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