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Geode H14000 User Manual

Table of Contents

INTRODUCTION TO CRYSTAL DIGITAL PCR™

Purpose of the document

Overview of the Crystal Digital PCR™ Workflow

Intended use of the naica® system

Citing the naica® system in scientific publications, presentations, seminars, etc.

MATERIALS AND EQUIPMENT

The packaging of the Geode contains:

Safety instructions for the naica® system

Labeling

Declaration of conformity

Specifications

Installation of the Geode

Materials required but NOT supplied

Crystal Digital PCR™ recommended detection system

The reference dye

SETTING

UP A CRYSTAL DIGITAL PCR™ EXPERIMENT

Preventing DNA contamination

Protocol for setting up Crystal Digital PCR™

Sample purification and pre-treatment

REACTION MIX PREPARATION

TIMIZATION OF CRYSTAL DIGITAL PCR™

CRYSTAL DIGITAL PCR™ GEODE PROTOCOL

Loading chips for Crystal Digital PCR™ on the Geode

Starting a Crystal Digital PCR™ run on the Geode

The Geode Crystal Digital PCR™ reaction steps

Additional protocols on demand

HOW TO USE THE GEODE SOFTWARE USER INTERFACE

Overview

Switch on/off the instrument

Create a new program

Edit a pre-existing program

Run

Pause a program

Abort a program

Import or export a program

Export Live Logs or system logs for troubleshooting support

Other functionalities

TROUBLESHOOTING

MAINTENANCE AND TECHNICAL SUPPORT

LICENSE INFORMATION

Содержание Geode H14000

Страница 1: ...STILLA Geode for the naica system User Manual Geode H14000 ...

Страница 2: ...ng from the use of this information Elements of the naica system and its uses are covered by US and corresponding non US patent claims owned by or under license to Stilla Technologies Details available at www stillatechnologies com patents Purchase of this product includes a limited non transferable right under such intellectual property for use of the product for internal research only No rights ...

Страница 3: ...A contamination 13 Protocol for setting up Crystal Digital PCR 14 a Sample purification and pre treatment 14 REACTION MIX PREPARATION 14 OPTIMIZATION OF CRYSTAL DIGITAL PCR 14 CRYSTAL DIGITAL PCR GEODE PROTOCOL 16 Loading chips for Crystal Digital PCR on the Geode 16 Starting a Crystal Digital PCR run on the Geode 18 a The Geode Crystal Digital PCR reaction steps 18 Additional protocols on demand ...

Страница 4: ...Geode H14000 User Manual 3 a Geode embedded software license 33 b Third party licenses 33 ...

Страница 5: ... these positive droplets to precisely extract the absolute quantity of nucleic acids With Crystal Digital PCR the combination of powerful image analysis and intuitive visual inspection offers an unmatched level of confidence in the digital PCR measurement yielding data you can trust Sample loading Generation of droplet crystal and PCR Reading and analysis Prepare the sample for the reaction mix St...

Страница 6: ...ologies com technical resources naica system prism3 The naica system is a laboratory instrument to be used by qualified personnel in a controlled environment Before using the naica system the user should be trained by a Stilla Technologies representative The naica system is intended for Research Use Only Not for use in diagnostic procedures Stilla Technologies recommends installing the devices in ...

Страница 7: ...ylus Sapphire chip and Opal chip Quick User Guides o For the kit of power cords Cable for Geode Cable for Prism3 Cable for the compressed air system ISPTLAPG3 Cable for naica PC and monitor o For the naica system accessory box Magnetic adapters for the Geode Fig 2 A An electronic level Fig 2 A Opal chip holder for the Geode Fig 2 A Electrostatic pen Fig 2 B Flashlight Fig 2 B Figure 2 The contents...

Страница 8: ...tilation of the device must not be covered Caution use If the device is used in a manner not described in this manual safety may be compromised Caution hot surface The thermal plate and chips quickly reach temperatures above 50 C thus there are risks of burning or scalding if the equipment is not operated properly Keep the lid closed until the temperature reaches 30 C or less Only use materials ch...

Страница 9: ...s not the hips Keep the head up the core muscles tight and do not twist the body Keep the load as close to the body as possible Wait until the load is secure to release the handhold If a part of the Geode chamber loosens or breaks then the Geode is not leakproof Pressure cannot build up so that there is no chance any parts are projected to cause harm If a part of the Geode chamber breaks while a 1...

Страница 10: ... of sample material in the laboratory must be followed by wearing the proper Personal Protective Equipment e g gloves and protective clothing For detailed instructions please refer to Decontamination instructions Mains supply voltage fluctuations 90 c Labeling i Labeling symbols Manufacturer Product reference part number Product serial number Read the User Manual before using the product Caution d...

Страница 11: ...ucture CE marking manufacturer s declaration that the product meets the requirements of the applicable EC directives ii Label type of the Geode d Declaration of conformity To view the declaration of conformity certificate please visit https www stillatechnologies com technical resources naica system prism3 ...

Страница 12: ...ax 1000m above sea level Noise level 37 dB A Storage Temperature 5 C to 40 C Relative humidity 10 to 95 non condensing Barometric pressure 700 hPa to 1060 hPa Waiting time until operation 8h Shipping Temperature 40 C to 60 C Relative humidity 10 to 95 non condensing Barometric pressure 700 hPa to 1060 hPa Waiting time until the operation 24h f Installation of the Geode i Operating requirements Pro...

Страница 13: ...ica system prism3 Any other enzymatic mix needs to be evaluated by the user before performing experiments as Stilla Technologies cannot guarantee the compatibility of any other enzymatic mix with the naica system h Crystal Digital PCR recommended detection system For the detection and quantification of the amount of target in the sample a fluorescent signal is measured The Crystal Digital PCRTM te...

Страница 14: ...stal Digital PCR when using TaqMan probes For EvaGreen based assays the basal fluorescence from the dye is usually sufficient to allow droplet detection in the blue channel However in case the red channel has to be used for droplet detection Alexa Fluor 647 can be added as a reference dye Stilla Technologies recommends adding Alexa Fluor 647 as reference dye to all EvaGreen experiments Please conf...

Страница 15: ...s recommends using the naica multiplex PCR MIX For the reaction mix composition using the naica multiplex PCR MIX view the detailed reaction preparation information in the corresponding IFU here https www stillatechnologies com technical resources naica system prism3 Please refer to the next section for guidelines on primer and probe concentrations For other compatible PCR Master mix compositions ...

Страница 16: ...oncentrations gradually up to 1 µM if needed for example to increase amplification efficiency see https www gene pi com item primers and probes 2 Note When optimizing primer and probe concentrations for a given target it can be beneficial to determine the limiting factor first For example if the primers are the limiting factor it is useless to increase probe concentrations Other important aspects ...

Страница 17: ...sure inlet behind the device Fig 3B The pressure tube coming from the pressure source compressed air system ISPTLAPG3 can be connected to the instrument by simply pushing it in the pressure inlet until it does not go any further 3 Switch on the pressure source wait for a minute and ensure that the pressure delivered to the Geode is between 1 250 50 mbars check the screen of the device or the scree...

Страница 18: ... of the respective magnetic frames is supported by a blue left and white white positioning indicator both on the magnetic frames as well as on the Geode instrument thermal plate framing Fig 5 Figure 5 Positioning of the Sapphire chip left and Opal chip right in the respective magnetic frame on the thermal plate of the Geode instrument 7 Close the lid of the Geode by pulling the black handle upward...

Страница 19: ...gital PCR To enable droplet generation pressure increases from atmospheric pressure AP to AP 1000 mbar followed by a drop to AP 950 mbar at the end of the partitioning step If a modification of the partitioning temperature is required please contact Stilla Technologies before proceeding For Sapphire chips the generated droplets have an average volume of 0 68 nL when using the naica PCR MIX and the...

Страница 20: ...ied Duration states indicative times variances may occur Table 5 Crystal Digital PCR template for RT PCR application called Template Stilla RT PCR 45 cycles with Quantabio qScriptTM XLT One Step RT qPCR ToughMix with Sapphire chips The total duration of the default program is approximately 2 hours and 30 min Step Temperature C Pressure mbar Duration Partition 40 AP to 950 12 min cDNA synthesis 50 ...

Страница 21: ...o start the program 4 Visualize the graphical progression of the partitioning and thermal cycling programs by pressing on Live Logs accessible from the main panel 5 Press on Run to go back to the remaining time estimation Note The remaining time of a program is indicative and relies on the effective temperature ramp rate of the thermal plate and the duration of the stabilization phase at each step...

Страница 22: ...oftware User Interface Additional protocols on demand Stilla Technologies continuously develops new protocols to support the optimal utilization of the variety of naica system applications All support protocols are accessible on our website https www stillatechnologies com technical resources naica system prism3 The Geode software is exclusively updated by a Stilla Technologist Service Specialist ...

Страница 23: ...eze Then press the black power button located at the rear of the instrument Create a new program 1 In the main panel press Programs and New Program Fig 9 Then define the name of the program as well as the author add comments or change the location for the program by default in local scripts Terminate by pressing the validate icon Figure 9 Create a New Program 2 Configure the new program steps by c...

Страница 24: ...late temperature at the set temperature value It can be used after Release to store the samples at a constant temperature until removal If the exact time of sample removal is uncertain activate the infinite field chip storing after Crystal Digital PCR under 20 C should be evaluated by the user Pressure Only for advanced users Please contact Technical Support for more help Wait Use this command to ...

Страница 25: ...on to save and start a program check that the lid is correctly closed before starting The templates folder cannot be modified thus programs created based on edited template programs should be saved in local scripts Four template programs recommended by Stilla Technologies are provided by default The Sapphire Template PCR 45 cycles js program to perform a PCR experiment for Sapphire chips based on ...

Страница 26: ...plate without time limitation Do not exceed 25 C for more than 20 min before starting a run 3 Close the lid and then press the play icon The remaining time indicative is displayed as well as the progression bar of each step based on the remaining time the current measured temperature of the thermal plate and the current measured pressure in the block Fig 11 Press the information icon to get a summ...

Страница 27: ...sure profiles at the end of a run would be necessary for optimal investigation Pause a program 1 During a run press the pause icon to interrupt the Crystal Digital PCRTM temporarily 2 Confirm the request in the appearing window and the program will be paused 3 Press the play icon to continue the program Abort a program 1 During a run press the stop icon to abort a run After confirming the request ...

Страница 28: ...on on the right side a new page is displayed 5 Press on the local scripts folder on the right panel 6 Press the validation icon To export a program on a USB key 1 Plug a USB key in the USB port at the front of the instrument 2 Wait for the popup indicating that the USB key has been recognized then press the validation icon 3 In the main panel Programs then the open icon Select the desired program ...

Страница 29: ...t 2 Wait for the popup indicating that the USB key has been recognized then validate 3 In the main panel press System then click on System Logs 4 Click on Send Log File to USB Stick 5 Always validate until the end 6 A syslog folder has been created on the USB key It contains all the information that may be necessary to the Technical Support for maintenance purposes Other functionalities All other ...

Страница 30: ...ponds partially e g no update of the Live Logs try to extract the live and system logs refer to the Export Live Logs or system logs for troubleshooting support then wait for the expected end of the run to potentially save the experiment if the program is still running correctly If the screen still does not respond or still responds partially try to stop the run click on Stop to preserve the crysta...

Страница 31: ...extract the live and system logs refer to Export Live Logs or system logs for troubleshooting support and contact Technical Support A temperature issue occurred The measured temperature is either lower or higher than the required temperature during the run If the experiment is running stop it click on Stop to preserve the crystal Make sure that the Geode is placed at 25 cm from any wall or objects...

Страница 32: ...technical support We will try our best to answer as promptly as possible If applicable Stilla Technologies offers to engage for remote troubleshooting by using the shared desktop application Team Viewer which is installed on the naica PC To enable remote software maintenance on the naica PC provided by Stilla Technologies check that the naica PC is turned on and connected to the Internet Then doub...

Страница 33: ...tronic waste l Shipment If shipping the Geode or the compressed air system ISPTLAPG3 is required use all the original packaging and cables provided upon reception of the naica system No chips Sapphire chip Opal chip must be left inside the Geode The original double packaging and protective foam should be used for the Geode To prepare the Geode for shipment proceed carefully as follows 1 Remove any...

Страница 34: ...ures b Third party licenses The software embedded in the Geode uses the following third party software components libqxt Linux Raspberry Pi QextSerialPort QSerialDevice Qt qtcopydialog Qwt The software version as well as the license information of all the third party software components is also accessible through the Geode user interface by pressing System in the main panel and the About ...

Страница 35: ...Villejuif FRANCE Phone 33 09 82 29 50 50 North American Office Stilla Technologies Inc 66 Cherry Hill Drive Suite 110 Beverly MA 01915 USA Tel 1 833 888 0150 For sales related queries please contact our local office in your region or refer to www stillatechnologies com Pat www stillatechnologies com patents MKT 00083 Rev A ...

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