CosMx Spatial transcriptome dataset of human gastric mucosa

This dataset contains the spatial transcriptome dataset of human gastric mucosa obtained by CosMx

A zip file contains the following folders and files:

Folders

- CellComposite folder: the composite immunofluorescent images of each FOV.

- CellLabels folder: the cell definitions images for each FOV determined during cell segmentation.

- CellOverlay folder: the cell boundary images for each FOV determined during cell segmentation.

- CompartmentLabels folder: the subcellular compartment images for each FOV determined during cell segmentation. The compartment types are as follows: 0. Extracellular, 1. Nuclear, 2. Membrane, 3. Cytoplasmic

- RawMorphologyImages folder: raw morphological TIF images for each FOV

Files

- Run5458_{sample_name}_exprMat_file.csv: cell expression matrix.

- Run5458_{sample_name}_fov_positions_file.csv: each FOV relative position within global structure.

- Run5458_{sample_name}_metadata_file.csv: the metadata of each cell.

- Run5458_{sample_name}_tx_file.csv: the transcript file for each target gene and its position.

- Run5458_{sample_name}-polygons.csv: the segmentation polygon file.

Citation

If you use this dataset for your research, please cite our paper.

Ayumu Tsubosaka, Daisuke Komura, Miwako Kakiuchi, Hiroto Katoh, Takumi Onoyama, Asami Yamamoto, Hiroyuki Abe, Yasuyuki Seto, Tetsuo Ushiku, Shumpei Ishikawa, Stomach encyclopedia: Combined single-cell and spatial transcriptomics reveal cell diversity and homeostatic regulation of human stomach, Cell Reports, Volume 42, Issue 10, 2023, 113236, https://doi.org/10.1016/j.celrep.2023.113236.