PBMC Dataset used in paper to produce Figure 6

[fbrundu]

Dear Vivian, I'd like to use the same dataset that you used in scImpute paper. However, I'm unable to infer which one it is from 10X webpage. The interested dataset is the one used to produce Figure 6:

The dataset contains 4,500 peripheral blood mononuclear cells (PBMCs) of nine immune cell types, with 500 cells of each type.

I am contacting you since the Fresh 68k PBMCs (Donor A) has 68k cells, the other ones have different size (not 4.5k cells), so I don't understand which one you used.

Edit Is the dataset the following: https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.3.0/pbmc4k ?

Thanks, Francesco

[Vivianstats]

Hello Francesco,

If you go to their website (https://support.10xgenomics.com/single-cell-gene-expression/datasets), you can see a list of cell types (Monocytes, B cells, etc.). For example, Monocytes data is distributed here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.1.0/cd14_monocytes

I randomly draw 500 cells from each type so that I can have true cell labels. I did not use the larger datasets since the true cell labels are missing.

[fbrundu]

Hi Vivian, Ok. How did you correct for batch effects?

[Vivianstats]

Hello Francesco, I'm aware that there are normalization methods developed for scRNA-seq data, but in my analysis I just normalized the raw data by total counts.

[fbrundu]

Ok, thanks.

[sophial05]

Hi Vivian, I was just wondering if you could please share the dataset that you used to produce Figure 6? Thanks!

[Vivianstats]

Hi Sophia,

You can directly download the data from 10x genomics website: https://support.10xgenomics.com/single-cell-gene-expression/datasets under section: Single Cell 3' Paper: Zheng et al. 2017

Best, Vivian

[sophial05]

Thank you so much!