatible C1000 or C1000 Touch thermal cycler. More than 1,000 typical PCR protocols can be stored onboard, making the system practical for laboratories running numerous established methods.

This Bio-Rad S1000 is available used and refurbished from American Instrument Exchange. AIE technicians inspect, clean, test, and verify major instrument functions prior to shipment, and the system includes a 90-day warranty from American Instrument Exchange.

Key Features

• Bio-Rad S1000 Thermal Cycler

• 96-Deep Well gradient reaction module

• Supports 96 x 0.2 mL PCR tubes

• Supports 48 x 0.5 mL tubes

• Supports one 96-well PCR plate

• Temperature range of 0°C to 100°C

• Maximum ramp rate of approximately 2.5°C/sec

• Average ramp rate of approximately 2°C/sec

• Temperature accuracy of ±0.2°C at 90°C

• Well-to-well uniformity of ±0.4°C

• Programmable thermal gradient

• Gradient range of 30°C to 100°C

• Gradient differential of 1°C to 24°C

• Peltier-based heating and cooling

• Adjustable heated lid

• Calculated and block temperature-control modes

• LCD interface

• Text-based programming

• More than 1,000 typical programs stored onboard

• Instant incubation function

• Four USB-A ports and one USB-B port

• Compatible with C1000 and C1000 Touch system control

• Interchangeable reaction-module architecture

• Suitable for conventional endpoint PCR

• Used and refurbished by American Instrument Exchange

• 90-day AIE warranty

Overview

Polymerase chain reaction requires precise and repeatable control of temperature as samples move through repeated denaturation, annealing, and extension steps.

Small differences in thermal performance can affect amplification efficiency, specificity, and reproducibility.

The Bio-Rad S1000 was designed as a modular PCR platform capable of supporting several interchangeable reaction modules while maintaining consistent Peltier-based temperature control.

This configuration includes the 96-Deep Well module, which offers greater vessel flexibility than Bio-Rad's standard 96-well fast block.

The system can be used as a standalone conventional thermal cycler or integrated into a larger multi-instrument Bio-Rad workflow.

Key Specifications

Specification	Details
Manufacturer	Bio-Rad
Model	S1000
Equipment Type	Conventional PCR Thermal Cycler
Reaction Module	96-Deep Well, Gradient Enabled
Sample Capacity	96 x 0.2 mL tubes
Alternate Sample Capacity	48 x 0.5 mL tubes
Plate Capacity	1 x 96-well PCR plate
Temperature Range	0°C to 100°C
Maximum Ramp Rate	2.5°C/sec
Average Ramp Rate	Approx. 2°C/sec
Temperature Accuracy	±0.2°C of programmed target at 90°C
Temperature Uniformity	±0.4°C well-to-well within 10 sec of reaching 90°C
Gradient Capability	Yes
Gradient Range	30°C to 100°C
Gradient Differential	1°C to 24°C
Temperature Control Modes	Calculated and block
Display	LCD
Programming	Text based
Protocol Memory	More than 1,000 typical programs
Heated Lid	Fully adjustable
Ports	4 USB-A, 1 USB-B
Instant Incubation	Yes
Dimensions	Approx. 13"W x 18"D x 8"H, chassis
Manufacturer Weight	Approx. 23 lb.
Input Power	Up to 700 W maximum
Frequency	50–60 Hz, single phase
Condition	Used / Refurbished
AIE Warranty	90 Days

Common Applications

The Bio-Rad S1000 is well suited for conventional PCR amplification, cloning, genotyping, mutagenesis, cycle sequencing, gene-expression research, assay development, primer optimization, molecular screening, sequencing preparation, and general nucleic-acid research.

Its programmable gradient capability makes it particularly useful for laboratories developing new PCR methods or troubleshooting amplification conditions.

Ideal Laboratory Types

The S1000 is a practical choice for biotechnology companies, pharmaceutical research laboratories, academic molecular biology laboratories, genomics facilities, university core facilities, contract research organizations, agricultural biotechnology laboratories, forensic research groups, and other facilities performing conventional PCR.

Its modular architecture also makes it useful in laboratories that already operate Bio-Rad C1000 or C1000 Touch systems and want to expand thermal-cycling capacity.

96-Deep Well Reaction Module

The 96-Deep Well module distinguishes this S1000 configuration from Bio-Rad's standard 96-Well Fast module.

It accommodates:

96 x 0.2 mL PCR tubes

48 x 0.5 mL tubes

or

one compatible 96-well PCR plate.

This expanded vessel compatibility can be useful for laboratories that perform a mixture of routine plate-based PCR and individual tube-based protocols.

Why the Deep-Well Block Matters

Many PCR thermal cyclers are optimized primarily around 0.2 mL tubes and standard PCR plates.

The S1000 Deep Well module provides additional flexibility by accommodating 0.5 mL tubes.

This can be useful for laboratories working with larger reaction volumes or legacy protocols that still use larger PCR vessels.

It also allows a single thermal cycler to support several common reaction formats without changing the entire instrument.

Peltier Temperature Control

The S1000 uses Peltier technology to heat and cool the reaction block.

Peltier systems allow rapid changes between programmed temperatures without the compressors or circulating fluids associated with older thermal-control technologies.

During a PCR run, the system repeatedly moves among temperatures used for:

Denaturation

Annealing

Extension

Final extension

and

Hold steps.

Precise electronic control helps maintain reproducible conditions through dozens of thermal cycles.

0°C to 100°C Temperature Range

The reaction module operates across a broad:

0°C to 100°C

temperature range.

This supports conventional PCR protocols as well as specialized incubation and hold steps.

Typical PCR programs may include:

94–98°C denaturation

50–65°C annealing

68–72°C extension

4°C final hold

Actual parameters should always be selected according to primers, polymerase, DNA template, amplicon length, and assay design.

Temperature Accuracy

Bio-Rad specifies temperature accuracy of:

±0.2°C of the programmed target at 90°C.

Accurate block temperature can help improve transferability of established protocols between runs and between compatible instruments.

This is particularly important when laboratories use tightly optimized annealing temperatures.

Temperature Uniformity

Well-to-well temperature uniformity is specified at:

±0.4°C within 10 seconds of arrival at 90°C.

Uniform block temperature helps ensure that samples positioned in different areas of the plate experience similar thermal conditions.

This can reduce one source of variation in multi-sample PCR experiments.

2.5°C/sec Maximum Ramp Rate

The 96-Deep Well module provides a maximum ramp rate of approximately:

2.5°C/sec

with an average ramp rate of approximately:

2°C/sec.

Although Bio-Rad's 96-Well Fast module can ramp more quickly, the Deep Well module prioritizes compatibility with multiple vessel formats.

For laboratories using 0.5 mL tubes or requiring the deeper block geometry, the tradeoff can be worthwhile.

Thermal Gradient Capability

The S1000 Deep Well module includes built-in gradient capability.

The gradient can be programmed across a range of:

30°C to 100°C

with a temperature differential between approximately:

1°C and 24°C.

This makes it possible to expose different rows of samples to different temperatures during the same PCR run.

Optimizing Annealing Temperature

Finding the correct annealing temperature is one of the most important steps in PCR optimization.

If the temperature is too low, primers may bind nonspecifically.

If the temperature is too high, amplification efficiency may decline.

A thermal gradient allows researchers to test several conditions simultaneously rather than running multiple separate experiments.

For example, researchers developing a new primer pair can evaluate several annealing temperatures within a single plate and then select the condition producing the strongest specific amplification.

Gradient PCR for Assay Development

Gradient capability can accelerate:

Primer optimization

New assay development

Troubleshooting

Mutagenesis protocols

Genotyping assays

Cloning workflows

Research PCR development

This makes the S1000 useful not only for established PCR protocols but also for laboratories frequently developing new assays.

Adjustable Heated Lid

The S1000 includes a fully adjustable heated lid designed to accommodate a variety of PCR vessels.

The heated lid helps reduce condensation on caps and plate seals during cycling.

Without adequate lid heating, water can condense at the top of the reaction vessel, altering the effective reaction volume.

Modern heated-lid systems generally eliminate the need for mineral-oil overlays that were common with older PCR instruments.

Calculated Temperature Control

The S1000 offers both:

Calculated temperature control

and

Block temperature control.

Calculated control estimates sample temperature based on thermal behavior rather than relying only on the physical block temperature.

This can help compensate for differences between the block and the actual reaction mixture during rapid temperature transitions.

Block Temperature Control

Block-control mode regulates the system according to the measured temperature of the reaction block itself.

This mode may be useful when transferring protocols from older thermal cyclers or when a method was originally validated using block-based control.

Having both modes provides additional flexibility when reproducing established PCR protocols.

More Than 1,000 Stored Protocols

The S1000 can store more than:

1,000 typical PCR programs

in onboard memory.

This is particularly useful in shared research laboratories where many different protocols are used.

Researchers can save established methods instead of re-entering:

Temperature steps

Cycle counts

Gradient settings

Extension times

and

Hold parameters

for each experiment.

LCD Interface

The S1000 uses an LCD display with text-based programming.

Although simpler than the touchscreen interface used on newer Bio-Rad systems, the controller provides direct access to protocol creation and execution without requiring a dedicated computer for routine standalone operation.

Instant Incubation

The S1000 includes an instant-incubation function.

This allows the thermal block to be held at a selected temperature without programming a complete PCR cycling protocol.

Potential uses include:

Sample incubation

Enzyme reactions

DNA denaturation

Temperature-controlled holds

Post-PCR incubation

This increases the utility of the instrument beyond conventional cycling alone.

Modular Reaction Block Design

One of the major advantages of Bio-Rad's 1000-Series architecture is its interchangeable reaction-module design.

The S1000 platform was offered with several modules, including:

96-Well Fast

96-Deep Well

Dual 48/48-Well Fast

384-Well

All are gradient capable.

This modular approach allowed laboratories to configure the platform according to sample format and throughput requirements.

S1000 96-Deep Well vs. 96-Well Fast

The 96-Well Fast module provides:

96 x 0.2 mL positions

and a faster maximum ramp rate of approximately:

5°C/sec.

The 96-Deep Well configuration provides:

96 x 0.2 mL tubes

48 x 0.5 mL tubes

or

one 96-well plate

with a maximum ramp rate of approximately:

2.5°C/sec.

The Deep Well module is therefore better suited for laboratories that value vessel flexibility, while the Fast module is preferable when maximum cycling speed is the primary requirement.

S1000 vs. Dual 48/48 Module

The Dual 48/48 Fast Reaction Module contains two independently controlled 48-well blocks.

That configuration allows two different PCR protocols to run simultaneously.

The 96-Deep Well configuration instead provides one unified 96-position thermal environment with compatibility for larger 0.5 mL tubes.

The appropriate configuration depends on whether the laboratory prioritizes:

Independent simultaneous protocols

or

Broader vessel compatibility.

S1000 vs. 384-Well Module

The 384-well module is optimized for higher throughput and smaller reaction formats.

It accommodates one 384-well PCR plate.

The 96-Deep Well module is better suited for routine PCR and laboratories that require compatibility with individual 0.2 mL and 0.5 mL tubes.

Standalone Operation

The S1000 can operate independently as a conventional PCR thermal cycler.

This makes it useful for laboratories that simply need reliable PCR amplification without requiring a larger networked system.

Researchers can program and run PCR methods directly on the instrument.

Integration with C1000 or C1000 Touch

The S1000 can also function as part of a larger Bio-Rad 1000-Series thermal-cycling system.

When connected to a compatible C1000 or C1000 Touch thermal cycler, multiple S1000 units can be controlled within a larger multi-bay configuration.

Bio-Rad documentation describes networked configurations of up to:

32 systems

under appropriate PC-controlled setups.

This can provide considerable PCR capacity for high-throughput molecular biology laboratories.

Conventional PCR vs. Real-Time PCR

The S1000 in this configuration is a conventional endpoint PCR thermal cycler.

It controls temperature but does not contain the optical fluorescence-detection system required for real-time PCR.

It is therefore ideal for workflows where amplified DNA is subsequently analyzed using techniques such as:

Gel electrophoresis

Fragment analysis

Sequencing

Restriction analysis

Cloning

Other downstream molecular methods.

Researchers requiring quantitative real-time amplification measurements should use a dedicated qPCR system such as an appropriate Bio-Rad CFX platform.

PCR vs. qPCR

Conventional PCR answers a basic question:

Was the desired DNA target successfully amplified?

Real-time PCR or qPCR additionally measures fluorescence during amplification and can provide quantitative information.

The Bio-Rad S1000 is designed primarily for conventional thermal cycling.

This makes it appropriate for cloning, genotyping, assay development, sequencing preparation, and many other workflows where real-time fluorescence detection is unnecessary.

Cloning Applications

PCR is central to many molecular cloning workflows.

The S1000 can support:

Insert amplification

Vector verification

Colony PCR

Construct confirmation

Site-directed mutagenesis

Sequence preparation

Its gradient capability can be particularly helpful when developing new amplification protocols for unfamiliar primer sets.

Genotyping Applications

The S1000 can be used for conventional PCR-based genotyping.

Typical applications may include:

Transgenic screening

Gene-editing confirmation

SNP-related assays

Animal-model genotyping

Plant-genetics research

Research cohort screening

The 96-position format provides practical throughput for routine genotyping laboratories.

Mutagenesis

Site-directed mutagenesis protocols frequently rely on precisely controlled PCR amplification.

The S1000's programmable temperature control and gradient capability can help optimize amplification when introducing specific sequence changes.

Cycle Sequencing

Bio-Rad also identifies cycle sequencing as an application for the S1000 platform.

Cycle-sequencing reactions use repeated temperature cycles in a manner similar to PCR, allowing the thermal cycler to support appropriate sequencing workflows.

Gene-Expression Research

Although the S1000 does not itself perform real-time gene-expression quantification, it can be used during supporting molecular biology workflows involving amplification, cloning, assay development, and sequencing preparation.

Quantitative expression analysis requiring fluorescence monitoring should be performed on a qPCR platform.

Pharmaceutical & Biotechnology Applications

Biotechnology and pharmaceutical research laboratories can use the S1000 for:

Molecular cloning

Assay development

Genotyping

DNA amplification

Mutagenesis

Sequencing preparation

Biomarker research

Research screening

The instrument's combination of gradient optimization and programmable cycling makes it useful during both early assay development and routine research.

Academic Research Laboratories

The S1000 is particularly well suited for academic laboratories because one system can support many different PCR workflows.

Researchers can save large numbers of protocols while the gradient capability allows students and investigators to optimize new assays without consuming multiple instruments.

PCR Teaching Laboratories

The straightforward LCD interface and conventional 96-well architecture also make the S1000 suitable for educational and teaching laboratories.

Students can learn fundamental PCR concepts including:

Denaturation

Annealing

Extension

Thermal gradients

Cycle numbers

Primer optimization

without requiring a more complex real-time PCR system.

High- and Low-Profile PCR Consumables

Bio-Rad's 1000-Series reaction modules support appropriate PCR consumables according to module geometry.

For the 96-Deep Well version, users can operate compatible:

0.2 mL tubes

0.5 mL tubes

and

96-well PCR plates.

Correct vessel selection and good thermal contact with the block remain important for consistent results.

Importance of Proper Plate Sealing

PCR plates and tubes should be properly sealed before cycling.

Correct sealing helps reduce:

Evaporation

Cross-contamination

Sample-volume changes

Condensation

and

Well-to-well inconsistencies.

The heated lid further helps control condensation during high-temperature cycling.

Refurbishment & Testing by American Instrument Exchange

PCR systems depend on accurate heating, cooling, timing, block performance, and electronic controls.

American Instrument Exchange tests used and refurbished laboratory equipment to confirm proper operation prior to shipment.

Evaluation of a Bio-Rad S1000 may include:

Instrument startup

LCD operation

Programming functions

Reaction-block heating

Reaction-block cooling

Temperature setpoints

Program execution

Gradient operation

Heated-lid function

Timing functions

USB interfaces

Block recognition

Electrical operation

Overall instrument condition

AIE technicians repair or replace components as necessary and thoroughly clean the instrument before shipment.

Refurbished Bio-Rad PCR Systems from American Instrument Exchange

A refurbished Bio-Rad S1000 can provide dependable PCR capability at substantially lower cost than purchasing a current-generation thermal cycler new.

American Instrument Exchange supplies used and refurbished molecular biology equipment for biotechnology companies, pharmaceutical laboratories, universities, research institutions, clinical research groups, and industrial laboratories.

Available molecular biology equipment may include PCR thermal cyclers, real-time PCR systems, centrifuges, microcentrifuges, electrophoresis equipment, incubators, shakers, laboratory refrigerators, freezers, ultra-low freezers, and related laboratory instruments.

This Bio-Rad S1000 includes a 90-day warranty from American Instrument Exchange.

Shipping & Installation

The S1000 chassis measures approximately:

13"W x 18"D x 8"H

and Bio-Rad lists the system weight at approximately:

23 lb.

The instrument requires a stable laboratory bench with adequate ventilation and access to appropriate electrical power.

Laboratories should also confirm they have compatible:

PCR tubes

PCR plates

Plate seals

Tube caps

and

Reaction racks

for the specific 96-Deep Well block.

Related Laboratory Equipment

Laboratories using the Bio-Rad S1000 may also require PCR workstations, clean benches for appropriate nonhazardous PCR setup workflows, microcentrifuges, benchtop centrifuges, vortex mixers, pipettes, electrophoresis equipment, gel documentation systems, laboratory refrigerators, freezers, ultra-low freezers, incubators, and real-time PCR systems.

American Instrument Exchange offers used, refurbished, and new equipment for molecular biology, biotechnology, pharmaceutical, academic, clinical research, and industrial laboratories.

Bio-Rad S1000 Frequently Asked Questions

What is the Bio-Rad S1000?

The Bio-Rad S1000 is a modular conventional PCR thermal cycler designed for DNA amplification, gradient PCR, cloning, genotyping, mutagenesis, cycle sequencing, and other molecular biology applications.

Which reaction module is installed on this S1000?

This system is equipped with the 96-Deep Well Reaction Module.

How many samples can the 96-Deep Well module hold?

It can accommodate up to 96 x 0.2 mL tubes or one compatible 96-well PCR plate.

Can it use 0.5 mL PCR tubes?

Yes. The deep-well module can accommodate up to 48 x 0.5 mL tubes.

Does the 96-Deep Well block use 2 mL tubes?

No. The manufacturer specifies 0.2 mL and 0.5 mL PCR tube formats, not 2 mL tubes.

What is the temperature range?

The module operates from approximately 0°C to 100°C.

What is the maximum ramp rate?

The maximum ramp rate for the 96-Deep Well module is approximately 2.5°C/sec.

What is the average ramp rate?

Approximately 2°C/sec.

What is the temperature accuracy?

Bio-Rad specifies approximately ±0.2°C of the programmed target at 90°C.

What is the temperature uniformity?

Well-to-well uniformity is approximately ±0.4°C within 10 seconds after reaching 90°C.

Does the S1000 have gradient PCR capability?

Yes. All of Bio-Rad's primary S1000 reaction modules include gradient capability.

What is the gradient range?

Approximately 30°C to 100°C.

How wide can the temperature gradient be?

The programmable differential can range from approximately 1°C to 24°C.

Why use a thermal gradient?

A thermal gradient allows researchers to test several annealing temperatures simultaneously, making it easier to optimize primers and new PCR protocols.

Does the S1000 have a heated lid?

Yes. It has an adjustable heated lid designed to reduce condensation and accommodate different reaction vessels.

How many programs can the S1000 store?

More than 1,000 typical protocols can be stored in onboard memory.

Can the S1000 operate without a computer?

Yes. It can operate as a standalone thermal cycler.

Can the S1000 connect to a C1000 Touch?

Yes. Bio-Rad designed the S1000 to integrate with compatible C1000 and C1000 Touch systems for expanded thermal-cycling capacity.

Is the S1000 a real-time PCR machine?

No. The S1000 itself is a conventional thermal cycler and does not contain fluorescence-detection optics for qPCR.

Can the S1000 quantify DNA during PCR?

Not directly. Quantitative real-time PCR requires an instrument with optical fluorescence detection, such as an appropriate Bio-Rad CFX system.

Can the S1000 be used for cloning?

Yes. It is well suited for insert amplification, colony PCR, construct verification, and related cloning workflows.

Is it suitable for genotyping?

Yes. Conventional PCR-based genotyping is one of the common applications for the S1000.

Can it be used for mutagenesis?

Yes. Its programmable thermal cycling and gradient capability can support site-directed mutagenesis and related amplification workflows.

Can it perform cycle sequencing?

Yes. Bio-Rad lists cycle sequencing among the applications for the S1000 platform.

What is the difference between the Deep Well and Fast 96-well modules?

The Deep Well module supports 0.2 mL and 0.5 mL tubes and has a maximum ramp rate of approximately 2.5°C/sec. The 96-Well Fast module supports 0.2 mL formats and can ramp at up to approximately 5°C/sec.

What are the dimensions of the S1000?

The chassis measures approximately 13"W x 18"D x 8"H.

How much does the S1000 weigh?

Bio-Rad specifies approximately 23 lb. for the S1000 system.

Is this Bio-Rad S1000 available refurbished?

Yes. American Instrument Exchange offers this S1000 used and refurbished.

What warranty is included?

The current AIE listing includes a 90-day warranty.