PF0870 Thermo Scientific PathoProof Mastitis Complete-12 assay PF1600 Thermo Scientific PathoProof Mastitis Complete-16 assay

Transcription

1 PF0870 Thermo Scientific PathoProof Mastitis Complete-12 assay PF1600 Thermo Scientific PathoProof Mastitis Complete-16 assay Instructions for use 1 1. Introduction Thermo Scientific PathoProof Mastitis Complete assays are designed for accurate same-day identification of mastitiscausing microorganisms from bovine milk using quantitative real-time polymerase chain reaction (PCR). PCR technology is used for amplifying DNA in a test tube enabling further analysis of DNA. In the PathoProof assays, real-time PCR detects the presence of DNA in a milk sample and identifies the bacterial species in question based on its unique DNA. The kit includes all the necessary reagents for bacterial DNA extraction and PCR. The test has been optimized for use with even the most challenging milk samples. Real-time PCR has become the gold standard method for food pathogen testing and quality assurance. Based on this advanced technology, PathoProof Mastitis Complete assays offer several advantages over the conventional bacterial culture method: Results are obtained substantially faster. Risk of carry-over contamination in the laboratory is minimized because the tests are performed in closed reaction vessels that are not opened after the run. Fewer no growth results because the test identifies and quantifies DNA, so it accurately detects viable, dead and growth-inhibited microorganisms. Applicable for use with preserved milk samples, thus eliminating the need for cooling during sample transportation. Can be integrated into milk recording programs using preserved milk. The PathoProof Mastitis Complete-12 assay identifies 11 mastitis-causing microorganisms species or species groups and the β-lactamase penicillin resistance gene in staphylococci (including Staphylococcus aureus and all major coagulasenegative staphylococci). The bacteria and the β-lactamase gene are detected in four separate PCR reactions. The PathoProof Mastitis Complete-12 assay can identify the following bacterial species and groups: Staphylococcus aureus Enterococcus spp. (including E. faecalis and E. faecium) Corynebacterium bovis Staphylococcal β-lactamase gene (the gene responsible for penicillin resistance in staphylococci) Escherichia coli Streptococcus dysgalactiae Staphylococcus spp. (including Staphylococcus aureus and all relevant coagulase-negative staphylococci) Streptococcus agalactiae Streptococcus uberis Klebsiella oxytoca and/or K. pneumoniae Serratia marcescens Arcanobacterium pyogenes and/or Peptoniphilus indolicus The PathoProof Mastitis Complete-16 assay identifies 15 mastitis-causing microorganisms and the β-lactamase penicillin resistance gene in staphylococci (including Staphylococcus aureus and all major coagulase-negative staphylococci). The microorganisms and the β-lactamase gene are detected in four separate PCR reactions. The PathoProof Mastitis Complete-16 assay identifies the following targets:

2 2 Staphylococcus aureus Enterococcus spp. (including E. faecalis and E. faecium) Corynebacterium bovis Staphylococcal β-lactamase gene (the gene responsible for penicillin resistance in staphylococci) Escherichia coli Streptococcus dysgalactiae Staphylococcus spp. (including Staphylococcus aureus and all relevant coagulase-negative staphylococci) Streptococcus agalactiae Streptococcus uberis Klebsiella oxytoca and/or K. pneumoniae Serratia marcescens Arcanobacterium pyogenes and/or Peptoniphilus indolicus Mycoplasma bovis Mycoplasma spp. Yeast Prototheca spp. Norden Lab Mastitis Studio General Edition is a software application designed for interpreting, reporting and storing the results obtained using PathoProof Mastitis Complete assays. This software facilitates data analysis and is highly recommended as an integral part of the procedure for the PathoProof Mastitis Complete assays. 2. Kit components and storage conditions The PathoProof Mastitis Complete assays contain all the necessary reagents (except ethanol) for DNA extraction and real-time PCR. The small reagent kits (small manual extraction and KingFisher Duo kits) are sufficient for 50 tests*, and the large kits (large manual extraction and KingFisher Flex kits) for 4x96 tests**. The kits are stable for six months from the packaging date when stored and handled properly. The small kits are suitable for laboratories handling small numbers of samples in each DNA extraction session. With small manual extraction kits, the sample amount can vary from 1 to 50. The extraction is performed in individual tubes. The KingFisher small kits use the Thermo Scientific KingFisher Duo instrument for sample preparation. The sample amount can vary from 1 to 12 or from 12 to 24, depending on the protocol used with the instrument ( PathoProof single plate or PathoProof two plates ). The large kits use a 96-well-format DNA extraction method by which 96 samples can be processed simultaneously. The large kits are designed for laboratories performing DNA extraction on large numbers of samples in each session. The KingFisher large kits use the Thermo Scientific KingFisher Flex instrument for faster and more convenient sample preparation. The KingFisher large kits are designed for high-throughput laboratories, or laboratories requiring a less hands-on time protocol. The tables in Section 2.1 list the components included in the kits. More detailed information on the components can be found in Section 2.2. * Sufficient for 50 reactions when at least 12 samples are analyzed per set ** Manual large kits are sufficient for 4 x 96 reactions when at least 20 samples are analyzed per set. The KingFisher large kits are sufficient for 4 x 96 reactions when at least 40 samples are analyzed per set. 2.1 Components included in the small and large kits The PF0870S and PF1600S kits consist of two separate boxes. The boxes contain the following components. Component Size Storage conditions Box QIAamp Mini Spin PF0870S, 50 RT Columns PF1600S Collection Tubes (2 ml) 150 RT PF0870S, PF1600S Buffer AL 1 12 ml RT PF0870S, PF1600S Buffer AW 1 (concentrate) 19 ml RT PF0870S, PF1600S BufferAW2 2 (concentrate) 13 ml RT PF0870S, PF1600S Buffer AE 12 ml RT PF0870S, PF1600S F-871S Lysis Solution ml RT PF0870S, PF1600S F-872S Lysis Solution 2 4x1.3 ml C PF0870SB, F-873S Proteinase K 2x1.8 ml C PF0870SB, F-882 PathoProof Master PF0870SB, 2x1.1 ml C Mix F-883S PathoProof Complete-12 Primer Mix 1 F-884S PathoProof Complete-12 Primer Mix 2 F-885S PathoProof Complete-12 Primer Mix 3 F-886S PathoProof Complete-12 Primer Mix 4 F-961S PathoProof Complete-16 Primer Mix 1 F-962S PathoProof Complete-16 Primer Mix 2 F-963S PathoProof Complete-16 Primer Mix 3 F-964S PathoProof Complete-16 Primer Mix 4 F-929 PathoProof Universal Amplification Standard 300 µl 300 µl 300 µl 300 µl 300 µl 300 µl 300 µl 300 µl from fight. PF0870SB PF0870SB PF0870SB PF0870SB 150 µl C PF0870SB, 1. Contains chaotropic salt. Not compatible with disinfecting agents containing bleach. 2. Contains sodium azide as a preservative.

3 3 The PF0870SKF and PF1600SKF kits consist of two separate boxes. The boxes contain the following components. The PF0870L and kits consist of three separate boxes. The boxes contain the following components. Component Size Storage conditions Box Buffer AW1 1 2x19 ml RT PF0870SKF, PF1600SKF Buffer AW2 2 2x13 ml RT PF0870SKF, PF1600SKF Tween ml RT PF0870SKF, PF1600SKF Buffer AE 15 ml RT PF0870SKF, PF1600SKF Buffer RLT 1 2x7 ml RT PF0870SKF, PF1600SKF MagAttract Suspension PF0870SKF, 2x1.6 ml RT G 2 PF1600SKF F-871S Lysis Solution ml RT PF0870SKF, PF1600SKF F-872S Lysis Solution 2 4x1.3 ml C PF0870SB, F-873S Proteinase K 2x1.8 ml C PF0870SB, F-882 PathoProof Master PF0870SB, 2x1.1 ml C Mix F-883S PathoProof Complete-12 Primer Mix 1 300µl F-884S PathoProof Complete-12 Primer Mix 2 300µl F-885S PathoProof Complete-12 Primer Mix 3 300µl F-886S PathoProof Complete-12 Primer Mix 4 300µl F-961S PathoProof Complete-16 Primer Mix 1 300µl F-962S PathoProof Complete-16 Primer Mix 2 300µl F-963S PathoProof Complete-16 Primer Mix 3 300µl F-964S PathoProof Complete-16 Primer Mix 4 300µl F-929 PathoProof Universal Amplification Standard from fight. PF0870SB PF0870SB PF0870SB PF0870SB 150µl C PF0870SB, 1. Contains chaotropic salt. Not compatible with disinfecting agents containing bleach. 2. Contains sodium azide as a preservative. Tween is a registered trademark of ICI Americas, Inc. MagAttract Lining is a registered trademark of the Qiagen Group. Component Size Storage conditions Box QIAamp 96 plates 4 RT S-Blocks 1 2 RT Collection Microtubes 4x96 RT (racked) Elution Microtubes CL (racked) 4x96 RT Caps for Collection Microtubes 4x55 RT Caps for Elution Microtubes 1x50 RT AirPore Tape 25 sheets RT Buffer AL 2 2x54 ml RT Buffer AW1 2 (concentrate) 95 ml RT Buffer AW2 3 (concentrate) 66 ml RT Buffer AE 110 ml RT F-871L Lysis Solution ml RT F-872L Lysis Solution 2 4x10 ml C F-873L Proteinase K 2x6 ml C PF0870L part 2, part 2 PF0870L part 2, part 2 F-882 PathoProof Master PF0870LB, 16x1.1 ml C Mix B F-883L PathoProof Complete-12 Primer Mix 1 F-884L PathoProof Complete-12 Primer Mix 2 F-885L PathoProof Complete-12 Primer Mix 3 F-886L PathoProof Complete-12 Primer Mix 4 F-961L PathoProof Complete-16 Primer Mix 1 F-962L PathoProof Complete-16 Primer Mix 2 F-963L PathoProof Complete-16 Primer Mix 3 F-964L PathoProof Complete-16 Primer Mix 4 F-929 PathoProof Universal A mplification Standard 2x1.1 ml 2x1.1 ml 2x1.1 ml 2x1.1 ml 2x1.1 ml 2x1.1 ml 2x1.1 ml 2x1.1 ml PF0870LB PF0870LB PF0870LB PF0870LB B B B B 150 µl C PF0870LB, B 1. Reusable, wash or autoclave after use. 2. Contains chaotropic salt. Not compatible with disinfecting agents containing bleach. 3. Contains sodium azide as a preservative.

4 4 The PF0870LKF and KF kits consist of three separate boxes. The boxes contain the following components. Component Size Storage conditions Box Buffer AW1 1 2x121 ml RT KF Buffer AW2 2 2x68 ml RT KF Tween x50 ml RT KF Buffer AE 110 ml RT KF Buffer RLT 1 3x35 ml RT KF MagAttract Suspension 21 ml RT G 2 KF F-871L Lysis Solution ml RT KF Collection Microtubes 4x96 RT (racked) KF Caps for Collection 1x55 RT Microtubes KF F-872L Lysis Solution 2 4x10 ml C KF F-873LKF Proteinase K 2x12 ml C KF F-882 PathoProof Master PF0870LB, 16x1.1 ml C mix B F-883L PathoProof Complete-12 Primer Mix 1 2x1.1 ml F-884L PathoProof Complete-12 Primer Mix 2 2x1.1 ml F-885L PathoProof Complete-12 Primer Mix 3 2x1.1 ml F-886L PathoProof Complete-12 Primer Mix 4 2x1.1 ml F-961L PathoProof Complete-16 Primer Mix 1 2x1.1 ml F-962L PathoProof Complete-16 Primer Mix 2 2x1.1 ml F-963L PathoProof Complete-16 Primer Mix 3 2x1.1 ml F-964L PathoProof Complete-16 Primer Mix 4 2x1.1 ml F-929 PathoProof Universal Amplification Standard PF0870LB PF0870LB PF0870LB PF0870LB B B B B 150µl C PF0870LB, B 1. Contains a guanidine salt. Not compatible with disinfecting agents containing bleach. 2. Contains sodium azide as a preservative. Tween is a registered trademark of ICI Americas, Inc. MagAttract is a registered trademark of the Qiagen Group.

5 5 2.2 Description of the real-time PCR reagents This section describes the real-time PCR reagents included in the kits. All other kit components are reagents for extraction of DNA from milk. PathoProof Mastitis Complete-12 assays: F-882: PathoProof Master Mix. PCR master mix in an optimized buffer, containing MgCl 2, deoxynucleoside triphosphates and hot start DNA polymerase. F-883: PathoProof Complete-12 Primer Mix 1. PCR primer mix for PCR reaction 1, including oligonucleotides for identification of S. aureus, Enterococcus spp., C. bovis and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-884: PathoProof Complete-12 Primer Mix 2. PCR primer mix for PCR reaction 2, including oligonucleotides for identification of staphylococcal β-lactamase (penicillin resistance) gene, E. coli, S. dysgalactiae and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-885: PathoProof Complete-12 Primer Mix 3. PCR primer mix for PCR reaction 3, including oligonucleotides for identification of Staphylococcus spp. (including all relevant coagulase-negative staphylococci), S. agalactiae, S. uberis and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-886: PathoProof Complete-12 Primer Mix 4. PCR primer mix for PCR reaction 4, including oligonucleotides for identification of Klebsiella spp., Serratia marcescens, Arcanobacterium pyogenes and/ or Peptoniphilus indolicus and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-929: PathoProof Universal Amplification Standard. Control DNA for all targets for use as a positive control and for calibration of Norden Lab Mastitis Studio General Edition with the real-time PCR instrument and the reagents. PathoProof Mastitis Complete-16 assays: F-882: PathoProof Master Mix. PCR master mix in an optimized buffer containing MgCl 2, deoxynucleoside triphosphates and hot start DNA polymerase. F-961: PathoProof Complete-16 Primer Mix 1. PCR primer mix for PCR reaction 1, including oligonucleotides for identification of S. aureus, Enterococcus spp., C. bovis, M. bovis and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-962: PathoProof Complete-16 Primer Mix 2. PCR primer mix for PCR reaction 2, including oligonucleotides for identification of staphylococcal β-lactamase (penicillin resistance) gene, E. coli, S. dysgalactiae, Mycoplasma spp. and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-963: PathoProof Complete-16 Primer Mix 3. PCR primer mix for PCR reaction 3, including oligonucleotides for identification of Staphylococcus spp. (including all relevant coagulase-negative staphylococci), S. agalactiae, S. uberis, Prototheca spp. and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-964: PathoProof Complete-16 Primer Mix 4. PCR primer mix for PCR reaction 4, including oligonucleotides for identification of Klebsiella spp., Serratia marcescens, Arcanobacterium pyogenes and/or Peptoniphilus indolicus, yeast and an Internal Amplification Control. Also includes Internal Amplification Control DNA. F-929: PathoProof Universal Amplification Standard. Control DNA for all targets for use as a positive control and for calibration of Norden Lab Mastitis Studio General Edition with the real-time PCR instrument and the reagents.

6 6 3. Materials needed but not supplied The materials needed but not supplied with the PathoProof Mastitis Complete assays are listed below. Most of the instruments and consumables needed are included in the PathoProof Starter Pack available from Thermo Fisher Scientific. Disposable powder-free gloves Ethanol (96 100%); do not use denatured ethanol Pipettes Sterile pipette tips with filter PCR vessels compatible with the real-time PCR Instrument Optically clear PCR vessel caps or sealers compatible with the real-time PCR Instrument Two incubators (+37 C and +55 C), or one fast-ramping incubator (not needed for the KingFisher Duo or KingFisher Flex kits) Vortex mixer Microcentrifuge and appropriate tubes and strip tubes Real-time PCR instrument for PathoProof Mastitis Complete-12 kits: 7500 Fast Real-Time PCR System (Applied Biosystems), Stratagene Mx3005P or Mx3000P QPCR System (Agilent Technologies) or Chromo4 Real-Time PCR Detection System (Bio- Rad Laboratories). Consult Thermo Fisher Scientific for compatible real-time PCR instrument software versions. Real-time PCR instrument for PathoProof Mastitis Complete- 16 kits: Stratagene Mx3005P QPCR System (Agilent Technologies). For the large kits: Decapping tool Plate centrifuge Thermo Scientific Heraeus Multifuge X3 centrifuge For the KingFisher large kits: Thermo Scientific KingFisher Flex instrument PF0450DW Microtiter Deepwell 96 Plate PF2534CO Kingfisher Flex 96 Tip comb PF3230CM Cap Mat for DW 96 Plate or PF0580SE Adhesive Plate seal For the KingFisher small kits: Thermo Scientific KingFisher DUO instrument PF3530CO KingFisher Duo Combi pack and strip tubes 5. General guidelines The following general guidelines should be followed throughout the PathoProof Mastitis Complete assay protocol: Use protective gloves. Thaw all frozen reagents thoroughly prior to use. Mix all solutions well before use. Spin down reagents after mixing. 5.1 Avoiding carryover contamination Due to their high sensitivity, real-time PCR assays are susceptible to carryover contamination of DNA. The contaminating DNA is typically an amplification product from a real-time PCR run, but can also originate from samples containing high quantities of bacterial DNA. The PathoProof Mastitis Complete assays do not require opening of the real-time PCR vessels once a real-time PCR program has been started. While this assay design significantly reduces the risk of cross-contamination, the following general guidelines should be followed, in addition to other precautions mentioned in this instruction manual, in order to minimize such risks. Designate physically separated working areas for: (1) DNA extraction (handling of milk samples or other samples containing bacteria); and (2) setup of the real- time PCR reactions. Use different laboratory equipment (disposable gloves, pipettes, pipette tip boxes, vortexes, centrifuges, laboratory coats etc.) in each working area. Change gloves frequently and always before leaving an area. Use aerosol-resistant pipette tips. Use new and/or sterilized plastic ware. After starting a real-time PCR run, do not open the realtime PCR vessels under any circumstances. Always dispose the real-time PCR vessels in a dedicated, closed trash container and make sure that the vessels do not open accidentally. If detecting a strong positive target in the samples (Ct-value ~20), please check that there is no crosscontamination from this sample in the proximate samples. 4. Sample material The PathoProof Mastitis Complete assays are intended for use with fresh, frozen or preserved milk samples.

7 Fluorescence Fluorescence Fluorescence Fluorescence Figure 1. Schematic illustration of the Pathoproof Mastitis Complete assay workflow. 1. DNA extraction: DNA is extracted from fresh or preserved bovin milk samples. The small kits are suitable for laboratories that process few samples per DNA extraction session; the large kits are suitable for large numbers of samples per DNA extraction session. The KingFisher kits require less hands-on-time due to semi-automated DNA extraction. 2. Real-time PCR setup: Extracted DNA and PCR solutions are used to set up reactions in a 96-well PCR plate. 3. Real-time PCR: Four PCR reactions are run for each sample hr. 30 min. +1 hr. 30 min Cycle Cycle Cycle A B C D E F G H The PathoProof Mastitis Complete-12 assay identifies 12 targets and the PathoProof Mastitis Complete-16 assay identifies 16 targets. Although a given milk sample is often positive for only one primary pathogen, the kit can identify all targets simultaneously. In the example illustrated here, a milk sample analyzed in wells A1 A4 is positive for a total of four targets: β-lactamase gene in Reaction 2 (A2), Staphylococcus spp. in Reaction 3 (A3), and Klebsiella spp. and S. marcescens in Reaction 4 (A4). The blue curve present in every reaction represents the Internal Amplification Control. 5. The obtained data is interpreted, reported and databased with Norden Lab Mastitis Studio General Edition (see instructions in Norden Lab Mastitis Studio instruction manual).

8 8 6. Workflow of the assay An overview of the laboratory workflow is presented in Figure 1. This section contains instructions for performing DNA extraction, real-time PCR setup and run. The instructions for performing realtime PCR instrument calibration and results analysis by Norden Lab Mastitis Studio software are given in the Norden Lab Mastitis Studio Instructions for Use. Important: When using PathoProof Mastitis Complete assays for the first time, it is necessary to calibrate the Norden Lab Mastitis Studio (see Norden Lab Mastitis Studio Instructions for Use). Calibration may also need to be performed when qpcr plastic type changes or when the real-time PCR instrument has undergone maintenance. The calibration runs and experiment runs must be performed using the same real-time PCR instrument, the same type of vessels and the same sealing method (sealers or caps). 6.1 DNA extraction DNA extraction for the small manual kits Things to do before starting: Buffers AW1 and AW2 are supplied as concentrates. Before using them for the first time, add the amount of ethanol (96 100%) indicated on the bottles. Heat two incubators: one to 55 C and one to 37 C, or use one fast-ramping incubator. Equilibrate Buffer AE to room temperature. If a precipitate has formed in Buffer AL, dissolve it by incubating at 55 C. 1. Prepare a fresh mix containing the following volumes per sample: 7 µl Proteinase K and 350 µl Lysis Solution 1. Calculate 1 2 extra reactions to ensure sufficient volume. 2. Vortex or shake the milk samples thoroughly. Add 350 µl of Lysis Solution 1/Proteinase K mix and 350 µl milk to each reaction vessel. Avoid pipetting milk clots into the reaction vessels. In addition to the milk samples, include at least one negative control (only reagents) in each DNA extraction. 3. Vortex briefly and incubate at 55 C for 5 min. 4. Centrifuge for 5 min at 5000 xg. 5. The presence of fat on top of the supernatant following centrifugation is normal. Remove the supernatant and fat by pipetting. Residual fat/liquid on top of the pellet is normal and does not need to be removed. 6. Resuspend the pellet in 100 µl Lysis Solution 2 by pipetting. 7. Incubate at 37 C for 10 min. 8. Prepare a fresh mix containing the following volumes per sample; 20 µl Proteinase K and 200 µl Buffer AL. Calculate 1 2 extra reactions to ensure sufficient volume. Add 220 µl of the mix to the reaction vessel. Mix by vortexing for 5 10 sec. 9. Incubate at 55 C for 10 min. Centrifuge for a few seconds. 10. Add 200 µl ethanol (96 100%) to the sample and mix by pulse-vortexing for 15 sec. It is essential that the sample, the Buffer AL and the ethanol are mixed thoroughly to yield a homogeneous solution. Do not use alcohols other than ethanol, as this may result in reduced DNA yields. After mixing, briefly centrifuge the reaction vessel to remove drops from inside the caps. 11. Remove the possible viscous clots from this mixture with a pipetter. Then, carefully apply the supernatant to the QIAamp Mini spin column (placed inside a 2 ml collection tube) without wetting the rim. Close each spin column to avoid aerosol formation during centrifugation. Centrifuge at 20,000 xg (~14,000 rpm) for 1 min. Place the QlAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the tube containing the filtrate. 12. Carefully open the QIAamp Mini spin column and add 500 µl Buffer AW1 without wetting the rim. Close the cap and centrifuge at 20,000 xg (~14,000 rpm) for 1 min. Place the QIAamp Mini spin column in a clean 2 ml collection tube (provided), and discard the collection tube containing the filtrate. 13. Carefully open the QIAamp Mini spin column and add 500 µl Buffer AW2 without wetting the rim. Close the cap and centrifuge at 20,000 xg (~14,000 rpm) for 3 min. 14. Place the QIAamp Mini spin column in a clean 1.5 ml microcentrifuge tube (not provided), and discard the collection tube containing the filtrate. Carefully open the QIAamp Mini spin column and add 100 µl Buffer AE. Incubate at room temperature for 1 min, and then centrifuge at 20,000 xg (~14,000 rpm) for 3 min to elute the DNA. 15. The purified DNA can be stored at +5 C for a few days and for longer times at C. Proceed to Section 6.2 for real-time PCR setup.

9 9 DNA extraction for KingFisher small kits Things to do before starting: Buffers AW1 and AW2 are supplied as concentrates. Before using them for the first time, add the amount of ethanol (96 100%) indicated on the bottles. Equilibrate Buffer AE to room temperature. Buffer RLT is provided in 7 ml bottles. To prepare the mixture used in step 11, add 7 ml ethanol (96-100%) and 1.4 ml MagAttract Suspension G to the Buffer RLT bottle. Vortex the MagAttract Suspension G for 3 min before using it for the first time and 1 min before subsequent use. The mixture is stable for one month. Alternatively the mixture can be prepared in smaller aliquots for every usage according to instructions in step 10. DNA extraction protocol for 1-12 samples 1. Prepare rows D-H of a 96 DeepWell Plate and Elution Strip according to the table below. Place a 12 Tip Comb into row B of the DeepWell Plate. The 96 DeepWell Plate and the Elution Strip are loaded into the KingFisher Duo instrument in step Mix sample thoroughly by vortexing or shaking. Depending on your sample type, prepare samples for centrifugation using the below instructions: 1. For individual quarter milk samples: Add 400 μl of Lysis Solution 1 and 400 μl milk into a 1.5 ml tube (or racked Collection Microtubes not provided in the kit, requires a plate centrifuge). Avoid pipetting milk clots into the reaction vessels. However, this may not always be possible as the quality of samples could vary remarkably. 2. For DHI samples: Prepare a fresh mix containing the following volumes per sample: 5 µl Proteinase K and 400 µl Lysis Solution 1. If using a multichannel pipette, calculate some extra to ensure sufficient volume. Add 400 µl of the Lysis Solution 1/Proteinase K mix and 600 µl milk into a 1.5 ml tube (or racked Collection Microtubes not provided in the kit, requires a plate centrifuge). In addition to the milk samples, include at least one negative control (only reagents) in each DNA extraction run. If using Collection Microtubes, seal the tubes using the caps provided for Collection Microtubes. 6. Resuspend the pellet well in 100μL Lysis Solution 2 by pipetting and transfer the sample into a well of the sample plate (into row A, containing Proteinase K) by pipetting. If the pellet does not resuspend well, 1000μL sterile water can be added to facilitate the resuspending. 7. Switch on the KingFisher Duo at the power switch. If using the KingFisher Duo through a computer, open the BindIt software from the computer which is connected to the KingFisher Duo instrument. 8. Select the PathoProof single plate protocol from the DNA/RNA menu under factory protocols. Press Start to start the protocol run. 9. Open the cover of the instrument and load the plate and the strip into the instrument as indicated on the KingFisher Duo display. Close the protective cover and start the run. 10. If the Buffer RLT/ethanol/MagAttract Suspension G mix has not been prepared in advance, then prepare a mix containing the following volumes for each sample: 200 µl ethanol (96-100%), 200 µl Buffer RLT and 40 µl MagAttract Suspenion G. Vortex the MagAttract Suspension G for 3 min before using it for the first time, and for 1 min before subsequent use. 11. When the extraction protocol pauses at the dispense step shake the mixture containing Buffer RLT, ethanol and MagAttract Suspension G thoroughly for 10 s and add 440μL to each well of the sample row. If dispensing the mixture into wells with a multichannel dispenser, make sure tips do not touch the well walls or the liquid in the wells. Load the plate back into the instrument and continue the run. The protocol will continue to the end. After the samples are processed remove the plate and strip as instructed by the KingFisher Duo display. 12. A small amount of beads in the eluted DNA is normal and does not affect the qpcr step. 13. The purified DNA can be stored at +5 C for a few days and for longer times at C. Proceed to Section 6.2 for real-time PCR setup. 3. Mix well and centrifuge for 3 min at 1500 xg. 4. The presence of fat on top of the supernatant following centrifugation is normal. Remove the supernatant and fat by pipetting. Residual fat/liquid on top of the pellet is normal and does not need to be removed. 5. Add 40μL Proteinase K per well into wells in row A of the 96 DeepWell plate according to your sample number.

10 10 Wash and elution rows and reagent volumes on DeepWell plate and Elution Strip Row name Plate Row Reagent Volume per well Wash 1 96 DeepWell D Buffer AW1 800 µl Wash 2 Wash 3 Wash 4 Wash 5 96 DeepWell 96 DeepWell 96 DeepWell 96 DeepWell E Buffer AW1 500 µl F Buffer AW2 500 µl G Buffer AW2 500 µl H Water containing 0,02 % Tween µl Elution Elution Strip Buffer AE 130 µl DNA extraction protocol for samples 1. Prepare rows D-H of two 96 DeepWell Plates and two Elution Strips according to the table below. Place a 12 Tip Comb into row B of the DeepWell Plate. The 96 DeepWell Plates and the Elution Strips are loaded into the KingFisher Duo instrument in step 9. 2.Mix sample thoroughly by vortexing or shaking. Depending on your sample type, prepare samples for centrifugation using the below instructions: the pellet does not resuspend well, 1000μL sterile water can be added to facilitate the resuspending. 7. Switch on the KingFisher Duo at the power switch. If using the KingFisher Duo through a computer, open the BindIt software from the computer which is connected to the KingFisher Duo instrument. 8. Select the PathoProof two plates protocol from the DNA/RNA menu under factory protocols. Press Start to start the protocol run. For individual quarter milk samples: Add 400μL of Lysis Solution 1 and 400μL milk into a 1.5 ml tube (or racked Collection Microtubes not provided in the kit, requires a plate centrifuge). Avoid pipetting milk clots into the reaction vessels. However, this may not always be possible as the quality of samples could vary remarkably. For DHI samples: Prepare a fresh mix containing the following volumes per sample: 5 µl Proteinase K and 400 µl Lysis Solution 1. If using a multichannel pipette, calculate some extra to ensure sufficient volume. Add 400 µl of the Lysis Solution 1/Proteinase K mix and 600 µl milk into a 1.5 ml tube (or racked Collection Microtubes not provided in the kit, requires a plate centrifuge). 9. Open the cover of the instrument and load the plates and the strips into the instrument as indicated on the KingFisher Duo display. Close the protective cover and start the run. 10. If the Buffer RLT/ethanol/MagAttract Suspension G mix has not been prepared in advance, then prepare a mix containing the following volumes for each sample: 200 µl ethanol (96-100%), 200 µl Buffer RLT and 40 µl MagAttract Suspenion G. Vortex the MagAttract Suspension G for 3 min before using it for the first time, and for 1 min before subsequent use. In addition to the milk samples, include at least one negative control (only reagents) in each DNA extraction run. If using Collection Microtubes, seal the tubes using the caps provided for Collection Microtubes. 3. Mix well and centrifuge for 3 min at 1500 xg. 4. The presence of fat on top of the supernatant following centrifugation is normal. Remove the supernatant and fat by pipetting. Residual fat/liquid on top of the pellet is normal and does not need to be removed. 5. Add 40μL Proteinase K per well into wells in row A of the 96 DeepWell Plates according to your sample number. 6. Resuspend the pellet well in 100μL Lysis Solution 2 by pipetting and transfer the sample into a well of the sample plate (into row A, containing Proteinase K) by pipetting. If

11 When the extraction protocol pauses at the dispense step shake the mixture containing Buffer RLT, ethanol and MagAttract Suspension G thoroughly for 10 s and add 440μL to each well of the sample row. If dispensing the mixture into wells with a multichannel dispenser, make sure tips do not touch the well walls or the liquid in the wells. Mixture is dispensed to both of the plates during the same dispense step; after dispensing to the first plate load the plate back into the instrument and press Start. After a short while the instrument will offer the second plate. Do not take the second plate out of the instrument before the instrument asks you to add the mix. After dispensing load the second plate back into the instrument and continue the run. The protocol will continue to the end. 12. After the samples are processed remove the plates and strips as instructed by the KingFisher Duo display. 13. A small amount of beads in the eluted DNA is normal and does not affect the qpcr step. 14. The purified DNA can be stored at +5 C for a few days and for longer times at C. Proceed to Section 6.2 for real-time PCR setup Wash and elution rows and reagent volumes on DeepWell plate and Elution Strip Row name Plate Row Reagent Volume per well Wash 1 96 DeepWell D Buffer AW1 800 µl Wash 2 96 DeepWell E Buffer AW1 500 µl Wash 3 96 DeepWell F Buffer AW2 500 µl Wash 4 96 DeepWell G Buffer AW2 500 µl Wash 5 96 DeepWell H Water containing 0,02 % Tween µl Elution Elution Strip Buffer AE 130 µl

12 12 DNA extraction for the large manual kits Things to do before starting: Buffers AW1 and AW2 are supplied as concentrates. Before using them for the first time, add the amount of ethanol (96 100%) indicated on the bottles. Heat two incubators: one to 55 C and one to 37 C, or use one fast-ramping incubator. Equilibrate Buffer AE to room temperature. If a precipitate has formed in Buffer AL, dissolve it by incubating at 55 C. Centrifugation of QlAamp 96 plates is performed on the Heraeus Multifuge X3 plate centrifuge. 1. Prepare a fresh mix containing the following volumes per sample: 7 µl Proteinase K and 350 µl Lysis Solution 1. If using a multichannel pipetter, calculate some extra to ensure sufficient volume. 2. Vortex or shake the milk samples thoroughly. Add 350 µl of Lysis Solution 1/Proteinase K mix and 350 µl milk into racked Collection Microtubes. Avoid pipetting milk clots to the reaction vessels. In addition to the milk samples, include at least one negative control (only reagents) in each DNA extraction. Seal the tubes using the caps provided for Collection Microtubes. 3. Vortex briefly and incubate at 55 C for 5 min. 4. Centrifuge for 5 min at 5000 rpm. 5. The presence of fat on top of the supernatant following centrifugation is normal. Remove the supernatant and fat by pipetting. Residual fat/liquid on top of the pellet is normal and does not need to be removed. 6. Resuspend the pellet in 100 µl Lysis Solution 2 by pipetting. Seal the tubes using new caps for Collection Microtubes. 7. Incubate at 37 C for 10 min. 8. Prepare a fresh mix containing the following volumes for each sample: 20 µl Proteinase K and 200 µl Buffer AL. If using a multichannel pipetter, calculate some extra to ensure sufficient volume. Add 220 µl of the mix to each sample, taking care not to wet the rims of the Collection Microtubes. Seal the tubes using new caps for Collection Microtubes. 9. Mix thoroughly by shaking vigorously for 15 sec. For efficient lysis, it is essential that the samples and Buffer AL are mixed immediately and thoroughly to yield a homogeneous solution. Hold the racked Collection Microtubes with both hands and shake up and down vigorously. 10. Incubate at 55 C for 10 min. Centrifuge briefly at 3000 rpm to remove drops from inside the caps. Stop the centrifuge as soon as it reaches 3000 rpm. 11. Add 200 µl ethanol (96 100%) to each tube. Seal the tubes using new caps for Collection Microtubes. Shake vigorously for 15 sec. Centrifuge briefly at 3000 rpm to remove drops from inside the caps. Stop the centrifuge as soon as it reaches 3000 rpm. 13. Seal the QIAamp 96 plate with an AirPore Tape sheet. Load the S-Block and QIAamp 96 plate onto the carrier, then place the carrier in the rotor bucket. Centrifuge at 6000 rpm for 4 min. 14. Place the QIAamp 96 plate on top of an empty S-Block. Remove the tape. Carefully add 500 µl Buffer AW1 to each well. Seal the QIAamp 96 plate with a new AirPore Tape sheet. Centrifuge at 6000 rpm for 4 min. 15. Place the QIAamp 96 plate on top of an empty S-Block. Remove the tape. Carefully add 500 µl Buffer AW2 to each well. Do not seal the plate, to ensure evaporation of residual ethanol in the following centrifugation step. Centrifuge at 6000 rpm for 15 min. The heat generated during centrifugation ensures evaporation of residual ethanol in the sample (from Buffer AW2) that might otherwise inhibit subsequent reactions. 16. Place the QIAamp 96 plate on top of a rack of Elution Microtubes (provided). To elute the DNA, add 100 µl Buffer AE to each well. Seal the QlAamp 96 plate with a new AirPore tape sheet, and incubate for 1 min. at room temperature. Centrifuge at 6000 rpm for 4 min. Seal the wells of the microtubes for storage using the caps for Elution Microtubes provided. 17. The purified DNA can be stored at +5 C for a few days and for longer times at C. Proceed to Section 6.2 for real-time PCR setup. DNA extraction for KingFisher large kits Things to do before starting: Buffers AW1 and AW2 are supplied as concentrates. Before using them for the first time, add the amount of ethanol (96 100%) indicated on the bottles. Equilibrate Buffer AE to room temperature. Buffer RLT is provided in 35 ml bottles. To prepare the mixture used in step 11, add 35 ml ethanol (96-100%) and 7 ml MagAttract Suspension G to the Buffer RLT bottle. Vortex the MagAttract Suspension G for 3 min before using it for the first time and 1 min before subsequent use. The mixture is stable for one month. Alternatively the mixture can be prepared in smaller aliquots for every usage according to instructions in step 10. The 96 Tip Combs are supplied as packages of 2. If opening a new package, store the other 96 tip comb on a 96 DeepWell Plate. Optional: Prefilling of DeepWell plates. Wash and elution plates can be filled, sealed with Cap Mats or Adhesive Plate Seals and preserved at room temperature for one month. If using Adhesive Plate Seals ensure that the rims of the plates are dry and clean before sealing. Ensure that no liquid has evaporated from the wells (especially the corner wells) before using the prefilled plates for extraction. Small amount of evaporation (10-25%) does not affect the efficiency of the extraction. Prefilled plates should not be shaken or heated. 12. Place the QIAamp 96 plate on top of an S-Block. Mark the plate for later identification. Remove the possible viscous clots from the mixture prepared in step 11 with a pipetter. Then, carefully apply the supernatant to the QlAamp 96 plate. Take care not to wet the rims of the wells to avoid aerosol formation during centrifugation.

13 13 1. Prepare six 96 DeepWell Plates according to the table on page 10. Place a 96 Tip Comb onto an empty 96 DeepWell plate. The 96 DeepWell Plates are loaded into the KingFisher Flex instrument in step Mix samples thoroughly by vortexing or shaking. Depending on the sample type, prepare samples for centrifugation using the instructions below: For individual quarter milk samples: Add 400μL of Lysis Solution 1 and 400μL milk into racked Collection Microtubes. Avoid pipetting milk clots into the reaction vessels. However, this may not always be possible as the quality of samples can vary remarkably. For DHI samples: Prepare a fresh mix containing the following volumes per sample: 5 µl Proteinase K and 400 µl Lysis Solution 1. If using a multichannel pipette, calculate some extra to ensure sufficient volume. Add 400 µl of the Lysis Solution 1/Proteinase K mix and 600 µl milk into racked Collection Microtubes. In addition to the milk samples, include at least one negative control (only reagents) in each DNA extraction run. Seal the tubes using the caps provided for Collection Microtubes. 3. Mix well and centrifuge for 3 min at 1500 xg. 4. Remove the supernatant by pipetting. The presence of fat on top of the supernatant following centrifugation is normal. Remove the fat by pipetting. Residual fat/ liquid on top of the pellet is normal and does not need to be removed. 5. Add 40μL of Proteinase K per well to an empty 96 DeepWell plate, corresponding to your sample amount. 6. Resuspend the pellet well in 100μL Lysis Solution 2 by pipetting and transfer the sample into a well of the sample plate (Containing Proteinase K) by pipetting. If the pellet does not resuspend well, 1000μL sterile water can be added to facilitate the resuspending. 7. Switch on the KingFisher Flex at the power switch. If using the KingFisher Flex through a computer, open the BindIt software from the computer which is connected to the KingFisher Flex instrument. 8. Select the PathoProof protocol from the DNA/RNA menu under factory protocols. Press Start to start the protocol run. 9. Open the cover of the instrument and load the plates into the instrument as indicated on the KingFisher Flex display. After each plate press Start and after the worktable has rotated load the next plate. After the last plate close the protective cover and press Start to initiate the run. 10. If the Buffer RLT/ethanol/MagAttract Suspension G mix has not been prepared in advance, then prepare a mix containing the following volumes for each sample: 200 µl ethanol (96-100%), 200uL Buffer RLT and 40 µl MagAttract Suspenion G. If using a multichannel pipettor, calculate some extra to ensure sufficient volume (for example for 20 samples prepare 4 extra reactions and for 96 samples prepare 10 extra reactions). Vortex the MagAttract Suspension G for 3 min before using it for the first time, and for 1 min before subsequent use. 11. When the extraction protocol pauses at the dispense step shake the mixture containing Buffer RLT, ethanol and MagAttract Suspension G thoroughly for 10 s and add 440μL to each well of the sample plate. If dispensing the mixture into wells with a multichannel dispenser, make sure tips do not touch the well walls or the liquid in the wells. Load the plate back into the instrument when the instrument asks you to insert the sample plate. Do not load the plate until this message appears on the interface. Press Start to continue the run. The protocol will continue to the end. 12. After the samples are processed remove the plates as instructed by the KingFisher Flex display. Press "Start after removing each plate. Seal the wells of the elution plate with a Cap Mat or an Adhesive Plate Seal for storage. 13. A small amount of beads in the eluted DNA is normal and does not affect the qpcr step. 14. The purified DNA can be stored at +5 C for a few days and for longer times at C. Proceed to Section 6.2 for real-time PCR setup. Wash and elution plates and reagent volumes Plate name Reagent Volume per well Wash 1 Buffer AW1 800 µl Wash 2 Buffer AW1 500 µl Wash 3 Buffer AW2 500 µl Wash 4 Buffer AW2 500 µl Wash 5 Water containing 0,02 % Tween µl Elution Buffer AE 150 µl

14 Real-time PCR setup An overview of the laboratory workflow is presented in Figure 1. Figure 2 illustrates the sample order in the real-time PCR setup necessary for PathoProof Mastitis Complete assays. Throughout the procedure, follow the general guidelines detailed in Section 5. Important points before starting: Use at least one negative (no template) PCR control for each of the four PCR reactions in each real-time PCR run. If all the samples are expected to be negative for the targets, it is advisable to include the PathoProof Universal Amplification Standard and/or a positive DNA extraction control (such as a milk sample previously tested positive with PathoProof Mastitis Complete assays) in each real-time PCR run. Note that the experiment runs must be performed using the same real-time PCR instrument, the same type of vessels and the same sealing method (sealers or caps) that were used for the calibration runs (see Norden Lab Mastitis Studio Instructions for Use). Vortex the thawed PathoProof Master Mix and PathoProof Primer Mixes 1 4 briefly and spin down. 1. Prepare four separate PCR solutions by combining PathoProof Master Mix and PathoProof Primer Mixes 1 4 in four separate microcentrifuge tubes. Use one of the formula sets presented below to calculate the volumes of the PCR solutions. Formula set for <20 samples PCR solution 1: Volume of PathoProof Master Mix = (N+2)x10 µl Volume of PathoProof Primer Mix 1 = (N+2)x5 µl PCR solution 2: Volume of PathoProof Master Mix = (N+2)x10 µl Volume of PathoProof Primer Mix 2 = (N+2)x5 µl PCR solution 3: Volume of PathoProof Master Mix = (N+2)x10 µl Volume of PathoProof Primer Mix 3 = (N+2)x5 µl PCR solution 4: Volume of PathoProof Master Mix = (N+2)x10 µl Volume of PathoProof Primer Mix 4 = (N+2)x5 µl N = Number of samples Including one or several of the following controls: Negative PCR control (necessary in every run) PathoProof Universal Amplification Standard (positive PCR control) Negative DNA extraction control Positive DNA extraction control The formulas provide excess volume to compensate for volume loss due to reagent pipetting. Formula set for 20 samples PCR solution 1: Volume of PathoProof Master Mix = Nx11 µl Volume of PathoProof Primer Mix 1 = Nx5.5 µl PCR solution 2: Volume of PathoProof Master Mix = Nx11 µl Volume of PathoProof Primer Mix 2 = Nx5.5 µl PCR solution 3: Volume of PathoProof Master Mix = Nx11 µl Volume of PathoProof Primer Mix 3 = Nx5.5 µl PCR solution 4: Volume of PathoProof Master Mix = Nx11 µl Volume of PathoProof Primer Mix 4 = Nx5.5 µl N = Number of samples Including one or several of the following controls: Negative PCR control (necessary in every run) PathoProof Universal Amplification Standard (positive PCR control) Negative DNA extraction control Positive DNA extraction control

15 15 The formulas provide excess volume to compensate for volume loss due to reagent pipetting. Figure 2. Illustration of a 96-well real-time PCR plate and the sample order necessary for PathoProof Mastitis Complete assays. 2. Vortex the PCR solutions briefly and spin down. 3. Prepare a 96-well PCR plate. Always allocate four consecutive wells in one row for the same sample (see Figure 2). For example, allocate wells A1 A4 for sample 1 Fill the wells of the plate in the direction A H, i.e. first down, then right, then down. Add 15 µl of PCR solutions 1 4 into the four wells allocated for each sample. For example, for sample 1, add PCR solutions 1, 2, 3 and 4 into wells A1, A2, A3 and A4, respectively (see Figure 2). Always add PCR solution 1 to plate columns 1, 5 and 9, PCR Solution 2 to columns 2, 6 and 10, PCR Solution 3 to columns 3, 7 and 11 and PCR Solution 4 to columns 4, 8 and 12. This order must be maintained for correct data analysis when using the Norden Lab Mastitis Studio software. If the PathoProof Universal Amplification Standard* is included, add 15 µl of PCR solutions 1 4 into the wells allocated for the PathoProof Universal Amplification Standard. Always allocate the last four wells for negative (no template) PCR controls (see Figure 2, example wells marked in red). 4. Add 5 µl of the eluate from the DNA extraction protocol (Section 6.1) into the four wells allocated for each sample. If the PathoProof Universal Amplification Standard is included, add 5μL of the standard into four consecutive wells. In the last four wells allocated for negative (no template) controls, add 5μL of sterile water or the Elution Buffer (AE) (Figure 2). 5. Close the 96-well PCR plate with a compatible optically clear sealer or optically clear caps, and spin the plate down with a plate centrifuge (3000 rpm, 5 s). 6. Place the 96-well plate in a real-time PCR instrument and start a real-time PCR program, following the instrumentspecific instructions in Section 6.3. *The PathoProof Universal Amplification Standard contains DNA for all targets of the PathoProof Mastitis Complete assays. It can be used as a positive control in the real-time PCR. It is also used for the calibration of the Norden Lab Mastitis Studio General Edition software. A B C D E F G H

16 Real-Time PCR instrument settings and run The PathoProof Mastitis Complete-12 assay is compatible with the following real-time PCR instruments: 7500 Fast Real-Time PCR System (Applied Biosystems), Stratagene Mx3005P or Mx3000P QPCR System (Agilent Technologies) and Chromo4 Real-Time PCR Detection System (Bio-Rad Laboratories). The PathoProof Mastitis Complete-16 assay is compatible with the Stratagene Mx3005P QPCR System (Agilent Technologies). Download ready-made instrument-specific template files from diagnostics.finnzymes.fi/. Save the templates on the computer connected to the real-time PCR instrument and follow the guidelines below. Applied Biosystems 7500 Fast Real-Time PCR System Instructions for Sequence Detection Software v 1.4 To start a run, open the template file (PathoProof_ template.sdt). Name the samples as needed (samples may be named after the run if preferred) and mark empty wells by selecting Omit Well in the Well Inspector. Verify that the settings are now as follows: Thermo Cycler Protocol: 1. Stage 1 (Reps 1) a. 10 min. at 95 C 2. Stage 2 (Reps 40) a. 5 sec. at 95 C b. 1 min. at 60 C 3. Stage 3 (Reps 1) a. 5 sec. at 25 C Sample Volume: 20 µl Run Mode: Fast 7500 Data Collection: during Stage 2, Step 2b ( min.) Save the file in.sds format. The instrument should now be connected to the software. Start the run by clicking the Start button. After the real-time PCR run, save the run data and the plate setup as two different files. Choose the Results menu. Choose Amplification plot and click Analyze. Go to the File menu, choose Export and then Delta Rn. Save the file in.csv format. In addition to the run data file, export the plate setup from the real-time PCR instrument software. Go to the File menu, click Export and then Sample setup Save the plate setup data in.txt format. Copy these files to the computer on which Norden Lab Mastitis Studio is installed. Now follow the instructions in your Norden Lab Mastitis Studio Instructions for Use in order to import the data into Norden Lab Mastitis Studio. Stratagene Mx3005P or Mx3000P QPCR System* *The following Stratagene Mx3005P or Mx3000P QPCR system instrument filters are compatible with the PathoProof Mastitis Complete assays FAM/SYBR Green, HEX/JOE/ VIC, ROX/Texas Red, CY5 and ATTO (for Mx3005P). If your Stratagene instrument does not have these filters, please contact Thermo Fisher Scientific. To start a run, open the template file (File -> Open -> PathoProof_template.mxp). Switch the instrument s lamp on by clicking the lamp icon. Verify that the settings are now as follows: Gain settings: 1x for CY5, 1x for ROX, 2x for HEX/JOE, 4x for FAM and 4 x for ATTO (Instrument -> Filter Set Gain Settings) Thermal Profile: 1. Segment 1 (1 cycle) a. 10 min. at 95 C 2. Segment 2 (40 cycles) a. 5 sec. at 95 C b. 60 sec. at 60 C, Endpoint read (End symbol on Step 2b) Verify that the lamp status field in the lower right corner of the window indicates Lamp Ready (green) or Warm- Up. Insert the PCR plate and name the samples as needed (samples may be named after the run if preferred). Select the empty wells and click Clear Selected Wells in the panel at the right. Save the run file in.mxp format and click Run to start the run. After the real-time PCR run, save the run data and the plate setup as one file.