Question: What would I observe if I mismatched Multiome ATAC and GEX data from different samples?
Answer: Below are two examples of correctly matched Multiome ATAC and GEX data. In the Cross-Sensitivities plot, barcodes called cells are on the top-right corner (green circles) with high UMI per barcode and high ATAC transposition events in peaks per barcode.
However, if you mismatched GEX and ATAC data from two different samples, the Cross-Sensitivities plot will look different from the correct match.
As a test, the GEX library from sample 1 above was analyzed with sample 2 ATAC data, and sample 2 GEX library was analyzed with sample 1 ATAC data. There are fewer barcodes called cells on the top-right corner (green circles). Most of the barcodes have high UMI with low ATAC transposition events or low UMI with high ATC transposition events (purple box, shaped like upside-down F).
When observing such signatures in the Cross-Sensitivities plot, there may be a mismatch of ATAC and GEX libraries from different samples.
Products: Single Cell Multiome ATAC + Gene Expression