Datasets for high resolution spatial mapping for SC2Spa

Title
Datasets for high resolution spatial mapping for SC2Spa
Author(s)
Linbu Liao
Categories
Bioinformatic methods development
Item type
dataset
Keyword(s)
Spatial transcriptomics, Spatial inference
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]. AdataMH2.h5ad is the processed mouse hippocampus spatial transcriptomics data file of puck_191204_01 from 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 dataset of Slide-seqV2[1]). C2L.zip is the cell2location data used in the analysis of SC2Spa manuscript. The datasets were used for the spatial mapping of SC2Spa.
Repositories The github website of SC2Spa: https://github.com/linbuliao/SC2Spa The github repository for SC2Spa analysis: https://github.com/linbuliao/SC2Spa_Notebooks Documentation The Read the Docs website of SC2Spa: https://sc2spa.readthedocs.io/en/latest/
References [1] Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F: Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature Biotechnology 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: Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain. Cell 2018, 174:1015-+. [3] Cable DM, Murray E, Zou LS, Goeva A, Macosko EZ, Chen F, Irizarry RA: Robust decomposition of cell type mixtures in spatial transcriptomics. 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: Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol 2022, 40:661-671.