Example Data & Notebooks

Last updated: 2024-07-16

This vignette provides an overview of the example data and accompanying notebooks available for the SDePER package. The example data includes pairs of spatial data (both simulated and real spatial transcriptomic (ST) datasets) with corresponding reference scRNA-seq data. The notebooks detail the description of the notebook, input data (with links to download the data), SDePER settings, running logs, and links to the corresponding results.

Simulated ST data

We generated 5 sets of simulated ST datasets, resulting in 14 combinations of simulated ST and various reference data. For each combination, we provide a link to the corresponding SDePER notebook, which includes links to documentation on the generation of simulated ST data and reference data preprocessing procedures, and links to download the corresponding ST and reference data.

Simulated ST data	Reference scRNA-seq data	Notebook
STARmap-based simulation	Internal reference	GO
	External reference	GO
	External reference with Vip missing	GO
	External reference adding irrelevant high intronic	GO
	Internal reference with downsampled Oligo	GO
	External reference with downsampled Oligo	GO
STARmap-based simulation with 5 cell types	Internal reference	GO
	External reference	GO
Sequencing-based simulation	Internal reference	GO
	External reference	GO
Sequencing-based simulation with 3x higher cell density	Internal reference	GO
	External reference	GO
Sequencing-based simulation with 6x higher cell density	Internal reference	GO
	External reference	GO

Real ST data

We collected 4 real ST datasets and their corresponding reference scRNA-seq datasets for cell type deconvolution. Details of these datasets, preprocessing procedures and SDePER notebooks are summarised as below:

	Mouse Olfactory Bulb (MOB)	Melanoma	Breast Cancer	IPF Lung
Spatial transcriptomics data source paper	Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. 2016, Science	Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma. 2018, Cancer Research	Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. 2021, Nature Communications	Our Paper
Spatial transcriptomic technology	Spatial Transcriptomics v1.0	Spatial Transcriptomics v1.0	Spatial Transcriptomics v1.0	10x Genomics Visium
Reference scRNA-seq data source paper	Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons. 2018, Cell Reports	A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. 2018, Cell	A single-cell and spatially resolved atlas of human breast cancers. 2021, Nature Genetics	Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. 2020, Science Advances
Reference scRNA-seq technology	10x Genomics Chromium Single Cell Gene Expression (droplet-based)	Smart-Seq2 (plate-based)	10x Genomics Chromium Single Cell Gene Expression (droplet-based)	10x Genomics Chromium Single Cell Gene Expression (droplet-based)
Preprocess for cell type deconvolution	MOB_preprocess.nb.html	Melanoma_preprocess.nb.html	Breast_Cancer_preprocess.nb.html	IPF_preprocess.nb.html
run SDePER on this real dataset	run_SDePER_on_MOB_data.ipynb	run_SDePER_on_Melanoma_data.ipynb	run_SDePER_on_Breast_Cancer_data.ipynb	run_SDePER_on_IPF_data.ipynb

Similarly, the links to download the ST and reference data are available in the notebooks.