Datasets for single-cell-resolution spatial mapping by 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

File description
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.

HC1_transfer_to_AMB.csv includes the predicted location of the scRNA-seq data (AMB_HC.h5ad). The columns "ClosestSC" and "Dis2ClosestBead" are used in the cell communication analysis tutorial.

ssHippo_RCTD.csv is the annotation for the AdataMH1.h5ad file by RCTD[3].

WDs_T2.csv includes the Wasserstain distance of genes between the scRNA-seq dataset[2] and the mouse hippocampus Slide-seqV2[1] dataset.

SI_T2_WD.h5 is the traned model for mapping mouse hippocampus cells to space. The model is trained using genes selected according to Wasserstain distance.

SI_T2.h5 is the spatial inference model trained on all shared genes between two datasets.

T2_stat.csv is a summary of SI_T2.h5. It contains genes' contribution to location prediction and Pearson's correlation between prediction and true gene expression.

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.

Cell2Location_ST.h5ad is the processed Visium adult mouse brain spatial transcriptomics data ST8059048 from Cell2Location paper[4].

Cell2Location_snRNAseq.h5ad is the processed snRNA-seq adult mouse brain data of 5705STDY8058280, 5705STDY8058281, 5705STDY8058282, 5705STDY8058283, 5705STDY8058284, 5705STDY8058285 from Cell2Location paper[4]. 80, 81, 82 are from male 1 (female). 83, 84, 85 are from mouse 2 (male)

ModelCell2Location_snRNAseq2ST_SC2Spa_WD.h5 is is the pretrained SC2Spa model for mapping snRNAseq to ST (Genes with a Wasserstein Distance greater than 0.1 was used for training)

WDs_snRNAseq2Visium.csv has the Wasserstain distance information of genes between the snRNA-seq data[4] and the Visium mouse brain data[4].

The datasets were used for the spatial mapping of SC2Spa.

CV_code.zip contains the benchmarking code along with scripts for cross-validation and cross-dataset validation.

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.