Data analysis: Scaling your data for dimensionality reduction
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Today we're talking about scales. Very boring, very important.
- May 3
- 4 min
Overnight staining for scRNA-Seq?
The idea? Combine overnight staining with RNA sequencing.
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- Apr 29
- 7 min
How to conjugate your own antibodies
When we conjugate an antibody to a fluorophore, we are performing a chemical reaction, creating a covalent bond between the fluorophore and
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- Apr 22
- 4 min
Data Analysis: EmbedSOM's party trick
Tired of trying to waiting for tSNE to run on large data sets? What if we could run any dimensionality reduction approach, but in a...
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- Apr 15
- 2 min
Optimizing cytokine staining--fixatives
In this post, I discussed the importance of testing and titrating the stimuli used for intracellular cytokine staining. Today let's look...
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- Apr 8
- 5 min
What's that cluster?
Today I'm going to talk about a feature in flowcytoscript--an R-based workflow for flow-cytometry analysis from the Liston Lab--that...
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- Apr 1
- 2 min
Optimizing cytokine staining--Ionomycin
Intracellular cytokine staining can be challenging to get right. The cells need to be in great condition to withstand the stimulation...
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- Mar 25
- 10 min
Data Analysis: Dimensionality Reduction
In this series, we're going to look at dimensionality reduction algorithms for use in the display and analysis of high parameter flow...
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- Mar 18
- 2 min
Panel Design: Build a backbone
I suggest starting by designing what I call a backbone for your panel. This is just the basic gating markers that will allow you to...
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- Mar 11
- 5 min
Panel Design: selecting fluorophores for spectral flow, part 2
How to pick the best fluorophores to use in your flow panels.
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- Mar 4
- 5 min
Panel Design: selecting fluorophores for spectral flow, part 1
Once we've decided which markers to include in our panel, the next step is to begin selecting the fluorophores that we want to use in the...
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- Feb 26
- 5 min
Panel Design: Dealing with spread
Spread is an inevitable consequence of multicolour fluorescence-based flow cytometry. When an excited fluorophore emits lower energy...
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- Feb 19
- 4 min
Panel Design: spectral viewer web-tools
Today let's look at web-tools for understanding fluorophore signatures. These spectral viewer tools can be very useful for designing flow...
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- Feb 12
- 3 min
Panel Design: Where to start?
A flow panel is all about choices. Our choices with the markers we include and the signals we attach to them via antibodies create a...
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- Feb 7
- 6 min
Identifying and fixing errors in flow data
Errors in flow data are all too common. The key to reducing errors lies in being able to recognize the symptoms and distinguish between...
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- Feb 1
- 6 min
How to test and titrate antibodies
Titration of antibodies means finding the optimal amount to use in order to maximize signal (specific binding) while minimizing noise...
1,785 views9 comments
- Jan 17
- 2 min
Tips & Tricks: Benchmarking controls
Today's topic is benchmarking. This is probably particularly relevant for anyone who manages a shared resource lab with an Aurora. On the...
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- Dec 21, 2023
- 2 min
Tips & Tricks: Stacking antibodies
Improve your signal by using more antibodies, not more antibody. If you have a marker that doesn't stain well, sometimes you can improve...
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- Dec 11, 2023
- 1 min
Data analysis: Comparing tSNE plots
Most of the time when people generate tSNE plots of flow data, they're interested in comparing how a treatment or condition affects the...
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- Dec 5, 2023
- 3 min
Tips & Tricks: Dealing with tandems
Tandems, tandems, tandems. We can't seem to avoid them in high parameter flow experiments--they're just too useful. How do we deal with...
1,149 views2 comments
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