Publicly Available CyTOF Data Containing Beads

[bumpCyto]

Hello,

Is anyone aware of publicly available CyTOF data where beads have not been removed? I'm interested in understanding bead normalization / studying a set of cells where there is no biological variability.

Thanks!

[mleipold]

HI Eric,

I can confirm that the Healthy Ctrl PBMC files in http://flowrepository.org/id/FR-FCM-ZYAJ still contain the EQ4 normalization beads.

There are 3 sets of files: Raw (no norm), Fluidigm-ver2 norm, and Finck norm. But in all cases, the EQ4 beads are still present (as are all the Debris, Doublets, Dead cells, etc).


Aside: I'm not sure what you mean by "studying a set of cells where there is no biological variability".....could you clarify?


Mike

[bumpCyto]

Thanks a lot Mike!

Sorry, poor wording on my part. What I really mean to say is that I am interested in understanding sources of variance in a population of cells. In live cells, that variance is a result of both biological variability and technical variability, and it is difficult to separate the two. With beads, my understanding is that any variability in the data is a result of technical variability. So, just looking at beads will help me understand, for instance, the relationship between mean and variance in the data.

[mleipold]

Hi Eric,

OK. In that case, would you be more interested in replicates of a single draw of a given donor? That way, biological variability is largely removed.

If so, this is maybe a better dataset: http://flowrepository.org/id/FR-FCM-ZY3Z

That's the data from the Multicenter study I was part of several years ago. Here's the paper that talks about it: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805584/
* note: this is CyTOF2 data, while the ZYAJ is Helios data.

This dataset has same-draw-same-donor Replicates, but are already Premessa-normd (barcoded sample, so normalized before debarcoding): http://flowrepository.org/id/FR-FCM-Z2YR
Formally, Beads are still included. However, the Bead Singlets (Ce140+ Ir191-) are discarded during the debarcoding process (since they're Barcode-negative). The only Beads remaining are Bead-Cell Doublets (Ce140+ Ir191+), and most of the Bead channels aside from Ce140 are also used for antibodies. But, you could look at the Ce140 channel.


There are also some replicate controls in some of the Immport SLVP015 studies: for example, SDY1464 ( https://www.immport.org/shared/study/SDY1464 ) has 4 replicates of the 885d5 donor (Raw, Ungated/uncleaned, Beads still included).

Mike

Mike

[sgranjeaud]

Hi,

Beads are not cells and if you have a CyTOF dataset, beads should be present in the raw files. Beads is an external control and allows to quantify the instrument variations.

It still not clear to me what variations you want to study, but it's up to you. My basic advice would be to draw the steps of an experiment from the labelling step up to the acquisition, in order to identify the variations you want to study.

P. Rybakowska et al. reviewed many sources of variation if you need a recent point of view.

Best.