Spatial gene expression data
In the spatial gene expression data submission, it is important for data interpretation that measured gene expression levels and spatial positions are related.
Submission of output files from the 10xGenomics Visium is explained in this section. Submit barcode sequences, position of spots containing the barcodes, tissue images, and scaling factors that converts pixel positions in the original, full-resolution images to pixel positions in the tissue image files.
Among the files indicated in the above page, submit the following files along with raw and processed data files. The other related files may also be included.
- tissue_hires_image.png, tissue_lowres_image.png: these files are downsampled versions of the original, full-resolution brightfield image provided by the user.
- scalefactors_json.json: scaling factor that converts pixel positions in the original, full-resolution image to pixel positions in the tissue image files.
- tissue_positions_list.csv: this text file contains a table with rows that correspond to spots.
After entering your data in D-way, please contact the GEA team before submitting.