Spatial gene expression

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.

Visium

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.

DRA

fastq or bam

Describe methods, name and version of kit (e.g., Smart-seq2, 10x, Drop-seq) used for single-cell library construction in Library Construction Protocol of the DRA Experiment. For 10x technology, describe version of 10x chemistry (e.g., v1, v2).

GEA

GEA processed data

GEX Matrix: gene expression data
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.
web_summary.html: Summary data (optional)
cloupe.cloupe: Loupe Browser file for data visualization and analysis (optional)

In CytAssist enabled Gene Expression (GEX), add the following files outputted in spatial sub-directory.

aligned_tissue_image.jpg (can be omitted when submitting web_summary.html)
cytassist_image.tiff

Submit these files in single tar file as GEA processed data.

Xenium

For spatial gene expression data generated from Xenium, submit output files archived and compressed by tar.gz as GEA processed data files. Select the “Submission Type: Microarray” and register dummy data files (md5: 5a3c1b7fe06fb47ffcf4b31ae87a8ee4) as raw data files. Enter “A-GEAD-11” (accession for the dummy array design) for Array Design Accession.