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Cancer immunotherapy was the focus of this year's participation in the MRC Festival of Medical Research, which took our researchers to shopping centres in Didcot, Reading and Oxford.
What do I do if my samples are contaminated with heavy metals?
Answer Make sure you comply with the prevention of sample contamination included in the section for contamination. If you follow all the rules for minimising contamination your samples during sample preparation think about what happens with your sample before. If these are patient samples there may be a fe…
How do I pick antibodies for my panel?
Answer When picking antibodies for your panel rules are very similar as for flow cytometry so you will need markers to discriminate your populations to find the population of interest and markers of interest that will give you answers to your research question/help you prove your hypothesis. In order to do this, y…
What do I do if I cannot purchase antibody in appropriate buffer or purified form?
Answer There are two options available for you. First, is to buy purified antibody in buffer containing additives and use kit to purify it (Abcam GOLD BSA Removal Kit – removes most of additives, not only BSA). Second, buy antibody conjugated with fluorescent dye that has an anti-dye antibody available and…
How do I validate my antibodies?
Answer In order to validate your antibodies, you will need a good positive and negative control for each antibody. It would be ideal if you can have a heterogeneous sample containing populations which you can easily discriminate and include some that express and some that do not express the particular…
What do I do if I don't have controls for my antibodies?
Answer Antibody validation is a crucial aspect of panel development and therefore it is very important to have appropriate controls. In some cases, this may be challenging if the marker is highly expressed in most of the cells (e.g. metabolic enzymes) or on the other hand its expression is very low. An option you…
How many cells do I start with?
Answer A standard mass cytometry protocol assumes starting with 1 to 3 million cells. Although if the population of interest is small you may need to start with more cells or think about previous enrichment of your samples. On the other hand, there are samples where recovery of a million of cells is an unreali…
What do I do if the cell count of my sample is very low (below 250000 cells)?
Answer If the cell count for the sample to be analysed on CyTOF is very low it will be beneficial to use different cells to create a bulk for staining. When choosing cells that will be used as a bulk it is important to remember to pick cells that will be easily available every time you need them, easily distinguishab…
What do I do if the population I am interested in is really rare?
Answer To detect really rare populations, you need either to acquire a lot of events, or enrich the samples for the population of interest. Acquiring high numbers of events in order to have reasonable count for the rare population of interest is highly inefficient and may be costly on CyTOF, thus the best optio…
Can I use FACS sorted samples?
Answer Yes, you can use FACS sorted samples for CyTOF analysis. The important issue you may want to consider if you are going to use the same markers for FACS staining and then for CyTOF staining is saturation of the epitope you stained for FACS. This can be solved in two ways by; finding antibody recognisi…
Can I use bead enriched samples?
Answer Yes, you can use bead enriched samples for CyTOF analysis. Most of the beads used for enrichment are not going to affect CyTOF analysis however there are a couple of things to consider. Some beads may be quite sticky and cause clumping of cells which in turn will decrease efficiency of sample prepa…
How long will the acquisition take?
Answer There are a few factors involved when it comes to the acquisition time. In general, acquisition is much slower in comparison to flow cytometer and varies from 100 to 750 events per second. This in turn gives 360,000 to 2,700,000 events per hour. The acquisition rate will depend on the quality of the sa…
How many samples can I barcode in one batch?
Answer Barcoding Kit supplied by Fluidigm allows for combination of up to 20 samples. It relies on the use of 6 different Palladium isotopes to create 20 various barcodes consisting of 3 isotope code.
Do I need to use specific slides?
Answer No – any microscope slide will work as long as it is made of glass.
How thick should I cut my sections?
Answer Standard 4-7 μm thickness is ideal. Thicker sections are likely to contain overlapping cells which may cause problems for accurate segmentation.
Can I use FFPE tissue?
Answer Yes, both FFPE tissue and frozen tissue can be used successfully with the Hyperion.
Can I use CyTOF antibodies for Hyperion staining?
Answer Antibodies that work for CyTOF staining will not necessarily work for Hyperion, particularly if you are using FFPE sections. However, in some cases, the antibody clone may work in both – we recommend that you check the antibody clone information to see if it is likely to work for normal immunohistoche…
How do I know what concentration to use?
Answer Antibody titration is a key to optimising a good panel and it is important that you check different dilutions in your tissue of interest to make sure that staining is optimal. If you know an antibody works for immunohistochemistry in your tissue this can be used as a rough indicator of where to start your titrat…
What controls will I need?
Answer In cases where you are unsure if or where your markers will be expressed, positive and negative controls are essential. The best positive and negative controls will be dependent on your markers of interest. In most cases, ‘minus one’ controls are not necessary but they can be used in cases where…