microSTRS: Spatial RNA-Sequencing of Microbiome-Host Interactions at One Micron Resolution

In situ polyadenylation combined with Sequencing based Spatial Transcriptomics allows the mapping of Microbiome + Total Host Transcriptome

Dependencies

The following software and packages were used to run this project:

• Python - Version 3.9.17
• Snakemake - Version 6.1.0
• STAR - Version 2.7.10a
• Kraken2 - Version 2.09
• Pandas - Version 2.1.3
• Scanpy - Version 1.9.3
• NumPy - Version 1.26.2
• SciPy - Version 1.11.3
• MuData
• Muon
• cell2location - Version 0.1.3
• ST_BarcodeMap
• anndata - Version 0.10.3

Alignment

• An earlier version (as found in the relevant subdirectory) for the slidesnake pipeline was used for alignment

Data generated for this paper:

Data will be made available upon publication under GEO accession numbers; GSE276866 for the low-resolution datasets, GSE277196, GSE277197 and GSE277255 for the high-resolution datasets.

Contact:

• Iwijn De Vlaminck (id93@cornell.edu)
• Yannis Ntekas (in68@cornell.edu)
• Lena Takayasu (lt425@cornell.edu)
• David W. McKellar (dmckellar@nygenome.org)

The pipeline is in active developement if you have issues/suggestions please contact us!