Published October 2, 2021
| Version v2
Dataset
Open
SSAM-lite test data
Description
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 file 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.
- a csv for a custom color palette for the provided cell types.
- and a README referencing the original publication the data was retrieved from as well as some dataset 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
Files
SSAM-lite_test_data.zip
Files
(26.1 MB)
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Additional details
Related works
- Is derived from
- Journal article: 10.1038/s41592-018-0175-z (DOI)
- Journal article: 10.1053/j.gastro.2020.11.010 (DOI)
- Is published in
- Preprint: 10.1101/2021.09.29.462194 (Handle)