Metadata Collected for Single-Cell ATAC-Seq (snATAC-seq)

1. Donor Metadata

Donor Identification

• RRID: Unique identifier assigned to the donor (e.g., RRID:SAMN37875593).
• Center Donor ID: Internal ID for the donor at the data collection center (e.g., SAMN37875593).

Demographics

• Self-Reported Sex: Biological sex of the donor (e.g., male or female).
• Age (years): Age of the donor at the time of tissue collection (e.g., 46 years).
• BMI: Body Mass Index, a measure of body fat based on height and weight (e.g., 35.36).

Medical and Clinical Information

• Living Donor: Whether the donor was alive at the time of tissue donation (e.g., false).
• Diabetes Status: Ontology term describing diabetes status (e.g., MONDO:0005148).
• Diabetes Status Description: Descriptive term for diabetes condition (e.g., type 2 diabetes).

Supplementary Information

• Data Available: List of datasets available for this donor, such as:
  • HLA typing
  • Islet function
  • CyTof data
  • Histology data for pancreas, spleen, and lymph tissues
• Other Tissues Available: Ontology terms for additional tissues provided (e.g., none specified).
• Description: Short description of the donor (e.g., Human donor SAMN37875593 in the HPAP database).
• Collections: Database or consortium collecting the data (e.g., HPAP).
• External Resources: Cross-referenced databases and IDs (e.g., PANC-DB:HPAP-158).
• Aliases: Alternate names or IDs assigned by collaborators (e.g., klaus-kaestner:HPAP-158).
• Identifiers: External references to the donor (e.g., PANC-DB:HPAP-158).

2. Biosample Metadata

Summary

• Sample Terms: Biological source or tissue type (e.g., islet of Langerhans).
• Taxa: Species (e.g., Homo sapiens).
• Description: Sample description and origin (e.g., Islet biosample from human donor SAMN22562810).

Sample Details

• Isolation Center: Institution where the sample was processed (e.g., University of Pennsylvania).
• RRID: Unique identifier for the biosample (e.g., RRID:SAMN22562810).
• Cold Ischaemia Time: Time between tissue removal and processing (e.g., 6.15 hours).
• Organ Source: Origin of the sample (e.g., deceased).
• Prep Viability (%): Viability percentage post-preparation (e.g., 95%).
• Purity: Composition details (e.g., 85% and 30%).
• Hand Picked: Whether the sample was manually selected (e.g., Yes).
• Islet Function Available: Availability of functional data (e.g., Yes).
• Islet Yield: Number of islets extracted (e.g., 504468).
• IEQ/Pancreas Weight: Islet Equivalent per pancreas weight (e.g., 5544).
• Islet Morphology and Histology: Information on islet structure (e.g., Yes).
• Preservation Method: Method used for preservation (e.g., UWStorage_Viaspan_SPS-1).

Provenance and Dates

• Sources: Contributor and institution (e.g., Klaus Kaestner, UPenn).
• Date Harvested: Collection date (e.g., June 24, 2021).

3. Measurement Set Metadata

Summary

• File Set Type: Type of data produced (e.g., experimental data).
• Summary: General description of the experiment (e.g., single-cell ATAC-seq).
• Assay Term: Type of assay performed (e.g., single-cell ATAC-seq).

Publications and Protocols

• Publication Identifiers: Related publications (e.g., PMID:31127054, PMID:36206763).
• Protocols: Link to protocols used in the study (e.g., https://hpap.pmacs.upenn.edu/explore/workflow/islet-molecular-phenotyping-studies?protocol=5).

Sample Summaries

• Sample Details: Description of the biosamples analyzed (e.g., islet of Langerhans cell, female, Homo sapiens).

4. Analysis Set Metadata

Intermediate Analysis Set

• File Set Type: Data processing type (e.g., intermediate analysis).
• Summary: Description of intermediate data outputs (e.g., intermediate analysis of snATAC-seq data).

Principal Analysis Set

• File Set Type: Final processed data (e.g., principal analysis).
• Summary: Description of processed data outputs (e.g., principal analysis of snATAC-seq data).