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. Author manuscript; available in PMC: 2023 Jun 7.
Published in final edited form as: Cell Syst. 2023 May 9;14(5):404–417.e4. doi: 10.1016/j.cels.2023.03.008

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Deposited data
Human Invasive ductal carcinoma spatial transcriptomics data 10x Genomics 10x Data: https://support.10xgenomics.com/spatialgene-expression/datasets/1.2.0/V1_Human_Invasive_Ductal_Carcinoma
Human Cutaneous squamous cell carcinoma spatial transcriptomics and single-cell RNA sequencing data Ji et al.17 GEO: GSE144240
Human cutaneous malignant melanoma spatial transcriptomics data Thrane et al.18 Spatial Research Lab Data: https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/
Human melanoma tumor single-cell RNA sequencing data Tirosh et al.19 GEO: GSE72056
Human HER2+, ER+ and PR- breast cancer spatial transcriptomics data 10x Genomics 10x Data: https://support.10xgenomics.com/spatialgene-expression/datasets/1.1.0/V1_Breast_Cancer_Block_A_Section_1
Human HER2+ breast tumor spatial transcriptomics data Andersson et al.45 GitHub Data: https://github.com/almaan/her2st
Mouse Posterior brain (sagittal) spatial transcriptomics data 10x Genomics 10x Data: https://support.10xgenomics.com/spatialgene-expression/datasets/)
Mouse kidney spatial transcriptomics data 10x Genomics 10x Data: https://support.10xgenomics.com/spatialgene-expression/datasets/
Human clear cell renal cell carcinoma primary tumors spatial transcriptomics data Meylan et al.44 GEO: GSE175540
Human breast cancer spatial transcriptomics data 10x Genomics 10x Data: https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
Software
TESLA This paper https://doi.org/10.5281/zenodo.7703260
BayesSpace Zhao et al.15 https://github.com/edward130603/BayesSpace
SpaGCN Hu et al.24 https://github.com/jianhuupenn/SpaGCN
RCTD Cable et al.23 https://github.com/dmcable/RCTD