{
"@context": "/terms/",
"@id": "/tissues/IGVFSM3939SHHK/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3939SHHK",
"age": "15-25",
"age_units": "month",
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject document [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject phenotype term [MONDO_0015924](/phenotype-terms/MONDO_0015924/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject treatment [612fd456-886b-412d-b935-c5cac7a1df21](/treatments/612fd456-886b-412d-b935-c5cac7a1df21/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "unexpected CCF ID",
"detail": "Tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has a `ccf_id` but is associated with a non-human donor. Non-human tissues are not expected to specify a common coordinate framework identifier (CCF ID).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM3939SHHK/"
}
]
},
"award": {
"@id": "/awards/HG012012/",
"component": "data coordination"
},
"ccf_id": "db06dea9-bba2-e923-4fc7-f67ae567a100",
"cellular_sub_pool": "AT9029",
"classifications": [
"tissue"
],
"collections": [
"ENCODE"
],
"creation_timestamp": "2023-04-25T13:57:50.715613+00:00",
"date_obtained": "2022-12-10",
"description": "Description of a tissue object",
"disease_terms": [
{
"@id": "/phenotype-terms/MONDO_0015924/",
"status": "in progress",
"term_name": "pulmonary arterial hypertension"
}
],
"documents": [
"/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO8570HWEN/",
"accession": "IGVFDO8570HWEN",
"status": "archived",
"strain": "B6XCast"
}
],
"embryonic": false,
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS1317BKCD/",
"accession": "IGVFDS1317BKCD",
"aliases": [
"lior-pachter:share_seq"
],
"file_set_type": "experimental data",
"lab": {
"title": "Lior Pachter, Caltech"
},
"preferred_assay_title": "SHARE-seq",
"status": "released",
"summary": "SHARE-seq (SHARE-seq)"
},
{
"@id": "/prediction-sets/IGVFDS3565IUJC/",
"accession": "IGVFDS3565IUJC",
"aliases": [
"igvf:prediction_set_2"
],
"file_set_type": "functional effect",
"lab": {
"title": "Alan Boyle, UMich"
},
"status": "in progress",
"summary": "functional effect prediction"
},
{
"@id": "/measurement-sets/IGVFDS5330YIDV/",
"accession": "IGVFDS5330YIDV",
"aliases": [
"igvf:basic_measurement_set"
],
"file_set_type": "experimental data",
"lab": {
"title": "J. Michael Cherry, Stanford"
},
"preferred_assay_title": "SUPERSTARR",
"status": "in progress",
"summary": "SUPERSTARR"
},
{
"@id": "/analysis-sets/IGVFDS3767BRBZ/",
"accession": "IGVFDS3767BRBZ",
"aliases": [
"buenrostro-bernstein:AnalysisSet_IGVFSM8883WYCA"
],
"file_set_type": "intermediate analysis",
"lab": {
"title": "Jason Buenrostro, Broad"
},
"status": "in progress",
"summary": "SHARE-seq"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/j-michael-cherry/",
"title": "J. Michael Cherry, Stanford"
},
"lot_id": "309",
"lower_bound_age": 15,
"lower_bound_age_in_hours": 10800,
"multiplexed_in": [],
"notes": "Previous taxa: Mus musculus will now be calculated. This biosample previously specified NIC0003291 as its NIC, but this property has been moved to the institutional certification object. Please submit there instead to specify certification.",
"origin_of": [],
"parts": [],
"pmi": 4,
"pmi_units": "week",
"pooled_in": [
"/tissues/IGVFSM2353PGIB/"
],
"preservation_method": "cryopreservation",
"product_id": "9301-A",
"release_timestamp": "2023-04-26T13:57:50.715613+00:00",
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002369/",
"status": "released",
"term_name": "adrenal gland"
}
],
"schema_version": "21",
"sex": "male",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/j-michael-cherry/",
"status": "current",
"title": "J. Michael Cherry, Stanford"
}
],
"starting_amount": 80000,
"starting_amount_units": "cells",
"status": "archived",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Kalina Andreeva"
},
"submitter_comment": "Comment on Tissue object",
"summary": "Mus musculus B6XCast (male, 15-25 months) adrenal gland tissue (cellular sub pool: AT9029) associated with pulmonary arterial hypertension, treated with 10 mM leucine for 6 hours",
"taxa": "Mus musculus",
"treatments": [
{
"@id": "/treatments/612fd456-886b-412d-b935-c5cac7a1df21/",
"depletion": false,
"purpose": "stimulation",
"status": "in progress",
"treatment_term_name": "leucine",
"treatment_type": "chemical"
}
],
"upper_bound_age": 25,
"upper_bound_age_in_hours": 18000,
"url": "https://data.igvf.org",
"uuid": "d8e781b3-3059-4c7b-9915-d5618bf748fc",
"virtual": false
}