How to handle the AmpliGrid System Pipetting the master mix
Transcription
How to handle the AmpliGrid System Pipetting the master mix
How to handle the AmpliGrid System Useful hints for set up and analysis. The purpose of this quick start guide is to help first time users to set up a successful experiment with the AmpliGrid system. Template Preparation Single cells can be deposited on the AmpliGrid using different techniques like: • Flow cytometry (e.g. Beckman Coulter MoFlo™ - see Quick Start Guides for the instruments) • Micromanipulation (use 0.05x PBS to micromanipulate the cells) • Laser microdissection • Pipetting dilutions If using a nucleic fluorescent staining, the deposition of the single cells on the reaction site can be controlled either manually or by using the Cell Detection software (OAX04117). Extracted template material can be used for amplification on the AmpliGrid. • DNA can be dried on the AmpliGrid before adding the PCR master mix • RNA must not be dried on the AmpliGrid; always prepare a second master mix solution incl. RNA Extracted template material should be diluted in water; high amounts of buffer with high salt concentration (especially PBS or Tris) can inhibit the PCR reaction and can lead to bubble formations in the master mix. Also residues of extractions / washing can inhibit PCR reactions (e.g. from columns, phenol extraction). Some extraction methods also contain ingredients which lead to bubble formation which induces droplet bursting during PCR. The concentration of the extracted nucleic acids should be used in the range of 100pg human genomic DNA equivalent (e.g. as positive control). For other sources of DNA and applications this may vary. Primer Primer can be either included into the PCR master mix or can be dried on the AmpliGrid before adding the PCR master mix. Primer can also be added if there is template material (cells or DNA) deposited already. The decision whether the primer should be dried or added to the master mix can be taken dependent on the workflow. It is recommended to add the primer to the master mix when only one primer pair (sense and antisense) is used and dried on the AmpliGrid when different primer pairs should be tested (take the advantage of only one master mix). Primer should be dried on the AmpliGrid by using 1 µL of approx. 0.6 µM primer (sense and antisense). It is not recommended to dry primers on cells when doing RNA analysis since the drying process might influence the quality of the RNA of the cells. Productinformation AmpliGrid #PI10012 Version 1.0 Pipetting the master mix • 1 µL of master mix should be pipetted on the AmpliGrid with deposited template (and primer). Do not exceed that volume. • We strongly recommend to use electronic multistep pipettes (e.g. Eppendorf XStream™ or Rainin AutoRep™) to avoid the creation of bubbles, which can lead to explosion of the reactions (air bubble expands due to heating and explodes under the oil – oil will spread and sample might be destroyed). • 5 µL of sealing solution should be applied on top of the aqueous phase with electronic multistep pipettes also. • Please do always release the PCR mix or oil droplet first, at the tip entry then deposit the droplet to the AmpliGrid reaction site. For some pipette tips the oil droplet is not clearly visible. Even in those cases move the pipette tip to the pre-deposited PCR mix. The oil will move to the correct position. Ideal pipetting angle is 90°. If the pipetting angle is lower than that, droplet deposition gets inaccurate. Downstream analysis PCR can be analysed by different techniques like: • gel electrophoresis (agarose gel (~2%) for high expressed genes or DNA amplification; polyacrylamide gels (8%) for lower expressed genes (we recommend to do polyacrylamide gel electrophoresis because of the superior detection limit). Pipette 4 µL of gel loading dye directly on the reaction site. Due to the higher density of the buffer it will move through the oil and merge with the sample. Use a standard 10µL pipette tip to aspirate the 5µL mixture of sample and buffer to load the gel. A minor transfer of sealing solution does not interfere with the gel analysis. • capillary electrophoresis; dilute the mix after PCR with 5 µL of water by just pipetting on top of the sealing solution. The water will merge with the PCR mix underneath the sealing solution. Pipette off the mix and transfer it to the capillary electrophoresis with an optional Sephadex column clean-up step. Please note, that a longer sample uptake time might improve the quality of the results. • qPCR: after pre-amplification or reverse transcription on the AmpliGrid the cDNA can be transferred to a real-time PCR system by either recovering the 1µL from underneath the oil or adding water to dilute the cDNA to a higher volume. For research use only. Not for use in diagnostic procedures. 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