Tool: Control data for cross-contaminations on C1 ATAC-seq.
gravatar for Charles Plessy
3.8 years ago by
Charles Plessy2.7k
Charles Plessy2.7k wrote:

Dear Biostars,

in the course of a project were we use the single-cell ATAC-seq protocol on the Fluidigm platform, it became important for us to assess the possibility of cross-contaminations, for instance by chromatin debris, so that we can appropriately quality-control and filter our data.

In line with some controls in single-cell RNA-seq experiments, we wanted a mixture control, with cells from different organisms, so that it can be crystal clear if one chamber contained DNA from other cells than the one on the capture site. Since such data did not seem to be available in public databanks, we made one dataset by ourselves, using mouse and human hepatocytes.

I have opened it to the public, in the hope that other single-cell ATAC-seq users may collaboratively contribute to the use of this datasets to make some robust quality standards. The data is described in the GitHub repository linked below.

I plan to add our own analysis "when it is ready", and I am eager to hear comments and feedback on the data itself in the meantime. I am aware that some of the experimental information is not yet presented in details, and please do not hesitate to underline which points need further description in priority.

tool atac-seq data single-cell • 1.8k views
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