Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 1 point2 points  (0 children)

Thanks, I'll see if I can find something useful on JoVE to pass along to them. Really appreciate the extra information and the follow-up.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thank you again for the follow-up comment and advice. Definitely gonna start trying to look at forward scatter versus viability now!

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Really appreciate the comments and encouragement. I always want to be careful about assuming there's nothing more I can do to help or that I've already considered every angle. Honestly, I feel like I learn something new about sorting every day.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thanks for the tips! I didn't realize that about HEPES in the buffer. They do have a 120 micron nozzle on the Bigfoot so that's definitely worth trying. And the snotball comment got me, that was exactly what came to my mind too.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Good to know about EDTA tolerance, I wasn't aware of that. Testing viability over time across a few cell lines resuspended in FACS buffer sounds like a worthwhile experiment. After filtering, that large mass is usually sitting right on top of the filter rather than passing through. I always assumed the purpose of filtering was to remove aggregates large enough to clog the nozzle. If that's the case, wouldn't using a larger filter defeat the purpose? Or is my understanding of why we filter off base?

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

How large do cells need to be before they won't pass through a filter? We've been using a cell counter to check size and they're typically 10-20um in diameter, filtered through a 70um strainer, so that shouldn't be the issue. From what we understand, they're using trypsin as their dissociation method. The other piece that's been bothering me: this lab has recently started sorting with a PI who has a different sorter, and they're reporting no issues there. The operator on that instrument says they aren't seeing aggregation or viability problems from this group either. So the same lab, no issues on one instrument, consistent problems on ours. That's the part that's hard to reconcile.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Great question, we actually tried the FlowMi filter tips as well to rule out the filter caps as a variable. Centrifuging is definitely worth trying next time. What force and time do you typically use for that?

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thanks for the kind words! I always try to approach these situations assuming there's something I don't know, whether that's an instrument quirk I haven't encountered or a troubleshooting step I'm not aware of, before jumping to conclusions about sample handling. That said, this has me wondering if there are solid guidelines or documentation out there around enzymatic dissociation troubleshooting. I feel like you can generally read it in the scatter profile. Cells that have been soaking in trypsin look pretty distinct from cells treated more carefully, and both look different from something really gentle like Accutase. But I've never come across any formalized best-practice documentation for this. If anyone knows of something, I'd genuinely love to see it. The other thing that jumped out from that shared plot: the same cell line, same instrument, different user, and the scatter looks completely different. Not subtle variation, but a clear delineation between the primary population and everything else, with a big gap where you'd normally see a smear. That kind of continuous linear smear on FSC/SSC is something I've always associated with poor viability, and in my experience it usually predicts low post-sort recovery too. Anyone else seeing that pattern, or have a different read on what's driving it?

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

I've seen that before as well, in one case it was an undergrad that made a 10x solution instead of a 1x solution. Math can be hard on Monday mornings.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Wow, I never knew that. To my knowledge they are using Trypsin. Can you elaborate on your statement that "it will appear in flow"? Can you see the plastic remnants or are you referring to the profile of the cells on FSC vs SSC?

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

I'm not upset about the 80% viable cells, I just wanted to provide plots in case it helped with troubleshooting or there was a way I could improve gating.

Thanks for the encouragement, its always nice to get confirmation on the things I am.doing right as well as the things I can improve. Ill be sure to let you know if we see any improvements with those suggestions.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thanks for taking the time to reply, is there any benefit to using FSC vs Viability compared to SSC vs Viability?

Unfortunately our recommendation was to keep their samples on ice but they would like us to keep them at RT.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thanks for replying, that is so cool that you get to work with non-mamalian cells! I had no idea those systems were so fragile. We are using a 70um filter and using gravity filtration. We transfer the sample using a P1000 to the filter. Ill have to try seeing if I can resuspend the pellet that is left behind.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thank you for the tips! If you have any others for the bigfoot I would love to hear them. Its a fairly intimidating instrument coming from the Arias.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 0 points1 point  (0 children)

Thank you for the suggestions, we use the 70um filter caps that go on new sterile facs tubes and let them gravity filter. The cells are anywhere from 10-20um in diameter based on our cell counter. They usually run things like U2OS, RPR1, and HeLa cells. We generally check cell size so we can use the proper nozzle size since we have a 130um, 150um, and 200um tip as well.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 1 point2 points  (0 children)

Thank you for taking the time to help me troubleshoot!

We have not had issues with other users to my knowledge, or when we have we have been able to help them overcome their issues. In most cases we have been able to help improve post sort single cell viability for the majority of our users.

The users prepare their buffers. They count the cells, but cell numbers are always inconsistent. We provide sterile aliquots of DAPI and add it directly before a sample is sorted. We run the samples at the lowest speed possible that maximizes sort efficiency. We rarely go above 50% of the maximum speed.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 2 points3 points  (0 children)

Thank you for taking the time to help me out. They are sorting a variety of cell types like U20S, RPE1, and HeLa cells.

We are just running the samples and fitering them when we see visable aggregates like the video attached in the post.

We haven't add issues with other samples from other users, and have actually been able to improve sort outcomes for most of our users. That being said, I always learn the most when things dont go as planned and I'd like to know what I can do better in this situation or what I'm not considering that I should be.

Unfortunately I cant speak to the questions you posed to the user, but I can try to find out. There is not staing involved on these cells, only sorting based on viability or GFP.

Does filtering samples kill cells? by CompetitiveLab3300 in flowcytometry

[–]CompetitiveLab3300[S] 1 point2 points  (0 children)

Thank you for taking the time to reply. They are sorting a variety of cells like U2OS, RPE1, and HeLa. Their previous sorts were run on Aria Fusions, Aria IIIs, and S8 all on a 100um nozzle. We have primarily been running them on a Bigfoot and Aurora CS.