Islet function experiment meta-data

This document outlines the recommended meta-data standards in PanKbase for reporting experiments involving purified pancreatic islets to measure function.

Schema URL: https://data.pankbase.org/profiles/measurement_set/

This data model is designed to capture comprehensive information about experiments performed to measure pancreatic islet function.

General meta-data fields

• Assay Term: Ontology term describing the experiment that was performed (OBI)
• Description: Plain text description of the experiment
• File set type: The category that best describes this measurement set.
• Auxiliary sets: Auxiliary file sets associated with the raw data for this experiment
• Control file sets: File sets that represent scientific controls for this experiment
• Data URL: Link to raw data for this experiment
• Protocols: Links to the protocol(s) for conducting the assay
• Samples: Sample used to perform the assay

Islet function-related fields

• Base media: Detailed composition of the perifusion media including supplements and buffering components
• Fraction collection time: Time interval set on the perifusion fraction collector for each fraction collection
• Hormone assay: Hormones measured in perifusion fractions (e.g., insulin, glucagon). See protocols.io — analysis of islet function by insulin ELISA
• Islet Diameter: Average islet diameter calculated as (longest + shortest) / 2 in micrometers
• Islet Endocrine Composition: Percentage breakdown of endocrine cell types within the islet preparation. See protocols.io — islet embedding for histology
• Islet Purification Method: Method used to purify islets before the functional assay (e.g., hand-picking to ensure purity and size consistency)
• Islet Purity: Percentage of target islet cells in the preparation used for the functional assay
• Islet Volume IEQ: Islet cell volume expressed as islet equivalents (IEQ). 1 IEQ = 1 islet with a diameter of 150 μm.
• Islets shipped: Whether the islets were shipped to a recipient lab before the experiment
• Perifusion flow rate: Flow rate of media through the perifusion system (e.g., mL/min, μL/min)
• Perifusion fraction volume: Flow rate of media through the perifusion system (e.g., mL/min, μL/min)
• Perifusion protocol: Flow rate of media through the perifusion system (e.g., mL/min, μL/min)
• Stimuli secretagogues: JSON object describing the temporal sequence of glucose and pharmacological stimulations during perifusion. Each key is a time range (e.g., '3-9 min') and each value is an array of stimuli applied.
• Total islets for assay: Total number of islets loaded into the perifusion chamber or tissue culture well for the functional assay