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meyer-lab / gc-valent

Exploring what valency does to IL-2.
http://asmlab.org
MIT License
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Analyze variation in receptor abundances within flow data #370

Closed aarmey closed 4 years ago

aarmey commented 5 years ago

Notes:

I figured out how to export gated populations as .fcs files. As a test case I exported the raw data for CD4+ T cells from our best run. It includes each gated population stained with the full set of antibodies (well A1), then each control well. Once we’re happy with the data I can generate the same output for CD8+ T cells, NK and NKT cells. I don’t know exactly how the software generates .fcs output so let me know if you see any issues with the data.

Controls for each receptor are unstained and stained with an isotype control carrying the same fluor. Controls for each receptor are separated into folders and each file is labeled as unstained or isotype control. Each control well is identical to the full stain, just with a single antibody omitted or swapped for isotype control.

I put together a few slides showing histograms for each receptor. The slides also summarize some of the issues around processing and visualization.

I’m happy to go through the data by phone if that helps make sense of everything. We’ll repeat the experiment, plus stain for IL-15RA, in the next few days. I hope to have IL-2 and IL-15 signaling data next week (single replicate, 1-2 more weeks for duplication). We’ve also got preliminary kinetic parameters for IL-2 muteins. We can start work through kinetics as soon as the agreement is in place.

aarmey commented 5 years ago

@hcrm-zot can you start to put some of the functions you've written into ckine/flow.py? We should review some of them to make sure the structure is setup in a way that will be useful to others.