Dataset used for "Transcriptome-scale spatial reconstruction reveals microenvironmental regulation of cell states with Emerge"

All datasets analyzed in this study are publicly available from the following sources. For MERFISH MOp dataset, the spatial transcriptomics dataset was obtained from the https://doi.org/10.35077/g.21, and the corresponding snRNA-seq dataset was accessed through the BRAIN Initiative Cell Census Network (https://assets.nemoarchive.org/dat-ch1nqb7). For Xenium breast cancer dataset, the Xenium in situ spatial data, matched scRNA-seq data and Visium spatial data were all obtained from 10x Genomics at https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast. For Merfish MBC Datasets, the spatial datasets and corresponding scRNA-seq (snRNA-seq) datasets of all twelve tissue slices were downloaded from the Single-Cell Portal at https://singlecell.broadinstitute.org/single_cell/study/SCP2702.