Data Deliverables

The following files are delivered when your project is completed:

• Fastq files
• Microscope image files
• 10X Genomics Spaceranger output

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 filesystem

Non-UMN users: a delivery email will provide instructions for downloading the deliverables from our download website

The following files are delivered when your project is completed:

Flat CSV files:

• Counts matrix (exprMat_file.csv.gz): matrix of target counts per cell (RNA) or target mean fluorescence intensity per cell (Protein)
• Cell metadata (metadata_file.csv.gz): various information associated with the CosMx run, which may include cell locations, cell areas / aspect ratios, marker intensity, etc.
• Transcripts (tx_file.csv.gz): tabulated transcript information, including local and global transcript pixel location, decoded target, compartment, and cell/FOV of origin. Large data. RNA assays only.
• Polygons (polygons.csv.gz): local and global coordinates of polygons outlining
• FOV positions (fov_positions_file.csv.gz): coordinates (in pixels and mm) of FOV centers.

Seurat Objects (Large Data)

• RDS file: file format readable by the Seurat package or other R-based open-source tools.
  • The provided Seurat object, by default, does not include transcript coordinates or polygon coordinates (large data). This information can be wrapped into the Seurat object on request.

FOV Image files

• Cell Labels TIFF: image indicating cell assignments of each pixel.
• Compartment Labels TIFF: image indicating compartment assignment (nucleus, cytoplasm) of each pixel.
• Cell Overlays JPG: image of segmentation outline overlays on DAPI nuclear stain.
• 2D Morphology TIFF: 5-channel raw images of FOV morphology stains.
• A python script and instructions will be provided that use the 2DMorphology TIFFs to create a composite image.

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 file system

Non-UMN users: The UIC offers external data delivery options through Globus, Box Secure Storage, and physical drives. Alternative delivery mechanisms can be discussed during project intake

The following files are delivered when your project is completed:

• Fastq files - some data repositories require uploading the fastq files for GeoMx projects, so be sure to download a copy when they are made available to you
• DCC count zip file
• LabWorksheet.txt and Config.ini
• ROI Report image export - A zip file for each slide containing a separate image of every ROI and every segment within that ROI, as well as an HTML summary of those images and a rendered scan image (full-color publication-quality image)
• Geomxqc.html summary report

GeoMx project data will be maintained on the GeoMx instrument for 1 year, after which it may be archived. Be sure to download all experimental data and securely store it on a local filesystem. 

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 file system

Non-UMN users: a delivery email will provide instructions for downloading the deliverables from our download website

The following files are delivered when your project is completed:

• Fastq files
• Curio Seeker analysis pipeline output:
  • sample1_Report.html - Run report
  • sample1_MoleculesPerMatchedBead.mtx - Expression table sparse matrix
  • sample1_barcodes.tsv - Expression table bead barcodes
  • sample1_genes.tsv - Expression table genes
  • sample1_MatchedBeadLocation.csv - Spatial coordinates of matched bead barcodes
  • sample1_seurat.rds - Seurat object with expression table, spatial coordinates, clustering results
  • sample1_anndata.h5ad - Anndata object with expression table, spatial coordinates
  • sample1_cluster_assignment.txt - Cluster assignment of bead barcodes
  • sample1_variable_features_clusters.txt - Top cluster defining genes
  • sample1_variable_features_spatial_moransi.txt - Top spatially variable genes
  • sample1_Metrics.csv - Run quality metrics
  • sample1_Report_files - Individual plots in sample1_report.html

UMN users: deliverables are copied to your group's data_delivery folder on the MSI Tier1 filesystem

Non-UMN users: a delivery email will provide instructions for downloading the deliverables from our download website