Thermal Cyclers ,PCR, qPCR
Contents
1. fey Microsoft PowerPor R MxPro Mx3005P Q r Well types shown c ESM HG 4 9 55 AM STLCC_CPLS Morrison 4 13 2015 Page 49 Thermal Cycler Stratagene MxPro Exporting Experiment Data Results to Excel Format 1 m File Edit View Document Comments Forms Tools Advanced Window Help x Pa Create PDF 7 i Combine Files 7 fa Export 7 E Start Meeting CE Secure 7 L Sign 7 ore Review amp Comment 7 P FEE i Ih File Edit View Insert Format Tools Data Window Help L Lm amp l v X A S x Z 1 ME 4 10c Arial B Z UE 23 PB ws t te He AT M f Segment AT B C DEF G H 1 Segment IFamp Flateau Ramp Plateau Well Dye Cycle Fluorescence Temperature 2 2P 2 1 FAM 1 21256 9 7 Es 21H 2 1 FAM 1 21 396 Sar d 21H 2 1 FAM 20893 3d a 21H 2 FAM 2 20957 Hu b 21H 2 1 FAM J 20964 s Pd 21H 2 1 FAM 3 20777 SJF B 21H 2 1 FAM 4 20878 d Z 21H 2 1 FAM 4 20064 s id 10 21H 2 1 FAM s 20946 3 3 LE xa raf P r MY Fi zl maaa A wr reuse 8 50x11 00in STLCC_CPLS Morrison 4 13 2015 Carola hx eels data far anl tall Aare oraminad lx FE DUXI TPT CA C b Page 50 From cindy jarv sdag lent com Sent Thursday January 21 2010 10 32 AM Ta Morrison Robert G St t Ge Boedeker Elizabeth D Staerk Becky K Schneider Scott E Norris Richa ra agene J E Subject RE Stratagene and MxPro at BRD2. Window Help ELE Thermal Profile Setup Standard 4 00e 0091 Standard 4 00e 0041 Standard 1 00e 001 T Ma200UD 4 filter set plate gt Standard Standard 4 00e 001 4 00e 001 Standard 4 00e 001 Standard d 00e 001 1 00e 001 Standard 4 00e 001 1 00e 001 Standard 4 00e 001 1 00e 004 4 006004 4 00e004 4 006001 Standard 4 00e 001 4 00e 001 4 00e 004 Standard 1 00e001 1 56e 001 1 56e 001 1 56e 004 1 58e 001 1 56e 001 1 56e 001 1 56e 004 Standard 1 00e001 Standard 1 56e 004 NTC Standard 1 00e 001 1 006004 2 50e 000 2 50e 000 2 50e 000 6 25e 001 2 50e4000 2 50e 000 2 50e 000 Standard 2 50e 000 2 50e 000 Standard amp 25e 001 1 56e 001 2 50e 000 6 258 001 1 568 001 Z 50e 000 6 25e 001 1 568 001 Standard 6 25e 004 6 25e 001 6 25e 001 Import Defaults bi Wall type Standard Show well Names Collect fluorescence data Reference dye none All well Assign Assay M ames Standard quantity al Auto Increment lk nanograms Identify replicates Auto Increment Standard units Replicate symbol Plate setup comments Full Screen Plate Nest gt Assays shown Assian Well Type and sau to selected wells The Ctrl key selects multiple wells 1 a
3. 7 5 60 38 60 54 60 74 419 421 419 418 30 NA 30 NA 30 NA 30 NA 0 60 44 0 60 62 J 5 60 84 7 2 61 01 5 2 5 2 424 424 423 421 10 10 10 10 2 3 2 5 7 5 12 5 3 3 3 3 60 32 60 51 60 69 8888 207 208 208 208 0 0 0 0 2 5 2 5 0 60 42 60 83 61 03 s5 o Thermal Cycler Smartcycler Exported Results File C13 Optic C13 Optics D C14 Ten C14 Optics C14 Opi C15 Temp C15 Opi C15 Optics C16 Temp C16 Optic 234 235 234 233 Page 24 Thermal Cyclers Smartcycler Misc Dye Info Cy3 and Cy5 are reactive water soluble fluorescent dyes of the cyanine dye family Cy3 dyes are green 550 nm excitation 7570 nm emission and therefore appear green while Cy5 is fluorescent in the red region 650 670 nm but absorbs in the orange region 7649 nm 3 4 They are usually synthesized with reactive groups on either one or both of the nitrogen side chains so that they can be chemically linked to either nucleic acids or protein molecules Labeling is done for visualization and quantification purposes They are used in a wide variety of biological applications including comparative genomic hybridization and in gene chips which are used in transcriptomics They are also used to label proteins and nucleic acid for various studies including proteomics and RNA localization 5 Texas Red or sulforhodamine 101 acid chloride is a red fluorescent dye used in histology for staining cell spec
4. 08 NEG 0 00 MEG aper spring 201 Cya CB gperspri UNEN UK FOS 19 69 NEG 0 00 MEG Ja Texas Red CH qncr spri UNEN UK FOS 22 56 NEG 0 00 MEG Uy Cr pcr spri UNEN UK FOS 23 53 NEG 0 00 MEG Standard CB qpcr spri UNKI UK POS 22 32 MEG 0 00 MEG CH gperspri UNKI UK POS 20 17 NEG 0 00 MEG C10 qpcr spri UNKI UK POS 70 60 NEG 0 00 MEG C11 aper spri UNKI UK POS 21 43 MEG 0 00 MEG MINNS TE Select Graphs View Another Run Delete Huns Update Analysis Import Std Curve Compare Run SS mI H O H 4 Thermal Cyclers Smartcycler Create Run Check Status Graph log STER Green threshold line gc of Malt temp gc of SYBR Green threshold lin TET CT LOG FAM CT 2ND FAM CT LOG FAM CT FAMITET Temperature SHR Green Malt FAN Cya Texas Red 5 Standard TET Hew Graph SILCC CPLS Morrison 4 13 2015 Graph Type Show Define Graphs Example Maintenance Page 23 Run Summary Run Nan Cheryl lab2 part 2 Started FH Number Results Table SiteID Protocol Sample ID C11 gpcr spring 2011 h Alu C12 gpcr spring 2011 h Alu C13 gpcr spring 2011 h Alu C14 gpcr spring 2011 h Alu C15 qpcr spring 2011 h Alu C16 gpcr spring 2011 h Alu D1 gpcr spring 2011 h Alu D2 gpcr spring 2011 h Alu D3 qpcr spring 2011 h Alu DA gpcr spring 2011 h Alu
5. D5 gpcr spring 2011 h Alu D6 gpcr spring 2011 h Alu D7 qpcr spring 2011 h Alu Analysis Settings Ch amp Dye Name Usage l FAM Assay 2 Cy3 Assay 3 TxR Assay d Cys Assay Melt Data Instrument C Smart Cycler 2 0d Sample Ty Note Status FAM Std Res FAM Ct Cy3Std Res Cy3Ct TxRStd ReTxRCt Cy5Std R Cy5 Ct OK OK OK OK OK OK OK OK OK OK OK OK OK UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN UNKN POS NEG POS POS POS POS POS POS POS POS POS POS NEG 28 99 NEG 0 NEG 21 86 NEG 21 52 NEG 31 76 NEG 29 92 NEG 33 75 NEOG 34 58 NEG 25 91 NEG 27 75 NEG 30 45 NEG 29 59 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG 0 NEG ce e a IR i e i a a Melt Peakl 81 96 62 42 61 64 82 13 82 97 82 31 82 33 82 71 82 27 83 03 82 25 82 58 Bkgnd Suk Bkgni Bkgnd Curve Analysi Thresh Se Manual Thre Auto Th Auto Min C Auto M Valid Min Valid M Boxcar Avg Target ON ON ON ON 2 2 5 2 40 Primary Curve Manual 40 Primary Curve Manual 40 Primary Curve Manual 40 Primary Curve Manual C11 Tem 11 Optics C11 Optics C12 Temp C12 C C12 Op C13 Temp 60 29 60 5 60 7 60 87 294 2 295 2 295 293 F 2 5 5 5 60 62 60 86 61 01 STLCC_CPLS Morrison 4 13 2015 105 108 109 111 10 10 7 5
6. Dx H 24x 44 x 21 9 x 17 5 x 8 Weight 10 kg 22 Ib Gradient Gradient accuracy 0 5 C of programmed target at end rows NIST traceable Row uniformity 0 5 C well to well within row within 30 sec of reaching target temperature Gradient range 30 99 C Temperature differential range 1 25 C STLCC CPLS Morrison 4 13 2015 Page 2 Thermal Cycler MyCycler HotLink to User Manual Plug in the unit to provide power there is no toggle on off switch Turn on by pressing the Stand by key once To put into Stand by mode conserving power hold down for gt 3 sec Turn off completely by unplugging the unit there is no on off switch STOP key will pause a protocol when running Pressing STOP again will terminate the protocol HELP menus are available From the HOME startup screen select F5 Help to review topics and display an index of features Hot link to Bio Rad MyCycler User Manual 45 pgs pdf STLCC_CPLS Morrison 4 13 2015 Page 3 Thermal Cycler Mycycler BioRad Quick Guide Page 1 2 1 Power up the MyCycler by either plugging in the instrument or pressing the standby key on the front panel of the instrument if in Standby mode After a quick diagnostic routine the Home screen will be displayed 2 Press F2 Create from the Home Screen A selection menu will appear 3 Select the Custom option from the selection menu it should be selected by default and press Enter You may also c
7. Morrison 4 13 2015 Page 16 Thermal Cyclers Smartcycler Define Protocol Example Define Graphs Maintenance Protocol Name SYBR Green for qPCR class 08 qPCR class Cyclo and other SMIT 2 ABI primer probes Copy af Alu human 2007 Alu human quantitation with melt qFactor 8 with Jaki per PER pcre auant Copy af STLCC 3 STLC E 2 D LE 2 Step bU 3 Step BU Er H PCR Fast 2 Step 60 Hew Protocol Delete Protocol Protocol Duplicate Protocol Protocol Rename Protocol Protocol Save Protocol Protocol Move To Move To Top STLCC_CPLS Morrison 4 13 2015 Page 17 Thermal Cyclers Smartcycler Define Protocol Enter View Stages Smart Cycler Sel User Logs Setup Tools Help Create Run View Results Define Protocols Define Graphs Maintenance Protocol Name 2 Step 60 lgpcr spring 2011 h Alu 13 Step pU amp 72 Irt PER 13 Step w Malt IFast 2 Step 60 Stage Z Stage 5 Repeat 35 times Unused ha 3 Temperature Cycle i S 60 0 95 0 Chi 0 2 Advance to Next Stage New Protocol Delete Protocol Duplicate Protocol Duplicate Protocol Rename Protocol Rename Protocol Protocol ann enine em Page 18 Thermal Cyclers Smartcycler Create Run Add Remove Sites 1 Enter Run Name AT amp Smart Cycle 1 2 Select Dye Set User Logs Setup Tools Help 3 S 4 Select Sites cells 5 Select Arrow to move to list 6 When done select
8. OK FAM Std Cy3 Std o Conc Cone Protocol Run Name test 1 22 Select Protocols and Sites Eer hAlu Sp 14 5 3 assay 2013 x hAlu new melt specs 20150124 hAlu 1 anneal 20130122 hAlu 20130116 phycal sybr green 2 phycal sybr green 1 esli 5 3 assay GPCR 20 BAE probe test KY e h Alu BAE 20120204 Protocol h amp lu Spy 4 h amp lu Spy 4 h amp lu Spy 4 Inm h amp Alu Sp 4 AS AAW Spy 4 AB hAlu Spy 4 Notes dl Add Remove Sites EEE Stes aT in Valid Max Boxcar Avg Target Cycle Dye Set FCTC25 ch Dye Usage Bk nd la Name sub Cycles a Fam assay jon j 8 60 Cy3 Assay JON 1 A9 B EE 1 D 2 M U sfa TR Assay JON j A10 s 60 D la cy5 Assay ON 1 11 B D A12 q 213 A14 Protocols Protocol Lot Number Select All Sites DEE Cancel Run Setup Report Run Setup Select Graphs Copy Run Setup c Smart Cycler p Documenti Microsof Search Desktop SC R L 7o A Ed 543 AM STLCC_CPLS Morrison 4 13 2015 Page 19 Thermal Cyclers Smartcycler Check Status Block Cell Errors e ML amp Smart Cycler TEK cu Home me I User Lo s Setup Tools Help n gg Cut f Find 54 Copy sap Replace isis F Format Pai k Select Clipboard Create Run View Results Define Proto
9. SILCC CPLS Morrison 4 13 2015 sample capacity Maximum ramp rate C sec Average ramp rate C sec Temperature range Temperature accuracy Temperature uniformity Input power Display Port Memory Dimensions Wx D x H Weight Gradient Gradient accuracy Row uniformity Gradient range Temperature differential range 96 x 0 2 ml tubes 0 2 ml tube strips or 1 x 96 well plate 4 2h 4 100 C 0 5 C of programmed target 0 5 C well to well within 30 sec af arrival at target temperature 100 150 VAC 50 60 Hz 220 240 VAC 50 60 Hz 700 W maximum 5 7 VGA color touch screen 1USBA 500 typical programs unlimited with USB flash drive expansion 26 X 47 x 23 cm 10 x 18 x 8 9 kg 20 Ib 0 5 C of programmed temperature 0 5 C well to well within row within 30 sec 30 100 C 1 25 C Page 6 Starting the Instrument Remove the T100 thermal cycler from the box and plug it in Turn on the power switch on the back of the instrument The T100 cycler will perform a quick T100 Thermal Cycler self test and then display the Home screen Figure 1 BIO RAD Thermal Cycler T100 Bio iin adh ni Rad Quickstart Setting the Date and Time First make sure the system clock is correct for your time zone so that all runs are accurately recorded in the run log 1 In the Home screen touch Tools and then Settings to display the instrument settings menu Figure 2 2 Touch the fields for Month Day Year Ho
10. Stande Temnd 361272011 Done Default User Jan 27 2011 04 57 E poet SE wires 7 Step 60 110127 1ChemlW Done Default User Jan 27 2011 04 56 SAEs 78 Melt rerun2JR 1 27 11 Done Default User Jan 27 2011 04 53 e a Fam rerun iriley 01 27 11 Done Default User Jan 27 2011 02 57 Start End Optics Deg Sec DegiSec i Jd oy3 aa12711 D one Default User Jan 27 2011 03 54 0 2 Status Done if Texas aper spring 2011 h A T10127 Done Default User Jan 27 2011 03 50 Cy5 gpcr spring 2011 h A 110127 Dione Default User Jan 27 2011 03 48 Notes if Standd JFT 27 11 Done Default User Jan 27 2011 03 46 1 pqut2711 Done Default User Jan 27 2011 3 43 h Alu standard curve bh 01 1 Done Default User Jan 18 2011 2 45 goer spring 2011 NTS Done Default User Jan 18 2011 5 12 pqu115811 Done Default User Jan 18 2011 06 10 4 gpcr spring 2011 h 4110118 Done Default User Jan 18 2011 05 08 gpcr spring 2011 h A110118 Done Default User Jan 18 2011 05 06 aw FAM Ct Cy3 Cy3 Ct T R qpcr spring 2011 h A 110118 Done Default User Jar 18 2011 05 04 Res Otdi Res S R qpcr spring 2011 h amp 110118 D ne Default User Jan 18 201105 02 k inu MEG D ag MEG goer spring 2011 h A110118 Done Default User Jan 18 20110500 Dye Set FCTC25 Tempd gpcr spring 2011 NR Done Default User Jan 18 2011 4 58 JInterca aper spring 2011 bae 01 18 Done Default U
11. system Requires 220V 20A L620P plug 11 20R receptacle STLCC_CPLS Morrison 4 13 2015 Page 33 Stratagene Mx3005P Thermal Cycler Agilent Stratagene Mx3005P Prepared by Bob Morrison FVCC Instrumentation Specialist June 09 Aug 09 STLCC CPLS Morrison 4 13 2015 Slide 34 Thermal Cycler Stratagene Mx30045E Sliding Door access to plate and heating elements CAUTION Avoid contact rr RS232 Serial out port to MxPro with anything other than plate computer controller Upper Light Green connected to host CPU Lower light Power on off On Off toggle at rear 5 E istrument lower near power plug gi Excitation source Quartz Tungsten Halogen lamp Detector 1 scanning photomultiplier tube PMT Multiplexing capabilities 4 targets in the same tube Link to Stratag ene Mx3000P Thermal system solid state Peltier based User Guide pdf Embedded computer safeguards data Filters Dual customizable filter wheels with four user selected filters Tube plate formats 200ul 96 well format optimized for 25ul sample size 96 WELL QPCR PLATES NON SKIRTED System Specifications T B onse Lr Dynamic Range 10 orders of magnitude Well Non Skirted Polypropylene ate for use wi T p Mx3000P Mx3005P QPCR Systems Compatible with our crar m e es Mx3000P Mx3005P Optical Strip Caps catalog number 401425 ene T L aL i Temperature Uniformity 25 C at 72 C 96 WELL OPCR PLATES SE
12. 0 QuickStart Guide pdf STLCC CPLS Morrison 4 13 2015 Page 9 Thermal Cycler PCR HYBAID Omn E 96 well STLCC CPLS Morrison 4 13 2015 Features Heat cool cycles for performing the polymerase chain reaction PCR in micro tubes 96 well heating block for 0 2 ml tubes power on off rocker switch in the back of Instrument LCD window for data display touch button data entry RS 232 port Overall dimensions of the unit width 7 in depth 11 height 8 5 Shipping weight is about 20 pounds Page 10 Thermal Cycler PCR Sprint HYBAID Limited 20 well Picture is similar to but not the Actual PCR Sprint device Model has 20 welis one with probe STLCC CPLS Morrison 4 13 2015 Page 11 Thermal Cycler Cepheid SmartCycler I and II Rapid real time thermal cycler used for identifying DNA RNA from prepared biological samples Delivers highly accurate and consistent test results in as little as 20 minutes Up to 16 independently programmable reaction sites can simultaneously run multiple experiments with different protocols and at different times Each independently programmable module performs four color real time fluorometric detection Specifications Weight 22 lbs Measurements 12 W x 10 Lx 12 H in Electrical 100 240 VAC 50 60 Hz 350 Watts Max current 7A Heating ramp rates max 10 C sec from 50 C to 95 C Cooling ramp rates max 2 5 C sec from 95 C to 50 C Temperature duration accur
13. 5 610 HEX JOE Filter 535 555 FAM Filter Set Plate setup comments oe shown Well types shown EE Well Type and il to selected wells The AU diz selects multiple wells E el 2 MxPro Mx3005P Q ej Microsoft PowerPoi c EMG Woe SE STLCC CPLS Morrison 4 13 2015 Page 46 Thermal Cycler Stratagene MxPro Tools Tab Preferences La MxPro Mx3005P Quantitative PCR HES SSE File Er dit Ins trument Too Osea Soc 3 e LE e HELE Preferences Colors Display Defaults MxPro Mx3005P data folder r utofilenaming Include in auto filename l Date tc MM DD rYYY C DDMMYYYY C YYYY MM DD W Time Example filename Quantitative PCR 07 06 2009 O9Hr 22Min r Export decimal using Point e g 34 32 Comma Flate setup eomments Full Screen Plate Next gt Door Closed BENE Eid GG HO Woe 0 77 AM imiz shown JE Well type
14. G Park Permission to Dear Bob You have permission to copy the software to the laptops indicated below CODy MxPro to Kindest regards Cindy Cindy Jarvis Laptops Agilent Technologies Account Manager 314 706 9945 Cindy jarvis agilent com From Morrison Robert G mailto BMorrison stlcc edu Sent Thursday January 21 2010 10 17 AM To JARVIS CINDY A LaJolla exl1 Cc Boedeker Elizabeth D Staerk Becky K Schneider Scott E Norris Richard J Subject Stratagene and MxPro at BRDG Park Cindy Last summer you helped with Betsy Boedeker s class getting us a loaner Stratagene and then obtained permission for us to copy the MxPro software to 8 laptops for student analysis functions At the end of the summer we replaced the loaner device with the new one we ordered and we now have all of that located at our new location at BRDG Park in the Center for Plant and Life Sciences The hardware and software we have is shown below In order to keep us and our I T people legally straight with the MxPro software that we placed on the laptops last summer we need a response in writing reply to this email is sufficient that we are allowed to populate that software to other specific laptops on our campus We anticipate the total number of laptops in our labs to be 18 eventually Can you have someone at Agilent or yourself give us this permission Thermal Cycler Agilent Stratagene Model Mx3005P SN DE92800456 Thermal Cycler Stratagene S
15. Ie Tum lamp on for warm up Dont show this again Door Closed LampOf ie Microsoft Powerbol Jf MyPro M33005P i lt EM aoe 0 15 AM nz Cycler Stratagene MxPro Plate Setup File Edit Instrument Tools Options Window Help Op Wag wv Air ERIE Thermal Profile Setup Import Defaults ag Quick Setup Show Wall Names Plate setup comments Full Screen Plate Newt gt Assays shown Well types shown Assian Well Type and Assays to selected wells The Ctrl key selects multiple wells Door Closed LPO Bu GR Woe 0 16 AM lrn C Fa ffe Microsoft PowerPor Bi MxPro Mx3005P Q STLCC CPLS Morrison 4 13 2015 Page 40 Thermal Cycler Stratagene MxPro Plate Quick Setup H MxPro Mx3005P Quantitative PCR New Expenment mxp File Edit Instrument Tools Options Section View Window Help L u E e 2 Z S 2 Setup Run Analysis PlateSetup id Thermal Profile Setup af 1 2 3 4 5 8 7 a8 9 1 n 2 dot O ey Quick Setup BEBEEEEEEEEE BENE M3UD5P 5 filter set plate ICY Negative Control JCS Negative Control _ G AD Negative Control THES Negative Control SY BR Negative Control CYS Positive Control CYS Positive Control angad ARDA Positive Control lentifu rd HEX Positive Control JSYER Positive Control Plate setup comments Fu
16. KXXXXXX a amp a hid Research PTC 220 BioRad Model PTC 1148 MJ Research Model PTC 150 Thermal Cyclers BioRad 1100 i a PCR gPCR delete this before publishing Introduction to Quantitative PCR vw uU C O pur x ig O lt x ye e o N U O Jus af D gt Stratagene gPCR Mx3005P amp STRATAGENE Ji Prepared by Bob Morrison HYBAID PCR Omn E STLCC CPLS Instrumentation Specialist STLCC CPLS Morrison 4 13 2015 June 2008 Latest Revision Feb 2013 Page 1 Thermal Cycler Mycycler Bio Rad w Gradient e A 96 well reaction module designed for use with 0 2 ml tubes or plates e Intuitive programming of temperatures times and protocol options e A user programmable sleep mode that saves power when the instrument is not in use Status and history of each run recorded in run and validation reports A self adjusting heated lid that accommodates standard 0 2 ml thin wall PCR tubes strips and plates Optional thermal gradient feature Sample capacity 96 x 0 2 ml tubes or 96 well PCR plate Speed of ramping Up to 2 5 C sec Temperature range 4 100 C Temperature accuracy 0 5 C of programmed target at 90 C NIST traceable Temperature uniformity 0 5 C well to well within 30 sec of arrival at 90 C Input power 100 150 VAC 50 60 Hz 220 240 VAC 50 60 Hz 670 W Maximum Display 12 cm 4 7 high resolution 1 4 VGA Ports 1 USB Memory 99 typical programs Dimensions W x
17. MI SKIRTED Temperature Ramp Rate up to 2 5 C second 96 Well Semi Skirted Polypropylene PCR Plate for use with 2407 Mx3000P Mx3005P QPCR Systems Compatible with our eni eyi H A b 46cm D x 17 Mx3000P8 Mx3005P Optical Strip Caps catalog number 401425 43cm H weight s 20 kilograms Page 35 STLCC CPLS Morrison 4 13 2015 Thermal Cycler Stratagene MxPro QPCR Software Perform multiple sub experiments on a single plate Real time amplification plots viewed and results analyzed during run e Standard curves plotted for multiple dyes on a single chart View all dyes on one amplification plot or view each single dye in multiplex experiments View and analyze data in multiple formats including amplification plots scatter plots fluorescence intensity screens final call results melting curves annealing range and text reports All results available as raw data Easily export data to Excel PowerPoint and text files Flexible analysis options amplification plots scatter plots standard curve charts fluorescence intensity final call results melting curve annealing range and text report View all dyes for multiplex experiments on one amplification plot and or standard curve chart or view individual plots for each individual dye Melting curve analysis with automatic melting temperature Tm calculation e Allelic discrimination by threshold cycle or by endpoint fluorescence values with auto call feature Expor
18. S Morrison 4 13 2015 Page 42 Thermal Cycler Stratagene MxPro Importing Well IDs from ogade w 28 B50f435 1 d j fl A second Microsoft Excel template format allows for up to two well name designation assignments e g gene name and sample ID per well Entries can be entered directly into the two plate setup tables provided see below For example if multiple samples have the same sample name but unique identifiers the sample name may be entered into the appropriate cells of one plate setup table and identification numbers may be entered into the appropriate cells of a second plate setup table in the Excel template file If only one well name designation 15 necessary the text in the second plate setup table can be deleted The template 1s stored n the MxPro data folder e g C Program Files Stratagene MxPro Storage Import Well Names trom Excel Plate Template xls and can be opened using Microsoft Excel Well D Well Name AT H1 LT Reference RNA 1 Reference ENA U Reference RMA 100 LI U LI LI Li LI LI Li Se XR ge re m Gere Sme frame pu ol E GarelSme name Diy gt D e a nane QW ar D area miz nima City gt D Gir S name ty ar area mize name Da gt D Gene Smo name Hu a KI GizrelEmg nine Pty ai D Gere mo name Hn ai D Well names may be mm from a Microsoft Excel file formatted as shown below with column A containing Well ID s and column B containing the wel
19. TLCC_CPLS Morrison 4 13 2015 Page 26 Thermal Cycler BioRad PTC 1148 Control Panel Figure 1 Front view of the MJ Mini thermal cycler LOD window screen hot key Black heatina cooling lights GE Selection keys Pause key 966 DOJ JOOS Proceed key EE 4 pi m Cancel key Figure 2 Control panel of the MJ Mini thermal cycler Thermal Cycler BioRad PTC 1148 Main Menu Understanding the Main Menu The Main Menu is the common access point to all programming and machine configuration screens RUN Executes a program NEV Allows new programs to be entered EDIT Allows modification of stored programs VIEW Accesses utilities that display a program s steps FILES Accesses file management utilities TOOLS Accesses machine configuration screens Using the Control Panel The control panel see fig 2 includes operation keys status indicator lights for heating and cooling an LCD window for displaying programming and machine status text and a numeric keypad for entering values into programs Operation Keys Select keys left right up down arrows Move the cursor one space or option in the LCD window Proceed Enter Accepts a selected menu or screen option during a protocol run advances the program to its next step Cancel Terminates a running protocol during program creation or editing cancels the last entry Pause Pauses a protocol during execution Inst
20. WelNames Download Data from Instrument lt mixed gt lt mixed gt mixed Discover Instruments n St r u m e nt Tab m Ni d m i gt Drop Menu units copies Plate setup comments Full Screen Plate Newt gt Assays shown Well types shown Y l zzi J z i le S MxPro My3005P Q fe Microsoft PowerPor lt Beets HO HG 6 20 AM STLCC CPLS Morrison 4 13 2015 Page 45 Thermal Cycler Stratagene MxPro Tools Tab O tics Confic LA f MxPro Mx3005P Quantitative PCR Mew Experiment mxp EUN vie Edit Instrument Tools L LA as I dl 3 RE 2 gt E 3L p P i IEEE C mus i Thermal Tele Setup E i i OOM m m a m 1 2 3 4 5 e 3 10 pa EN Tools Optics Menu Buick Setup Show Well Names r Collect fluorescence data 1 mix P mixed lt mixed J R TI ST lt MD Options Section View Window Help Optics Configuration Dyes amp Fiters Dye Assignment Scan Order instrument Selection r ptical path dye assignments Excitation Emission Dye Filter set wavelength nm wavelength nm CY5 Filter Set 635 665 CY3 Filter Set 545 558 ROX Filter Set 58
21. acy 1 0 sec from programmed time Temperature accuracy 0 5 C from 60 C to 95 C Melt curve programmable ramp rates 0 1 C sec to 1 0 C sec On Off switch on Top OK Block ID other info displayed REAR LOWER e USB connectors and e 110V AC Power STLCC_CPLS Morrison 4 13 2015 Page 12 Thermal Cycler Cepheid Smartcycler Configuration Setup Computer P C use bs m am e If using more than one Block use a daisy chain with USB connections as shown above It is not required to daisy chain 110V power If used do not connect more than 2 blocks Note that the USB on Blocks 1 and 2 should be directly connected to the computer Connect each Block to an 110 V AC power source DO NOT TURN ON YET Turn on in sequence Block 1 first then Block 2 then Block 3 and Block 4 if appropriate Activate the Smart Cycler Software on the Computer Splash screen on each block will blink and then switch to a sequence of A B C etc o0 E EN a 5 Letter A will appear on Block 1 and B on Block 2 etc 6 CLOSE Software before turning off or disconnecting any Blocks QTI CC CPI S Marrican 4 12 9015 Page 13 Thermal Cycler SmartCycler I Core Module Features I CORE Module Auto Advance Multiplex PCR Detecting multiple targets m Internally controlled assays A October 17 2005 22 STLCC_CPLS Morrison 4 13 2015 Thermal Cycler SmartCycler Reaction Tube Featu
22. adient and Ramp rate select a step and touch Options Figure 5 Program tne required parameters as needed f Touch Save to select a folder location and save the protocol B Touch Run to start the protocol You can also run a protocol without saving it by touching Run at any time while editing Running and Editing a Saved Protocol 1 In the Home screen touch Saved Protocols The T100 cycler organizes all the protocols into folders A preinstalled library of standard protocols is in the MAIN folder Figure 6 2 Select a folder from the Folders column then select a protocol file from the Files column 3 Review the selected protocol using the Preview column on the right 4 Touch Run to start the run or touch Edit to edit the protocol For more information visit www bio rad com web T100QuickGuide This product is covered by ona or mora of tha following U S patents or their foreign counterparts owned by Eppendorf AG U S Patent Numbers 6 767 512 and 7 074 367 wo Le M NS MII be I VN RM R R IMN RR T IV eV IY inten hep Fi 4 insert tep window 000 Thermal y J Cycler NS WERT T100 Bio E M D Rad See Quickstart Guide pg 2 of 2 Felder Ope ne LFS Opens Fig 6 Saved Protocols screen showing the preinstalled library of standard protocols in the MAIN folder Page 8 Thermal Cycler T100 Biorad User Manual QuickstartGuide Hot link to Bio Rad 1100 User Manual pdf Hot link to Bio Rad T10
23. ant Initiates a program that sets up the MJ Mini as a simple incubator Thermal Cycler BioRad PTC 1148 Running Protocol Running a protocol on the MJ Mini thermal cycler involves two steps 1 Choosing a stored protocol to run 2 Setting up the temperature control method Either a custom designed protocol or one of the factory installed resident protocols may be run See appendix A for descriptions of the resident protocols which may be edited to fit your needs see chapter 7 tor instructions on editing stored programs All the factory installed protocols are stored in a single folder called the MAIN folder at the time of shipping Choosing a Stored Protocol to Run With the Main Menu displayed select Run then press Proceed One of two types of screen will be displayed depending on whether custom protocols have been stored in the MAIN folder or in custom falders If all protocols have been stored in the MAIN folder A screen listing the protocols will be displayed Custom protocols are listed first followed by the factory installed programs Run PROGRAMS MATIN IPHFTKb IPHFSkb IPHF1Skb LONG 2 LONG 3 Thermal Cycler BioRad PTC 1148 Key Features Thermal gradient technology that permits simultaneous incubation at 8 different temperatures for optimizing reactions in a single run Ability to upgrade to the MiniOpticon 2 color real time PCR system e Superior temperature performance that matche
24. cols Define Graphs Maintenance Editing Views 4 Protocol Name Results Table gpcr spring 2011 h Alu Jf Analysis Settings gpcr spring 2011 Alu OMH11012 1 lys T Brotacals i Temperature Stage 2 Stage 4 User Default User i Intercalate i Repeat 35 times f Melt 5 Started Jan 27 2011 05 0 PM FAM Degsec Finished Jan 27 201105p2PM E5 Ay DM ee 2 i Texas Red Status Done cys i Standard Notes MR Protocol SamplelD Sample Status FAM FAMCt cya Cy3Ct TAR StdiRes B lRes Bie Error POS 31 80 NEG 0 00 INEG Error POS 1584 NEG 000 NEG OK POS 14 60 NEG 000 NEG OK POS 685 NEG 000 NEG OK Pos 1832 NEG 0 00 NEG OK POS 20 08 NEG 000 NEG Uk X POS 185 58 MEG 0 00 MEG Uk POS 22 58 MEG 0 00 MEG Uk POS 23 53 MEG 0 00 MEG OK POS 7237 NEG 0 00 NEG UK POS 20 17 MEG 0 00 MEG OK FOS 20 60 MEG 0 00 MEG OK POS 2143 MEG 0 00 MEG Words 0 Thermal Cyclers Smartcycler View Results Select Run wp us me User Logs Setup Tools Help Maintenance Sla rm h 4 rn ii i an Damlarg har ee pe Create Run he Graphs select a Kun Run Name ae12720111 sick nick 1 27 11 gpcr spring 2011 Alu DIMHT 1 Done Done Default User Default User Jan 27 2011 05 05 Jan 27 2011 0503 Status BR r ag12720111 Done Default User Jan 27 2011 05 19 if
25. ernet v a Microsoft Po Wav 9 40 AM olLUUC UCPLo5 Morrison 4 13 2019 Page 37 Thermal Cycler Stratagene MxPro Software About MxPro Mx3005P Mx Pro Mx 3005P v4 01 Build 369 Schema 80 2007 Stratagene All rights reserved Instrument versions Q5 v6 22 Control v4 40 Firmware v110 61 Experiment last saved under not available Trademarks United States MxPro is a trademark of Stratagene STBR is a registered trademark of Molecular Probes Inc Eva reen is a trademark of Biotium Inc ALEXA Hour 350 is a registered trademark of Molecular Probes FAM TET HEX VIC JOE TAMRA and ROX are trademarks of Applera Corporation or its subsidiaries in the US Siia E Cy 3 and Cy 5 are trademarks of Amersham Biosciences Microsot and PowerPoint are registered trademarks of I Microsoft STLCC CPLS Morrison 4 13 2015 Page 38 Thermal Cycler Stratagene MxPro Software Startup Jelal D Nev Koeriment IVIOGC aE a Tac Hi MxPro Mx3005P BLIES gw ec Y New Options Select experiment project type Realtime Quantitative PCR Multiple Standards Cancel t Comparative Quantitation Calibrator L SYBR Green with Dissociation Curve L EvaGreen with Dissociation Curve Allele Discrimination SNF s Real Time Molecular Beacon Melting Curve Plate read C Quantitative Plate Read Plate Read Allele Discrimination Project type L
26. hoose to edit a Bio Rad template protocol listed in this menu if the template protocol is similar to your desired protocol 4 Edit the fields of the protocol The default custom protocol is a simple three step amplification protocol 30 seconds at 95 C 30 seconds at 55 C followed by 0 seconds at 2 C To add or delete a step or cycle press F4 Add Del and select the appropriate option Note that vertical lines demarcate different cycles and that steps with in the same cycle are not separated by vertical lines Cycles are numbered sequentially in the bottom left corner of their first step s display Use the arrow keys to move the selection box between the different fields for each step of your protocol Set point temperature fields are shown Immediately above the temperature plot line whereas dwell time fields are shown immediately below the temperature plot line The repeats field which specifies the number of times a cycle is to occur followed by an x is shown in the bottom right corner of the last step of a cycle STLCC CPLS Morrison 4 13 2015 Page 4 Thermal Cycler MyCycler Biorad QuickGuide Page 2 2 Use the arrow keys to move the selection box between the different fields for each step of your protocol Set point temperature fields are shown Immediately above the temperature plot line whereas dwell time fields are shown immediately below the temperature plot line The repeats field which specifies the n
27. imens for sorting cells with fluorescent activated cell sorting machines in fluorescence microscopy applications and in immunohistochemistry 1 2 Texas Red fluoresces at about 615 nm and the peak of its absorption spectrum is at 589 nm making it more purple than red actually The powder is dark purple Solutions can be excited by a dye laser tuned to 595 605 nm or less efficiently a krypton laser at 567 nm The absorption extinction coefficient at 596 nm is about 85 000 M 1cm 1 FAM is the most commonly used fluorescent dye for oligonucleotides attachment It exhibits high quantum ylelds and it is compatible with most fluorescence detection equipment Since it has decreased fluorescence below pH it is typically used in the pH range 7 5 8 5 STLCC CPLS Morrison 4 13 2015 Page 25 Thermal Cycler BioRad Model PTC 1148 On Off switch on Membrane Keypad Rear panel l Controls setup and operation Optional USB and Firewire ports on rear panel The MJ Mini 48 well gradient thermal cycler offers individual researchers the quality and features of advanced cyclers The MJ Mini cycler offers thermal gradient technology allowing you to optimize reactions for maximum efficiency and accurate quantitation And with the addition of the MiniOpticon two color real time PCR detection system the MJ Mini cycler is converted to the most compact real time system available Hotlink to Biorad MJ Mini Gradient User Manual 85pgs pdf S
28. l Names b Export Instrument Data K m standard quantity F Export Chart Data j Auto Increment 10x v Export Text Report b TT copes gt Standard units copies Export to PowerPoint CIO Identify replicates Export to Image File Ctrl I Replicate symbol E Convert to New Experiment Type eker Mail Experiment rri 1 Print Page Setup Print Ctrl F Plate setup comments Print Screen Alt T Print Report Print Preview 1 SYBR Green 05 01 2009 12Hr 24Min 2 2 SYBR Green 05 01 2009 12Hr 24Min 3 Joonbae_SYBR Green 04 24 2009 11Hr 13Min 4 SYBR Green 04 24 2009 11Hr 13Min Full Screen Plate Hest gt 5 Joonbae SYBR Green 04 23 2009 11Hr 10Min L well types shown 6 SYBR Green Uniformity Example TE i Door Closed ME Z aal 1 Exit soft PowerPor lt Beets ER IE DESERT STLCC CPLS Morrison 4 13 2015 Page 44 Thermal Cvcler Stratagene MxPro Instrument tab Fi MxPro Mx3005P Quantitative PCR New Experiment mxp File Edit Tools Options Section View Window Help B ms lultiple Instrument Control b Add Instruments 5 filter set plate NE Rename Remove Instruments F Qualificati est IIIS acd Change Connected Instrument aa M M RR RT TRS HT N Lamp Reset and Utilities M EN Filter Set Gain Settings TT Update Filter Configuration Shww
29. l names to be imported The Well ID s may appear n any order but must contain the syntax Al H12 or A01 H12 An Excel template associating Well ID positions to well names 15 stored in the MxPro data folder e g C Program Files Stratagene MxPro Storage Import Well Names from Excel Well ID Template xls and can be opened using Microsoft Excel Excel Templates B Find L Mafio Flacc deng H RR e DE Eg EE S a i eee anasanat varman n vanf EET FEEL G anasanat OE terete eto Randi pram ale E ED GU TEES DEE EE EE ED RE GET GER ER GE S GAR Gm EEE nigel nsf yn ER EEE POMS enri Sra rara Ge tel Smp nin dai eee eet Sees TET RR e CMe ES Fre S pm ni e mtn enki S e Du e mes E seret vind nen ranjecietznpran E TD om Zmpn 1m inci mr p rum mS E EE pm SN DENE Genel nane QW ar ID f E GerelSme name Pty lt D Dx rel mo name Diu a D Rida nans Rug ur D a ww Ee Mut Cvcler Stratagene MxPro File Tab Options Aa CE Mx3005P PCR Mew a ll TEE Fei tew Winda Help New CtrleN EM gn i ir MeS005P 5 filter set plate lt Ope Ctrl 0 49 FP 7 Wap 6 fiter set plate setup Run Analysis Close Save Ctr pos RE RE EE RE Imo aus 7 Save As Ctrl Quick Setup Show well Names New Project Multiple Experiment Analysis Open Project Save Project Save Project As Add Experiment to Project Remove Experiment from Project Import Wel
30. ll Screen Plate Hest gt Assays shown Well types shown Assian Well Type and Assays to selected wells The Ctrl key selects multiple wells Door Closed brampotf M S T a en 7 A mm im r ye R MxPro Mba005P Q RE Microsoft PowerPor Bees NA NOE 9 17 AM STLCC CPLS Morrison 4 13 2015 Page 41 Thermal Cycler Stratagene MxPro Setup Well Annotation H MxPro Mx3005P Quantitative PCR New File Edit Instrument Tools Options Section View Window Help 5 um l WIC e Hd FH Z S S wssose 5 fiter set plate Setup Run Analysis Thermal Profile Setup es ec BEN es es BET BET HEFE mot Defauts gt B m O T TT TANS Click on Wellto h e Well type Mban lt identify details 00 ShowWelNames CY5 ROX YT SYBR Well Information 9 Well annotation tani Y 5 Mame Enter Well Description PA T Er Comments TREE copies lt eplicate symbo none Assign assays within selected wells _Auteinerement Dye Assay Assay Color Clear Selected wells CrS Cys RU HE Plate setup comments SYER Use for all wells Remove Assays Close Full Screen Plate Next gt Assays shown Well types shown Asslan Well Type and Assays to selected wells The Ctrl key selects multiple wells DoorOpen Lamp 0 i A am 7 Aa S MxPro Mx3005P Q fe Microsoft PowerPor dci Bh Wo 6 32 AM STLCC CPL
31. oftware Stratagene MxPro QPCR 401454 6400 Ver 4 1 Vista or XP Bob Morrison STLCC FV and BRDG Instrumentation Specialist Cell 314 971 3795 Email bmorrison stlcc edu STLCC_CPLS Morrison 4 13 2015 Page 51
32. operation Hot Bonnett optional lid Hot Bonnett spring loaded internal seal lid Features Fast Ramping 60 up to 1C sec 96 up to 1 4C sec Memory stores up to 80 programs Method of heating cooling Peltier Joule Temperature control methods Block or calculated Heated lid optional Available on new units or can be factory retrofit Thermal If there is a beeping alarm when range 0C 105C Temperature accuracy The Hot bonnet is in use there is 0 3C of programmed target at 90C NIST f traceable Temperature uniformity 0 4C usually an issue that the tubes are well to well within 30 sec of arrival at 90C not pressing squarely on the bonnet Block 16 x 0 5 ml tubes internal lid This internal spring loaded lid must be depressed enough to indicate that a good seal is present You may consider adding a heat resistant washer or thin flat liner to add thickness to the overall tube height and thus seal the hotbonnet lid Hotlink to MJ Research PTC 150 User Manual 3 5mb pdf STLCC CPLS Morrison 4 13 2015 Page 32 Thermal Cycler PG MEN Bio Rad DYAD PTC 200 EST i Model PTC 220 SN DY002678 Alpha SN AL063359 AL062992 From FV to BRDG Aug 2010 Dual block DNA Engine thermal cycler features numeric keypad with 1 4in VGA screen and touch pad to move cursor arrow in the VGA screen USB mouse port RS232 and Ethernet port 200 250V 50 60HZ 1600W alpha units are available for this
33. res SmartCycler Reaction Tube Designed for e High surface area to volume ratic e Superior thermal response contr large S race e Max fluorescence signal Temperature Area i i with thin wall e Entire volume interrogated enclosure n e No X contamination e Indestructible T Optic Reflectors October 17 2005 23 Optic windows with 90 optics path STLCC CPLS Morrison 4 13 2015 Thermal Cyclers Smartcycler Create Run Example 4 STU ck Status Stop Run view Results Define Protocols Define Graphs Maintenance C Site IL Protocol sample ID Sample Type Motes FAM Std TET Std TxR Std C5 Std Run Name Wi Conr Cont Cone Corie Hotes JE Add Remove Sites Dye Set FITC25 2 Ch Ove Usage Bkgnd Bkgnd Bkgnd Curve Analysis Thresh Setting Manual Thresh Auto Thresh Auto Min Auto Max Valid Min We Mame sub Min Cycle Max Cycle Fluar Units 5D s Cycle Cycle Cycle A 1 FAM Assay JON 5 40 Primary Curve Manual 30 0 NA D 10 3 bU sil z TET Assay ON 5 40 Primary Curve Manual 30 0 NA 5 10 3 60 EL ML LLLI xn assay ON fe 40 Primary Curve Manual 30 0 NA 5 10 3 B0 cM CyS Assay ON 5 40 Primary Curve Manual 30 0 NA 5 10 3 B Graphs Cancel Run Setup Cancel Run Cancel Run Setup Report Run Setup Report Run Setup Run Setup Select Graphs Select SelectGraphs CopyRun Setup CopyRun Setup Setup STLCC CPLS
34. s or exceeds that of high performance 96 well thermal cyclers High performance cycling options including calculated or block temperature control automatic temperature increment automatic time extension and adjustable ramp rates e Fully adjustable heated lid that accommodates both full height and low profile vessels for low volume reactions lt 20 ul e Durable thermoelectric Peltier modules for lasting performance A 6 x 8 sample array that accommodates 0 2 ml tubes tube strips 48 well plates and up to twelve 0 5 mi tubes Memory for up to 400 typical programs e Large 64 x 128 backlit semigraphical display with graphical editing for rapidly modifying programs Power protection so programs will resume after power outages STLCC CPLS Morrison 4 13 2015 Page 30 Thermal Cycler Gradient PTC 1148 Control Options The MJ Mini cycler offers two easy programming options A graphic mode allows you to quickly modify basic cycling parameters while a menu based text mode allows you to efficiently enter advanced options During a PCR run pressing a single key changes the display to show a list of the program s steps a graphical representation of the protocol s progress with real time displays of the block lid and sample temperatures or the time remaining in the run STLCC CPLS Morrison 4 13 2015 Page 31 Thermal Cycler Mini MJ Research Model PTC 150 Membrane Keypad On Off switch on controls setup and Rear panel
35. s shown Assian well Type and az kaya to selected wells The E key selects multiple v wells a eC S MxPro M 3005P Q ffe Microsoft PowerPor STLCC_CPLS Morrison 4 13 2015 Page 47 Thermal Cvcler Stratagene MxPro Thermal Profile Setup S MxPro Mx3005P Quantitative PCR New Experiment mxp File Edit Instrument Tools Options Section View Window Help B p mi e Z E 2 DAP 5 filter set plate Setup Run Analysis pee Sep Cemaes Thermal Profile Estimated Run Time 02 26 05 Thermal Profile Design Y Standard f Custom Pre Melt AT Segmenti 1 Plateau 2 Plateaus 3 Plateaus Amplification Segment Fast 2 Step Normal 2 Step Normal 3 Step Dissociation Melt Segment Dissociation 2 Melt Thermal prafile comments Temperature segment 1 segment 2 1 Cycle 40 Cycles Full Screen Profile To edit select plateaus ramps or segment boundaries Door Closed Lamp Off DE 6 E W MxPro MGD0SP Q ffe Microsoft PowerPor lt 17 F LM 0 34 AM STLCC CPLS Morrison 4 13 2015 Page 48 Thermal Cycler Stratagene MxPro QPCR 4 Plex Example Plate setup W MxPro Mx3005P Quantitative PCR l PCR 4 Plex Example mxp File Edit Instrument Tools gt ri Plate Setup DNEEREREHEEEEENNEENEENENER Standard Standard A A Options Standard View Standard 4 00e 001
36. ser Jan 18 2011 04 53 Protocols i Melt Protocol Lot Number f FAM TEE Texas Cy o Cancel Humber of Sites 1 Eee 4 Export Report Select Graphs View Another Run Delete Run s Update Analysis Import Std Curve Compare Run i Q E EB ER E pa Om Ml Page 21 Words 0 THE PEEN 4 13 2015 smart Cycler IY User Logs Setup Tools Help Create Run Thermal Cyclers Smartcycler View Results Run Selected Display View Results Define Protocols Define Graphs Maintenance Views 4 Protocol Name Run Name aper spring 2011 h Alu ar in 2011 Alu DMHT10127 i Temperature Stage 1 Stage 2 Staged User Default User Intercalate of Melt Started Jan 27 201105 03PM FAM Temp secs Optics Degisec Finished Jan 27 20110552PM 03 SEMEN m i Texas Red Status Done TSE f Standard Notes Views Site Protocol Sample ID Sample Notes Stats FAM FAM Ct Uy Cy CI TER ID Type BtiRes ShiRes o S N RE B15 upcr spri UNEM Error POS 31 80 MEG 0 00 MEG 1 B1B iqpcr spri UNEN Error POS 15 84 NEG 0 00 MEG Dye Set FCTC25 Temperature C1 gaper spri INEN UK POS 14 60 MEG 0 00 MEG f Intercalate C2 pcr spri UNEM UK POS 15 85 NEG 0 00 MEG Pratacals helt Ca gperspri UNEN UK FOS 18 32 NEG 0 00 MEG E EN FAM C4 gpcr spri UNEN UK FOS 20
37. t chart and text report data directly from display screen to Microsoft Excel PowerPoint text and image fl e Software can link up to six 6 Mx3005P and Mx300P instruments with one computer Link to Stratagene Introduction to Quantitative PCR pdf Agilent website Thermal Cycler Stratagene MxPro Video Training A variety of online seminars and tutorials is available online in streaming video format You must access the site below and register or login as ID bmorrison sticc edu Password 15agilent Link to Stratagene Video Training Website http www stratagene com onlineseminars SeminarsAnd Turorials aspx catid 8 e Stratagene Online Seminars and Tutorials Microsoft Internet Explorer gt D x File Edit View Favorites Tools Help ae pack lt ix E A j Search S Z Favorites Oi iw rel 3 Address http www stratagene com onlineseminars SeminarsAndTurorials aspx catid 8 STRATAGENE i An Agilent Technologies Division About Us Contat Y E3e Links PRODUCTS TECHNICAL RESOURCES SPECIAL OFFERS SHOP FREEZER PROGRAM EVENTS By Application ByName New Products QPCR The following section contains training movies The presentations are provided in a WebEx movie format wrf and require a Windows operating system with a sound card The movies can be streamed over a high speed Internet connection or downloaded for offline viewing with a s
38. tandalone WebEx movie player Streaming the presentations may require the installation of 4 viewer plug in so please make sure you download and install the WebEx player from http www webex com p player download html Online Seminars Stream Video Module 1 Mx Instrument System and Software Seminar covers the optical and thermal systems of the Mx instrument line with discussion of the considerations that went into the instrument design Time will also be spent on a tutorial of the software used for both systems covering experimental setup well types standards replicates and thermal profile setup Stream Video Module 3 Probe and Primer Design Seminar discusses the criteria involved in designing primers for SYBR Green I and probe based QPCR assays as well as designing Taqman and Molecular Beacons probes Dye and quencher selection is covered briefly and guidelines are provided on how primers and probes should be tested and how reaction conditions can be optimized Stream Video Module 4 Stratagene Mx Software Demonstration Seminar walks through the software interface used for the Mx instrument line Covers experimental setup well types standards replicates and thermal profile setup Also includes demonstration nf how tn analyze amnlificatinn nlats as well as set haselines and thresholds L 7 start Jj e e x fa By fw C note gadge S Bmorrison hoc 3 Morrison Pr 2 Microsoft SIE T Int
39. umber of times a cycle is to occur followed by an x is shown in the bottom right corner of the last step of a cycle To add an increment or decrement option for either time or temperature put the selection box on the desired time or temperature field press F3 Option and select the desired option After selecting the desired option a new field will pop up in the display In this new field input the amount of time or degrees Celsius by which you want to increment or decrement each repeat When you are finished editing the protocol press F5 Done 5 oavethe protocol by choosing Save Protocol As from the selection menu Name the protocol using the alphanumeric keys as described in section 1 5 and press Enter when finished 6 The Home screen will appear Press the F1 Protocol Library to access the Protocol Library Using the arrow keys select the protocol you just created and press Enter selection menu will appear Select Run Protocol 7 The Run Setup screen should appear Specify whether or not you want a hot start and the hot start temperature if you picked Y ES and which temperature measurement mode you want and the sample volume if you picked Algorithmic Measurement 8 Press F5 Begin Run to begin the run s xii 00in af meli STLCC CPLS Morrison 4 13 2015 Page 5 Thermal Cycler T100 BioRad Description Specs Power on switch on back of unit Follow screen menu for setup and functions
40. urs and Minutes and edit the values using the ed o s pop up keypad Guide 3 Touch Save to save the changes or RS EO i L 4 Touch Home to return to the Home screen Dil dolo MM Dg 1 of 2 Creating a New Protocol 1 To create a new protocol touch New Protocol in the Home screen 2 The New Protocol screen displays a graphical view of the protocol Figure 3 Edit the value of any of the following parameters by touching the corresponding field Temperature Hold time Number of repeats in the GOTO loop Starting step for the GOTO loop Sample volume Lid temperature 3 To select a step touch anywhere outside the temperature box The step becomes highlighted to indicate that it is selected Once a step is selected you can insert a new step after the selected step delete the selected step or configure the options for the step Fig 3 New Protocol screen showing graphical view of a protocol Page 7 4 To insert a step touch Insert The screen will display the type of steps to insert Figure 4 Select Temperature for a temperature hold step Gradient for a thermal gradient for protocol optimization or GOTO to insert a GOTO step that will loop back to repeat the specified steps in your protocol typically denaturation annealing and extension 5 To delete a step select the step and touch Delete 6 To configure advanced parameters for a step such as Temperature Increment Time Extend Gr
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