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RIDA

CYCLER

Version 1.0

User manual

Acknowledgement of Registered Trademarks

Adobe

and

Reader

are both registered trademarks of Adobe Systems Incorporated, San Jose

CA USA

Bluetooth

is a registered trademark of the Bluetooth SIG, Kirkland WA USA

CAL Fluor

, Quasar® and BHQ

are registered trademarks of Biosearch Technologies,

Petaluma CA USA.

Eclipse

is a registered trademark of Epoch Biosciences Inc., Bothwell WA USA.

Eva Green

is a registered trademark of Biotium, Hayward CA USA.

Hex™, NED™, ROX™, Cy™, FAM™, TET™, TAMRA™ and JOE™ are trademarks, and VIC

is a

registered trademark of Applera Corporation, Foster City CA USA.

Iowa Black

is a registered trademark of Integrated DNA Technologies Inc., Coralville IA USA.

LC Green

is a registered trademark of Idaho Technology Inc., Salt Lake City UT USA.

is a registered trademark of Roche Holding AG, Basel Switzerland.

LUX

probes, Texas Red

, SYTO

, SYBR

, PicoGreen

, and RiboGreen

are registered

trademarks of Life Technologies, Carlsbad CA USA

Plexor

is a registered trademark of Promega, Madison WI USA

Scorpion

probes are a registered trademark of Sigma-Aldrich Corporation, St. Louis MO USA.

Windows

is a registered trademark of the Microsoft Corporation, Redmond WA USA

Summary of Contents for Rida Cycler

Page 1: ...R Biopharm AG RIDA CYCLER User Manual BILD...

Page 2: ...RIDA CYCLER Version 1 0 User manual 2...

Page 3: ...RIDA CYCLER Version 1 0 User manual 3...

Page 4: ...express prior written consent Subject to technical changes Technical changes deviations in illustrations and errors reserved 2018 R Biopharm AG Darmstadt User manual RIDA CYCLER ZRCYCLER Version 1 0 2...

Page 5: ...RIDA CYCLER Version 1 0 User manual 5 User manual...

Page 6: ...d 19 5 1 Loading tubes 19 5 2 Removing tubes 22 6 Software overview 22 6 1 Tool bar 23 6 1 1 Help icon 23 6 1 2 Open run files 24 6 1 3 Instrument icon 24 6 1 4 Instrument Communication Icon 26 6 2 Fi...

Page 7: ...a template 52 11 During a run 52 11 1 Modifying a profile during a run optional 53 11 2 Data 53 11 3 Messages 54 12 Analysis 54 12 1 Cycling analysis 55 12 1 1 Graph types 55 12 1 2 Cycling analysis p...

Page 8: ...Instrument 73 EC Declaration of conformity CE Mark 73 Type Plate Symbols 74 Disposal Information 74 Annex 1 Temperature verification system TVS 75 Annex 2 Error messages and warnings 76 Annex 3 Toshib...

Page 9: ...accessories or external equipment other than that specified Safety warnings must be adhered to at all times to avoid risk in personal injury and or damage to the instrument If the equipment is used i...

Page 10: ...RIDA CYCLER Version 1 0 User manual 10 ATTENTION Follow the instructions to ensure optimal instrument performance...

Page 11: ...rning Do not clean the chamber with flammable liquids The chamber can reach temperatures above 100 C 212 F Any flammable liquids in the chamber could be a fire risk Hot Surface In the event of a user...

Page 12: ...RIDA CYCLER Version 1 0 User manual 12 Keep the side vents free from obstruction to prevent interference with the cooling of the instrument...

Page 13: ...s inside the instrument Service should only be performed by an authorized party Intended use The RIDA CYCLER instrument is intended to be used to perform qPCR for molecular biology research applicatio...

Page 14: ...ptor into the back of the instrument To avoid electrical arcing ensure that the power adapter is not plugged into a wall socket before plugging into the instrument Plug the power cord into a wall sock...

Page 15: ...RIDA CYCLER Version 1 0 User manual 15 Ensure that the PC has Bluetooth enabled if this is the preferred connection...

Page 16: ...cted instruments are now ready to be used 1 3 Updating software Please check the website www r biopharm com periodically to see if new software and firmware updates are available or contact your R Bio...

Page 17: ...d shut during a run to protect the user from moving parts Fig 2 RIDA CYCLER Top view 4 Lid Provides access to the rotor 5 LED indicator When illuminated blue indicates that the instrument is powered O...

Page 18: ...trument Mic SBS robotic loading block Art No ZRC MIC SBSLB SBS dimension loading block to fit most liquid handling systems Loads 2 x 48 well Mic racks Fig 4 Consumables and accessories 4 LED Indicator...

Page 19: ...correctly oriented into the loading block and instrument Fig 5 Closing the tubes Use the provided loading rack to pipette reagents and samples into each tube The tubes are pre packed into a loading ra...

Page 20: ...RIDA CYCLER Version 1 0 User manual 20 Fig 6 Loading rack set up...

Page 21: ...d water tubes in unused wells No tubes empty tubes and tubes with different volumes of liquid all have different thermal loads on the metal rotor Variations in thermal load around the rotor can cause...

Page 22: ...the lid for at least 5 minutes until the chamber has cooled The rotor within the chamber could be above 40 C 104 F To avoid personal injury do not touch the rotor for at least 5 min Remove the tube c...

Page 23: ...the tool bar Instrument Communication Detect available instruments via USB or Bluetooth 6 1 1 Help icon The Help icon is used to access the following options Fig 10 Help icon overview RIDA CYCLER Manu...

Page 24: ...he type of communication achieved The serial number or name of the instrument is displayed next to the communication symbol The status of the instrument is also displayed beneath the name Idle Instrum...

Page 25: ...RIDA CYCLER Version 1 0 User manual 25...

Page 26: ...tware upgrades Temperature Verification Allows you to determine if the instrument is within specification using the Temperature Verification System TVS See Appendix A on how to operate the TVS This op...

Page 27: ...e associated tab Use the down arrow to view files that might be out of view if multiple tabs are open at the one time Fig 15 File tab overview 6 3 Navigator bar To the left hand side of the main user...

Page 28: ...1 0 User manual 28 Fig 16 Navigator bar 6 4 File active windows In the central area of the user interface are segmented windows that are active for a specific section of the navigator bar Fig 17 Cycl...

Page 29: ...RIDA CYCLER Version 1 0 User manual 29...

Page 30: ...an and standard deviation or as individual wells 6 4 1 CSV Export or Copy to Clip Board Each Result table and Samples editor will have two options for copying the data for easy export to third party s...

Page 31: ...lication purposes For larger posters e g A0 the images may appear slightly grainy Fig 18 Result image as bitmap 6 4 4 Result Table Organization Each column can be sorted in both Ascending and Descendi...

Page 32: ...area to view more detail within the graph To zoom back out double click anywhere on the graph Pan Combining the Zoom function with Pan allows you to move the display around a magnified field of view...

Page 33: ...and displaying the name of the sample in a small text box along with the well number The sample bar in the Samples selector is also highlighted in black Similarly hovering over a sample in the Samples...

Page 34: ...RIDA CYCLER Version 1 0 User manual 34 View icon located on the sample selector There is also an option to Show All or Hide All...

Page 35: ...mples Selector Grouping icon to view the sample selector based on Assay Sample Name or None well order Fig 25 Sample grouping This option makes it easier to view or hide samples based on grouped types...

Page 36: ...emplate for the new run from the drop down list Fig 27 Template window 8 1 Adding assays Select the Assays required for the run by selecting the Add button You can select from any library of assays di...

Page 37: ...Fig 29 Shortcut library You can create a new assay library Shortcut Select the button next to Personal Shortcuts then browse and select the location of the new directory you wish to use as a personal...

Page 38: ...le will be adjusted to match the run This may also add melt steps to the run s profile if required by the assay Add Without Modification The selected assay will be added without modification The assay...

Page 39: ...ual 39 8 3 Updating Changes to an Assay Further changes in the Information fields can be made to the assay These changes can be saved to a new or existing Assay file by clicking on the Save icon locat...

Page 40: ...ure that the lid is closed prior to starting the run A lid sensor will detect if the lid is open and will prevent the instrument from starting while a warning will notify you of the fact Double check...

Page 41: ...ersion 1 0 User manual 41 The instrument will automatically lock the lid centrifuge the samples down and then the run profile will begin The LED indicator will turn green to notify a user the instrume...

Page 42: ...lect from the options below A B C D E F G 2 3 4 5 1 6 H 8 9 10 11 7 12 96 well plate Mic block Left half Right half By column By row Fig 35 Well layout Display wells as either numerical 1 2 3 or alpha...

Page 43: ...ut different assays will be linked based on the type of analysis chosen You can highlight multiple cells within a column and enter the same characters to annotate replicates Alternatively enter the na...

Page 44: ...k on the Auto fill icon The names will be sequential based on the first two inputs and the replicates for each will be automatically filled in too Fig 36 sample name options 9 1 5 Type Select the samp...

Page 45: ...RIDA CYCLER Version 1 0 User manual 45 To change multiple cells at once highlight the cells use the F2 key on your keyboard and then select from the following options...

Page 46: ...or for contamination of the assay and is helpful in preventing false positives Unlike the NTC the negative control can contain an internal amplification control template to ensure the PCR is working 9...

Page 47: ...the cells required to complete the dilution series and replicates Click on the Auto fill icon The concentrations will be filled based on the first two inputs and the replicates for each will be automa...

Page 48: ...cate an assay to a sample will result in the sample not being analyzed Link one Assay to a sample Select the required samples by highlighting the cells in the Assays column Use Ctrl Click to highlight...

Page 49: ...de a RNA integrity number for each input RNA Comment provide additional information about the samples Fig 40 Select visible sample data columns 9 1 10 Import samples Import sample information from a n...

Page 50: ...rnings Various warnings will be displayed if annotations have not been completed correctly Some examples include If standards have been selected as Type but no values have been entered into the Standa...

Page 51: ...RIDA CYCLER Version 1 0 User manual 51 Fig 44 Information window...

Page 52: ...As button 10 2 Opening a template Install Template Help button on the tool bar In the New button on the tool bar select the template The run will open with all the saved parameters including sample an...

Page 53: ...run Use this function if you believe you required more cycles to thoroughly complete amplification You can only add another five cycles while the cycling is still running up to a maximum of 60 cycles...

Page 54: ...uantification Analysis specific parameters are provided for edit and report tables are displayed along with various graphs depending on the analysis type We have taken care to provide the most robust...

Page 55: ...ny other analysis type that uses cycling data Standard Curve and Absolute Quantification allowing you to adjust parameters associated with generating Cq and efficiency values By selecting Cycling Anal...

Page 56: ...RIDA CYCLER Version 1 0 User manual 56 Fig 50 Cycling analysis options Linear y axis display the baseline corrected cycling data with the y axis in linear scale by selecting the Linear y axis icon...

Page 57: ...re first cycles use this setting if there is a significant deviation in the baseline at the start of the run These changes can occur due to many factors including too much template or insufficient den...

Page 58: ...dyes The default level is set to 5 Auto Exclusion If the sample is excluded its Cq value is not determined and it is not included in the window of linearity calculation Depending on the exclusion set...

Page 59: ...on samples may also be excluded from the window of linearity calculation if The second derivative maxima occur at the extreme of the data range The logarithm of the normalized fluorescence trace is no...

Page 60: ...le can be compressed by hiding the individual sample results using the triangle at the top of each replicate row or selecting the Full Collapse option in the Sample table selector for the whole table...

Page 61: ...esented in the associated parent analysis Fig 54 Floating window Select the delete icon in the top left corner of the floating window to close the floating window 12 3 Standard curve using absolute qu...

Page 62: ...andard annotated in the Samples editor A line of best fit is generated for the data plot from which the slope of the line is determined Fig 55 Efficiency calculation Efficiency From the slope of the l...

Page 63: ...le location as a micsc file This file can be imported into any run containing cycling data and used as part of the Absolute Quantification analysis Fig 56 Exporting the standard curve 12 3 2 Standard...

Page 64: ...ly paired with and will appear beneath the Standard Curve Analysis in the navigator bar Use Cycling Analysis to make modifications to analysis parameters such as Method or Ignore first cycles The same...

Page 65: ...rve will be displayed on a dashed line Samples outside the limits of a standard curve should be treated with caution To avoid having samples outside the limits of the standard curve ensure that your s...

Page 66: ...w of the report will be displayed to the right and can be configured to show only certain parts of the run 13 1 Report configuration Each report is divided into two standard sections Run Properties an...

Page 67: ...rsion of software used The run name will be displayed in the page header Fig 61 Report preview 13 2 1 Run properties The Run Properties section will display the following Name The name of the run File...

Page 68: ...rations and Assay All 48 samples will be displayed 13 2 3 Analysis Each analysis will be displayed depending on the information provided for the analysis Only the targets selected will be displayed To...

Page 69: ...page and Last page Export Export the report using one of the available file formats including PDF XLS and Text file Each export will have a set of options to choose from Send Email a report using one...

Page 70: ...ormation Contains information about the software version file location operator start and finish times along with the run logs Samples The Samples editor is reproduced in Excel format Assays Informati...

Page 71: ...RIDA CYCLER Version 1 0 User manual 71 Fig 63 Excel workbook...

Page 72: ...mperature Input Range 35 99 o C min 40 o C when cycling Optical Detectors High sensitivity photodiode per channel Excitation Sources High energy light emitting diode per channel Channels Green Ex 465...

Page 73: ...ic instrument including the chamber and tube clamp can be decontaminated using a solution of sodium hypochlorite NaOCl A solution containing 1 gL 1 available chlorine will be suitable for sanitation i...

Page 74: ...for Laboratory Equipment CE Marking The device is in compliance with the essential requirements and other relevant previsions of Low Voltage Directive 2006 95 EC Disposal Information European Union EU...

Page 75: ...erified to your computer and switch it on Take the TVS out of the protective case and connect it to your computer through USB Open the RIDA CYCLER software Version must be at least 1 0 Verification Pr...

Page 76: ...and place it back into the protective case Annex 2 Error messages and warnings The following error messages and warnings are possible The selected assay is not compatible with the run The assay s pro...

Page 77: ...ooth adapter Select the Bluetooth section header and a number of child items will appear In Windows 8 select the Bluetooth VX Module where X is a version number as the Bluetooth adapter In Windows 7 s...

Page 78: ...will break the signature resulting in a notification by the software The Data Integrity can be found in the Information page of the run file b The ability to generate accurate and complete copies of...

Page 79: ...rovided by organization document management system see note below h Use of device e g terminal checks to determine as appropriate the validity of the source of data input or operational instruction Th...

Page 80: ...RIDA CYCLER Version 1 0 User manual 80...

Page 81: ...alating LC Green 455 495 HRM dye SYTO 9 483 503 HRM dye FAM best 494 515 Conjugated label SYBR Green I 494 521 Intercalating RiboGreen 500 520 RNA label PicoGreen 502 523 ds DNA label Eva Green 503 52...

Page 82: ...RIDA CYCLER Version 1 0 User manual 82 Quasar 705 690 705 x Conjugated label...

Page 83: ...AM TET TAMRA and JOE are trademarks and VIC is a registered trademark of Applera Corporation Foster City CA USA Iowa Black is a registered trademark of Integrated DNA Technologies Inc Coralville IA US...

Page 84: ...using real time quantitative PCR and the 2 Delta Delta C T Method Methods 25 4 402 8 3 Ramakers C Ruijter J M Lekanne Deprez R H and Moorman A F M 2003 Assumption free analysis of quantitative real t...

Page 85: ...ation cycle CV Coefficient of variation IAC Internal amplification control LoD Limit of detection NTC No template control PCR Polymerase chain reaction qPCR Real time PCR RIN RNA integrity number RT q...

Page 86: ...ather than another nonspecific target Use of NTC s helps determine analytical specificity Hydrolysis probes are short oligonucleotides with a fluorescence reporter dye at the 5 end and a quencher mole...

Page 87: ...LER Version 1 0 User manual 87 Bio Molecular Systems Pty Ltd Unit 5 3 Northward Street Upper Coomera QLD 4209 Australia Phone 61 02 9332 1694 E mail support biomolecularsystems com www biomolecularsys...

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