Human hg38 reference genome analysis set was downloaded from the University of California Santa Cruz (UCSC) ftp site (Kuhn et al., 2013 (link)). Human hg38 reference genome Ensembl gene annotations were obtained using the UCSC Table Browser Tool (Karolchik et al., 2004 (link)).
For each sequenced scRNA-Seq pool, Cellranger software (version 3.1.0) from 10 × Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest ) was used to process, align and summarize unique molecular identifier (UMI) counts against hg38 human reference genome.
Similarly, Spaceranger (version 1.0.0) software from 10X Genomics was used to process, align and summarize UMI counts against hg38 human reference genome for each spot on the Visium spatial transcriptomics array.
Corresponding antibody libraries were processed separately using CITE-Seq Count (version 1.4.3) to obtain antibody tag UMI counts for each cell barcode using the following parameters: -cbf 1 -cbl 16 -umif 17 -umil 28 -T 8 -cells 200000. Read UMI counts were summarized using 16-base barcodes for TotalSeq antibody libraries and 12-base barcodes for the in-house conjugated antibody libraries (see Fawkner-Corbett et al., 2020 (link)] for barcode sequences). Antibody UMI count matrices were then further filtered against the 10X cellular barcode whitelist for the corresponding 10x version 3.0 chemistry.
For each sequenced scRNA-Seq pool, Cellranger software (version 3.1.0) from 10 × Genomics (
Similarly, Spaceranger (version 1.0.0) software from 10X Genomics was used to process, align and summarize UMI counts against hg38 human reference genome for each spot on the Visium spatial transcriptomics array.
Corresponding antibody libraries were processed separately using CITE-Seq Count (version 1.4.3) to obtain antibody tag UMI counts for each cell barcode using the following parameters: -cbf 1 -cbl 16 -umif 17 -umil 28 -T 8 -cells 200000. Read UMI counts were summarized using 16-base barcodes for TotalSeq antibody libraries and 12-base barcodes for the in-house conjugated antibody libraries (see Fawkner-Corbett et al., 2020 (link)] for barcode sequences). Antibody UMI count matrices were then further filtered against the 10X cellular barcode whitelist for the corresponding 10x version 3.0 chemistry.
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