SSAM-lite test data

Spatially resolved transcriptomics datasets prepared from different publications to be used as sample data sets for the SSAM-lite tool.

Each folder contains a dataset including:

• one (or more) files for mRNA locations, formatted as a comma separated file adhering to the DecodedSpots format defined by the Starfish pipeline (https://spacetx-starfish.readthedocs.io/en/mcai-api-additions/help_and_reference/spacetx-format/output_formats/DecodedSpots/index.html). This format is intuitive, with fields for the target mRNA, the x-coordinate and the y-coordinate.
• a gene signature file, containing expected mRNA expression profiles for cell types, formatted as a comma separated file with rows as cell types, columns as genes, with the matrix populated with numerical or binary values associating mRNA expression to cell types.
• and a README referencing the original publication the data was retrieved from as well as some datset specifications.

Datsets specifications:

• Codeluppi_osmFISH
  • method: osmFISH
  • tissue: mouse brain somatosensory cortex
  • mRNA spots: 1802589
  • genes: 33
  • signatures: 31 cell types
  • DOI: 10.1038/s41592-018-0175-z
• Tosti_ISS_Pancreas
  • method: ISS
  • tissue: human pancreas
  • mRNA spots: 461078
  • genes: 138
  • signatures: 16 cell types
  • DOI: 10.1053/j.gastro.2020.11.010