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The first large-scale genetic study of people in Papua New Guinea has shown that different groups within the country are genetically highly different from each other. Scientists at the Wellcome Trust Sanger Institute, University of Oxford and the Papua New Guinea Institute of Medical Research reveal that the people there have remained genetically independent from Europe and Asia for most of the last 50,000 years, and that people from the country’s isolated highlands region have been completely independent even until the present day. The study, published in Science, also gives insights into how the development of agriculture and cultural events such as the Bronze or Iron Age could affect the genetic structure of human societies. The study used DNA samples collected by Prof John Clegg and Prof Sir David Weatherall in the 1980s, a collection housed at the WIMM.
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 few things to consider. Please have a look at the list below organized according to metal: Iodine – iodine solution is used as disinfectant during surgeries, some dyes used by pathologists may contain it as well Barium – may be present on reusable parts of medical equipment, rarely patients are given contrast for some medical assessments which contain a lot of this metal Platinum - Cisplatin is one of the most common cancer treatments but it is also used for Live/Dead discrimination in CyTOF experiments. If patients that you collect samples from were treated with Cisplatin you will need to use alternative Rhodium staining for CyTOF Other – example being Yb, Sn, Pb can come from environmental contamination, water, solutions that may have contact with the sample before it gets to you
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, you can use all information that is available in literature or from your previous research, including not only FACS and mass cytometry but also other techniques like immunohistochemistry, mass spectrometry. Antibodies that are used for flow cytometry and work well for you should be your first choice. However, the antibodies that you are interested in but you haven’t try in flow cytometry or even are not available as mass/flow cytometry antibodies may still work for your CyTOF experiment. Always bear in mind that it is very important to validate your antibodies so you and later your reviewer will be convinced that they are specific and the staining is free of artefacts.
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 use two step staining.
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 marker.
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 may need to consider is looking for a knockdown or overexpressing cell line respectively.
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 unrealistic dream then you may want to think about creating a bulk out of other cells that will ensure that the cell recovery after an extended staining protocol is still good.
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 distinguishable from your sample and will not catch/‘eat’ antibodies you use for staining. A good option also would be to barcode and pool your samples together. This is probably viable for samples with cell counts well below 1 million down to 100,000.
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 option would be to enrich the samples for the population of interest by FACS sorting or using bead-based enrichment methods.
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 recognising a different epitope of the same marker or using secondary antibody against fluorescent dye that the FACS antibody was conjugated to.
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 preparation and may also cause clogging of the mass cytometer during acquisition. If the sample contains a lot of the beads they may accumulate on internal parts of the machine and therefore affect the analysis. If it is possible it may be best to do negative selection with the beads or try FACS sorting the cells.
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 sample. The more metal contamination, debris and overstaining present in the sample the more we will need to decrease the acquisition rate. Also, we will have to acquire sample slower if the cells are sticky or big due to clogging issues. Once we know how much we can acquire it will be important to think how many events per sample we will need to analyse, bearing in mind that the count for the smallest population of interest should not be lower than 300.
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 immunohistochemistry before attempting to validate for use in the Hyperion. If no information is available to suggest whether a suspension CyTOF clone will work but there are alternative clones available known to work in immunohistochemistry, then we would recommend using these alternative clones first as there is a greater likelihood of success.
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 titration. However, it is likely that the antibody concentration will need to be higher for use the Hyperion compared to standard immunohistochemistry. This is because, in general, secondary antibodies are not used for Hyperion staining so the signal will not be amplified.
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 you are unsure whether a signal is due to spill-over in a particular channel.