Giotto_Suite_manuscript

Repository containing all files related to the Giotto Suite manuscript. The scripts repository contains all the code used to generate the figures presented.

important links

• Giotto Suite repo
• Giotto Suite preprint

folder structure

• scripts - main directory containing reproducible scripts and associated subdirectories

  • CREATE - intermediate and additional files
    • EXT_DATA - pre-made additional files
    • OUTS - intermediate files, some of which are provided with the repo
  • SOURCE - scripts to source for additional functionality
  • Xenium_coregister - files used with xenium co-registration

• terrabio_startup_scripts - directory containing .sh scripts that can be uploaded to Terra cloud platform for creating a cloud environment with Giotto installed. There is a master.sh file for creating the cloud environment with the previous version of Giotto and suite.sh for creating the cloud environment with the most recent version of Giotto suite.

data used

The following spatial datasets were used in this manuscript:

• Spatial Genomics Mouse kidney fresh frozen: https://spatialgenomics.com/data/.
• DBiT-seq mouse embryo E10.5: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137986.
• Nanostring CosMx FFPE Non-Small Cell Lung Cancer (lung sample 12): https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/
• Seq-Scope liver: https://deepblue.lib.umich.edu/data/concern/data_sets/9c67wn05f.
• Vizgen MERSCOPE/MERFISH FF mouse brain (data release v1.0, May 2021): https://info.vizgen.com/mouse-brain-data
• Vizgen MERSCOPE/MERFISH FFPE breast cancer: https://info.vizgen.com/ffpe-showcase
• 10X Genomics Xenium human breast cancer: https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
• 10X Genomics multi-modal Visium CytAssist Human Tonsil: https://www.10xgenomics.com/resources/datasets/gene-protein-expression-library-of-human-tonsil-cytassist-ffpe-2-standard
• 10X Genomics Visium Mouse Brain Section (Coronal): https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain
• Stereo-seq Mouse Embryo E16.5_E2S6 bin1 matrix (i.e. *_GEM_bin1.tsv.gz): (https://db.cngb.org/stomics/mosta/download/)
• Imaging Mass Cytometry Intensity images of human lymph node FFPE: (Bost et al. 2023) https://data.mendeley.com/datasets/ncfgz5xxyb/1
• Single Cell Mouse Brain Dataset (Manno et al. 2021): http://mousebrain.org/development/downloads.html
• Single-cell Atlas of the Human Tonsil (Massoni-Badosa et al 2024) annotated SpatialExperiment object: https://github.com/massonix/HCATonsilData.