I am reading Saunders et al. (2018).

In the methods' subsection "ICA based analysis and clustering" (independent component analysis), a set of independent components from ICA is labelled as "Artifact" with the following explanation:

Artifact (n = 315), in which either: (a) cell scores showed obvious replicate-specific biases, or (b) the top loading genes largely intersected with those observed to vary strongly with digest time (Figures 3 and S3), or contained many heat-shock proteins;

Aside from a possible typo (Figure S3 instead of S2) I couldn't find a list of genes that vary with digest time. The list of genes they found in few technical components is shown in Fig. S2 (D-H). The legend of the figure indicates:

Example of digest-related ICs from FC co-analysis of under- and over-digested cells. Left, cell loadings color-coded by digest condition. Right, gene-loading plots for the 10 top and bottom loading genes. IC 15 (cluster 2, Syt6+ deep-layer glutamatergic) and IC 68 (cluster 1, Nptxr+ upper-layer glutamatergic) show contributions from similar genes. Genes related to ATP synthesis and Calmodulins (eg., Cox6a1, Ndufa4, Calm2) load on the under-digested cells, while another set of genes including the nuclear-enriched Meg3 and Malat1 load highly onto the over-digested condition.

However, a full list of genes associated with digestion is not provided. I searched for other articles reporting such genes but I was unable to find any. Is there such a resource or well-known characterization of genes associated with technical signal in scRNA-Seq?


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