Spatial transcriptomics

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Providing data

Providing data for basic processing - VisumHD

Use the following checklist of files/data that should be provided if RIC is performing basic processing of the data.

NOTE: If data are being generated by the UIC SGT core, RIC and SGT will coordinate sharing of data. There is no need for you to manage which files are being shared.

If your lab is providing image files for VisiumHD, please review 10X's image recommendations at https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/image-image-recommendation before providing any images. If the data are being provided by the UIC SGT core, RIC and SGT will coordinate these data and there is not need for you to review these recommendations.

• (REQUIRED) Sequencing data (FASTQ files)
• (REQUIRED) Cytassist images. Should be in TIFF format.
• (REQUIRED) Visium slide serial number and location.
• (OPTIONAL) Microscopic image. Can be one of the following and should be in BigTIFF (.btf) format.
  • Brightfield (H&E) image
  • Fluorescence Image. Typically dark field image. Can be grayscale or colorized

Providing data for analysis

NOTE: If the RIC is performing basic processing, or if Xenium data are being generated by the UIC SGT core, RIC and SGT will coordinate sharing/management all of the necessary files. There is no need for you to manage which files are being shared.

VisiumHD

• (REQUIRED) Provide the entire outs directory from SpaceRanger. Best to provide as either a ZIP or tar.gz file. A typical outs directory would have the following.
  • barcode_mappings.parquet
  • binned_outputs directory
  • feature_slice.h5
  • metrics_summary.csv
  • molecule_info.h5
  • spatial directory

Xenium

• (REQUIRED) Gene expression matrix in sparse format, typically in a directory named cell_feature_matrix. This directory should contain 3 files:
  • (REQUIRED) barcodes.tsv.gz.
  • (REQUIRED) features.tsv.gz.
  • (REQUIRED) matrix.mtx.gz.
• (REQUIRED) Transcript coordinates, typically named transcripts.parquet or transcripts.csv.gz.
• (REQUIRED) Cell coordinates, typically named cells.parquet or cells.csv.gz.
• (REQUIRED) Cell boundary coordinates, typically named cell_boundaries.parquet or cell_boundaries.csv.gz.
• Nucleus boundary coordinates, typically named nucleus_boundaries.parquet or nucleus_boundaries.csv.gz.
• Morphology image file, typically named morphology.ome.tif.
• Note that the final two files are required for submission to online repositories like Gene Expression Omnibus (GEO) prior to publication, but may not be required for our analysis. All together these files are the "raw data" for the Xenium platform.