Space Ranger, printed on 06/20/2021
The Visium for FFPE assay uses probes targeting protein coding genes in the human or mouse transcriptomes. Each probe consists of a pair of oligonucleotides hybridized to the targeted transcript and are subsequently ligated. A human transcriptome probe set is available currently, and a mouse transcriptome probe set will be available shortly.
Gene IDs and probe sequences are defined in the probe set reference CSV input file for
spaceranger count. Two supporting files are provided: a BED file listing the reference genome coordinates for each probe, and a CSV file listing probes with predicted off-target activity, which are excluded from analysis by default.