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

Giotto Module Versions Used:

• {Giotto} v4.2.1
• {GiottoVisuals} v0.2.12
• {GiottoClass} v0.4.7
• {GiottoUtils} v0.2.4
• {GiottoDB} v0.0.0.0001

Archive branches for these modules can be found by clicking the version numbers above.

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_supporting_files - files used with xenium co register and segmentation

• 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 dataset. The mouse kidney fresh frozen dataset was downloaded from the Spatial Genomics website at https://db.cngb.org/stomics/mosta/download/.
• DBiT-seq dataset. The mouse embryo E10.5 dataset was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137986.
• Nanostring CosMx dataset. The CosMx FFPE Non-Small Cell Lung Cancer dataset for lung sample 12 was downloaded from the Nanostring website at https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/
• Seq-Scope dataset. The Seq-Scope liver dataset was downloaded directly from the following link, https://deepblue.lib.umich.edu/data/concern/data_sets/9c67wn05f.
• Vizgen dataset. The MERSCOPE/MERFISH FF mouse brain (data release v1.0, May 2021) and FFPE breast cancer (May 2022) datasets were downloaded directly from the Vizgen website at https://info.vizgen.com/mouse-brain-data and https://info.vizgen.com/ffpe-showcase, respectively.
• 10X Genomics Xenium dataset. Xenium, corresponding images and Visium datasets for human breast cancer were downloaded directly from the 10X website at https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast.
• 10X Genomics multi-modal Visium CytAssist Human Tonsil dataset. The multi-modal Visium CytAssist Human Tonsil dataset was downloaded from the 10X genomics website at https://www.10xgenomics.com/resources/datasets/gene-protein-expression-library-of-human-tonsil-cytassist-ffpe-2-standard.
• 10X Genomics Visium Mouse Brain Section (Coronal) dataset. The Visium Mouse Brain Section (Coronal) dataset was downloaded from the 10X Genomics website at https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Adult_Mouse_Brain.
• 10X Genomics Visium HD Human Colorectal Cancer. The Visium HD Human Colorectal Cancer (FFPE) dataset was downloaded from the 10X genomics website at https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc.
• OpenST adult mouse hippocampus dataset. The OpenST adult mouse hippocampus dataset was downloaded from https://rajewsky-lab.github.io/openst/latest/examples/datasets/.
• Slide-seq mouse brain. The processed counts of the Slide-seq mouse brain were downloaded from the NeMO database using the following link https://data.nemoarchive.org/biccn/grant/rf1_macosko/macosko/spatial_transcriptome/cellgroup/Slide-seq/mouse/.
• Stereo-seq dataset. The bin1 matrix files (i.e. *_GEM_bin1.tsv.gz) were downloaded from the CNGB portal at the following link (https://db.cngb.org/stomics/mosta/download/).
• Imaging Mass Cytometry dataset. Intensity images of human lymph node FFPE tissue were downloaded from a repository created by Bost et. al https://data.mendeley.com/datasets/ncfgz5xxyb/1.
• Single Cell Mouse Brain Dataset. A single-cell reference dataset published by Manno et al. 2021 was used to identify developmental mouse brain cell types for spatial DWLS deconvolution with Stereo-seq data in this study. This data can be downloaded in the form of a .loom file from the Mousebrain.org website (http://mousebrain.org/development/downloads.html).
• Single-cell Human Tonsil Dataset. The Atlas of Cells in the Human Tonsil published by Massoni-Badosa et al 2022 containing the annotation of >357,000 cells was used for spatial DWLS deconvolution of Visum CytAssist data in this study. The annotated SpatialExperiment object was downloaded from https://github.com/massonix/HCATonsilData.
• Spatial RNA-ATAC seq mouse embryo ME13. The Mouse embryo ME13 spatial RNA-ATAC seq was originally published by Zhang et al. 2023 and downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205055.