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For sequencing-based spatial transcriptomics data, the gene-spot count matrix is highly sparse. This feature is similar to scRNA-seq. The goal of this paper is to identify whether there exist genes that are frequently under-detected in Visium compared to bulk RNA-seq, and the underlying potential mechanism of under-detection in Visium. We collected paired Visium and bulk RNA-seq data for 28 human samples and 19 mouse samples, which covered diverse tissue sources. We compared the two data types and observed that there indeed exists a collection of genes frequently under-detected in Visium compared to bulk RNA-seq. We performed a motif search to examine the last 350 bp of the frequently under-detected genes, and we observed that the poly (T) motif was significantly enriched in genes identified from both human and mouse data, which matches with our previous finding about frequently under-detected genes in scRNA-seq. We hypothesized that the poly (T) motif may be able to form a hairpin structure with the poly (A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during Visium library preparation.

It is (or should be) well-known that the Hawking flux that reaches spatial infinity is extremely sparse, and extremely thin, with the Hawking quanta, one-by-one, slowly dribbling out of the black hole. The typical time between quanta reaching infinity is much larger than the timescale set by the energy of the quanta. Among other things, this means that the Hawking evaporation of a black hole should be viewed as a sequential cascade of 2-body decays.