• Suspension of NCBI/EBI SRA data mirroring

Genomic Expression Archive

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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.

10x Genomics 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.

  • What format of 10x Genomics data should I submit to NCBI GEO/SRA?
  • Space Ranger Spatial Outputs
  • Understanding Space Ranger Outputs

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.

10x Genomics Xenium

  • Submission Type: Microarray
  • Array Design: A-GEAD-246 (Xenium)

Metadata

  • IDF sample collection protocol: Describe the protocol used to prepare the tissue.

For both Raw and Processed data, please submit a single tar archive containing the following files.

Raw data files

  • morphology.ome.tif: High-resolution morphology images
  • transcripts.parquet: Decoded transcripts (parquet or csv format)

Processed data files

  • barcodes.tsv, features.tsv, matrix.mtx OR cell_feature_matrix.h5: Transcript count (MEX or HDF5 format)
  • cells.parquet: Cell summary (parquet or csv format)
  • cell_boundaries.parquet: Cell segmentation (parquet or csv format)
  • nucleus_boundaries.parquet: Nucleus segmentation (parquet or csv format)
  • rds: Seurat object (optional)

Related pages:

  • Understanding Xenium Outputs
  • Archiving Xenium Data

MERFISH

For MERFISH or MERSCOPE submissions, processed data are necessary.

  • Submission Type: Microarray
  • Array Design: A-GEAD-247 (MERFISH)

The raw image data for MERFISH studies are too large for GEA to archive. You are welcome to submit the raw image files and .vzg files to a generalist archive.

Raw data files

  • Register the dummy data file (md5: 5a3c1b7fe06fb47ffcf4b31ae87a8ee4)

Processed data files

  • Identified transcripts (text or parquet format)
  • .vzg files are not accepted by GEA