Supplementary data for thesis "Methodologies in Resolving Spatial Transcriptomic Signals and Applications"

<p dir="ltr">Chapter 3 titled "Spatially Resolved Analysis of Human Ovarian Tissue Responses to Cryopreservation" (in revision)</p><ul><li>This study constructs a spatially resolved molecular map of human ovarian tissue using high-resolution Stereo-seq to characterize how the two principal cryopreservation strategies, slow-freezing and vitrification, affect different functional regions of the organ. </li><li>The code provided here illustrate the analysis pipeline.</li></ul><p dir="ltr"><br></p><p dir="ltr">Chapter 4 titled "Mitochondrial Single Nucleotide Polymorphisms Resolve Clonal Architecture and Progressive Lineage Expansion in Colorectal Cancer" (in preparation)</p><ul><li>This study asks whether mitochondrial single-nucleotide polymorphisms captured by single-cell ATAC sequencing can serve as endogenous lineage barcodes for reconstructing clonal expansion in colorectal cancer.

We developed a reproducible computational workflow integrating mitochondrial variant calling, clone identification, cell-type annotation, chromatin-accessibility analysis, and copy-number inference. </li></ul><p dir="ltr">Chapter 5 titled "CLEAR-ST: Physics-informed Probabilistic Decontamination of Spatial Transcriptomics by Modeling mRNA Lateral Diffusion" (submitted)</p><ul><li>This study addresses lateral mRNA diffusion in sequencing-based spatial transcriptomics, where transcripts may spread during tissue permeabilization and contaminate neighbouring capture locations.