Spatial Transcriptomics

HiFi-Slide

Prepare your metadata based on the latest metadata schema using one of the template files below. See the instructions in the Metadata Validation Workflow document for more information on preparing and validating your metadata.tsv file prior to submission.

Related files:

This link lists the set of fields that are required in the OME TIFF file XML header.

Metadata schema

Version 2 (use this one)


Directory schemas

Version 2.0 (use this one)
pattern required? description
extras\/.* ✓ Folder for general lab-specific files related to the dataset.
extras\/microscope_hardware\.json ✓ [QA/QC] A file generated by the micro-meta app that contains a description of the hardware components of the microscope. Email HuBMAP Consortium Help Desk help@hubmapconsortium.org if help is required in generating this document.
extras\/microscope_settings\.json   [QA/QC] A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk help@hubmapconsortium.org if help is required in generating this document.
raw\/.* ✓ All raw data files for the experiment.
raw\/fastq\/.* ✓ Raw sequencing files for the experiment
raw\/fastq\/RNA\/.* ✓ Directory containing fastq files pertaining to RNAseq sequencing.
raw\/fastq\/RNA\/[^\/]+_R[^\/]+\.fastq\.gz ✓ This is a GZip’d version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2).
raw\/Spatial_barcodes\/.* ✓ Files containing spatial barcodes and coordinates.
raw\/Spatial_barcodes\/[^\/]+\.gene ✓ Information about each gene.
raw\/Spatial_barcodes\/[^\/]+\.mtx ✓ The raw count matrix (reads per spot that map to each gene:spot x gene).
raw\/Spatial_barcodes\/[^\/]+\.spo ✓ The spatial coordinates for each spot.