Datasets for single-cell-resolution spatial mapping by SC2Spa

<strong>Title</strong><br> Datasets for high resolution spatial mapping for SC2Spa<br> <strong>Author(s)</strong><br> Linbu Liao<br> <strong>Categories</strong><br> Bioinformatic methods development<br> <strong>Item type</strong><br> dataset<br> <strong>Keyword(s)</strong><br> Spatial transcriptomics, Spatial inference <br> <strong>File description</strong><br> AdataMH1.h5ad is the processed mouse hippocampus spatial transcriptomics data file of puck_200115_08 from Slide-seqV2 paper[1]. AMB_HC.h5ad is a processed mouse hippocampus scRNA-seq data file[2]. The datasets are saved in Anndata format. ssHippo_RCTD.csv is the annotation for the AdataMH1.h5ad file by RCTD[3]. SI_T2_WD.h5 is the traned model for mapping mouse hippocampus cells to space. WDs_T2.csv includes the Wasserstain distance of genes between the scRNA-seq dataset[2] and the mouse hippocampus Slide-seqV2[1] dataset. <br> AdataMH2.h5ad is the processed mouse hippocampus spatial transcriptomics data file of puck_191204_01 from the Slide-seqV2 paper[1]. slideSeq_Puck190926_03_RCTD.csv is the annotation file for AdataEmbryo1.h5ad. AdataEmbryo1.h5ad is preprocessed file of puck_190926_03 (a mouse emrbyo Slide-seqV2[1] dataset). C2L.zip is the cell2location[4] data used in the analysis of SC2Spa manuscript. The datasets were used for the spatial mapping of SC2Spa. <br> <strong>Repositories</strong> The github website of SC2Spa: https://github.com/linbuliao/SC2Spa The github repository for SC2Spa analysis: https://github.com/linbuliao/SC2Spa_Notebooks <strong>Documentation</strong> The Read the Docs website of SC2Spa: https://sc2spa.readthedocs.io/en/latest/ <br> <strong>References</strong> [1] Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F: <strong>Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.</strong> <em>Nature Biotechnology</em> 2020. [2] Saunders A, Macosko EZ, Wysoker A, Goldman M, Krienen FM, de Rivera H, Bien E, Baum M, Bortolin L, Wang SY, et al: <strong>Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain.</strong> <em>Cell</em> 2018, <strong>174:</strong>1015-+. [3] Cable DM, Murray E, Zou LS, Goeva A, Macosko EZ, Chen F, Irizarry RA: <strong>Robust decomposition of cell type mixtures in spatial transcriptomics. </strong>Nat Biotechnol 2021. [4] Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Elmentaite R, Lomakin A, Kedlian V, Gayoso A, et al: <strong>Cell2location maps fine-grained cell types in spatial transcriptomics.</strong> <em>Nat Biotechnol</em> 2022, <strong>40:</strong>661-671. <br>