QuickSRT: Quick Access to Spatially Resolved Transcriptomics (SRT) Datasets

SRT Studies:

• 14204217 – Triple Negative Breast Cancers
• 14620362 – Kidney and Lung Cancer with Tertiary Lymphoid Structures
• 4739739: Human Breast Cancers
• 7760264 – Colorectal Cancer Consensus Molecular Subtypes
• DLPFC: Dorsolateral Prefrontal Cortex
• GSE175540: Tertiary Lymphoid Structure
• GSE193460: Mouse Model of Lung Adenocarcinoma
• GSE213688: Cellular Plasticity in Human Breast Cancer Subtypes
• HER2-Positive: Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer
• MOB: Mouse Olfactory Bulb

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SRT Data Structure:

Each study's samples have the following files:

• data/SCE_sampleID.h5ad (HDF5 AnnData):

  • sce: SingleCellExperiment (R) / adata: AnnData (Python)
    • assay(sce, "counts") / adata.X: Gene-by-spot count matrix
      • Batch-corrected count matrix for study 14204217
    • reducedDims(sce)$S / adata.obsm['S']: Spatial coordinate matrix
    • colData(sce)$z / adata.obs['z']: Annotations

• images/HE_sampleID.jpg or .png:

  • Hematoxylin and Eosin (H&E)-stained histological image