Question: Can I combine data from Visium CytAssist for FFPE and Visium for FFPE (direct placement) if I am using the Mouse Transcriptome v1 probe set?
Answer: We do not recommend or officially support combining data from these modes. While the probe set for mouse transcriptome is the same between these CytAssist for FFPE and direct placement FFPE approaches, the barcodes are different between direct placement slides (v1) and slides for CytAssist (v2). Information about different Visium slide versions and compatible assays can be found here. Sample preparation also differs greatly. For direct placement, the probes are applied to the tissue surface, diffused through the tissue, and captured by oligos below the tissue. For CytAssist, the probes are sandwiched between the tissue and the capture oligos and transferred to the Visium slide via the CytAssist machine. Due to this chemistry difference, we do not officially support combining data from these modes. However, spaceranger aggr does enable combining the datasets.
Please see our Analysis Guide here for related information about correcting batch effects in Visium data. See our Tech Note here for comparisons between direct placement versus CytAssist-enabled data.
Products: Visium for FFPE, Visium CytAssist for FFPE