Measurement Set
Title
Measurement Set
Description
A file set for a distinct measurement, such as the sequencing of a genomic library generated by an experiment performed on a cell line. A measurement set contains the raw data files generated by the measurement.
Required
assay_term, award, file_set_type, lab, samples
Identifying Properties
accession, aliases, alternate_accessions, uuid
Highlight properties with matching names, “title” attributes, or an enum of those properties. Matching properties might be non-submittable.
array[string]
Lab specific identifiers to reference an object.
linkto
The assay used to produce data in this measurement set.
array[linkto]
The auxiliary sets of files produced alongside raw data from this measurement set.
linkto
Grant associated with the submission.
string
Detailed composition of the perifusion media including supplements and buffering components
array[linkto]
File sets that can serve as scientific controls for this measurement_set.
string
Link for downloading the functional assay data (if publicly available)
array[string]
Identifiers from external resources that may have 1-to-1 or 1-to-many relationships with IGVF file sets.
string
A plain text description of the object.
array[linkto]
Documents that provide additional information (not data file).
array[string]
Method used for mapping the data to the donor it came from.
string
Links to the external site where images produced by this measurement are stored.
string
The category that best describes this measurement set.
string
Time interval set on the perifusion fraction collector for each fraction collection
array[string]
Hormones measured in perifusion fractions (e.g., insulin, glucagon). See https://www.protocols.io/view/analysis-of-islet-function-by-insulin-enzyme-linke-bz7bp9in
number
Average islet diameter calculated as (longest + shortest) / 2 in micrometers
string
Percentage breakdown of endocrine cell types within the islet preparation. See https://www.protocols.io/view/islet-embedding-for-histology-261ge455dv47/v1
string
Method used to purify islets before the functional assay (e.g., hand-picking to ensure purity and size consistency)
number
Percentage of target islet cells in the preparation used for the functional assay
number
Islet cell volume expressed as islet equivalents (IEQ). 1 IEQ = 1 islet with a diameter of 150 μm.
boolean
Whether the islets were shipped to a recipient lab before the experiment
linkto
Lab associated with the submission.
array[linkto]
The platform used to construct the library sequenced in this measurement set.
integer
The number of datasets included in the multiome experiment this measurement set is a part of.
string
Flow rate of media through the perifusion system (e.g., mL/min, μL/min)
string
Volume of each fraction collected over a defined time interval (e.g., mL, μL)
string
Link to the protocols.io protocol for the dynamic cell perifusion assay
string
The custom lab preferred label for the experiment performed in this measurement set.
array[string]
Links to the protocol(s) for conducting the assay
array[string]
The publication identifiers that provide more information about the object.
array[linkto]
The sample(s) associated with this file set.
array[string]
The version or type of sequencing chemistry used.
array[string]
Description of the libraries sequenced in this measurement set.
string
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.
string
Additional information specified by the submitter to be displayed as a comment on the portal.
array[linkto]
A list of genes targeted in this assay. For example, TF ChIP-seq attempts to identify binding sites of a protein encoded by a specific gene. In CRISPR FlowFISH, the modified samples are sorted based on expression of a specific gene. This property differs from small_scale_gene_list in Construct Library Set, which describes genes targeted by the content integrated in the constructs (such as guide RNAs.)
integer
Total number of islets loaded into the perifusion chamber or tissue culture well for the functional assay
Supported by National Institutes of Health (NIH) grants U24 DK138515, U24 DK138512
Supplemental funds from the NIH Office of Data Science Strategies
Supplemental funds from the NIH Office of Data Science Strategies
