Project description:Several ovarian cancer tumors from different anatomical sites and therapy statuses. A GUI to explore the data can be found at: https://visium-shiny-9hzfl.ondigitalocean.app/ Code to run the shiny app (same output as the GUI): https://github.com/kwells4/visium_public_shiny Code to replicate the analysis can be found: https://github.com/kwells4/visium_ovarian_cancer
Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).
Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".
Project description:8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples obtained from the ovaries during the interval debulking surgery
Project description:To reveal the spatial distribution and the difference gene expression pattern of cancer cells in colorectal cancer, Visium spatial transcriptomics of four CRC patients was applied
Project description:We investigated the mechanisms by which inflammatory responses generated by tumor-specific T cells delivered to ovarian tumor-bearing mice alone or after oncolytic vaccinia virus-driven immunogenic cancer cell death affect antitumor efficacy using spatial transcriptomics.