For the Gabitto et al manuscript, was any sort of ambient RNA detection performed for the query MTG?

1

For the Gabitto et al manuscript, was any sort of ambient RNA detection performed for the query MTG?

Thanks,

2

No ambient RNA correction was used. We benchmarked cellbender extensively and found it (1) did not change much generally (I suspect because we sort nuclei before loading them onto the 10x controller) or (2) would sporadically fail to identify the empty droplet plateau and return very weird counts matrices.

Here’s two libraries illustrating this effect:

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The effect on MALAT1 has widespread effects on other genes because of its high relative abundance in single nucleus data (& has weird cell type specificity):

Without cellbender:

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With cellbender (Note randomly large effects on L5 IT and VLMC):

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3

Thanks you for getting back to me. Much appreciated! I see the effect with MALAT1