PKBDS5789FZQV
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS5789FZQV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS5789FZQV",
"aliases": [
"pankbase-consortium:bulkRNA_GSE248853_SAMN20478103_alphaCell_RFX6shRNA_MeasurementSet"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has in progress subobject human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/PKBDS5789FZQV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has in progress subobject primary cell [PKBSM2595VQBS](/primary-cells/PKBSM2595VQBS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/PKBDS5789FZQV/"
},
{
"category": "validation error",
"detail": "Treatment [9b713a06-8215-4af1-8426-03b72c16075b](/treatments/9b713a06-8215-4af1-8426-03b72c16075b/) has schema error {'lab': '00eadba4-bed5-4ffd-a4bf-9a5c16c87cc6', 'award': '2e63d0a1-1cc1-4654-8f19-4968a5ca9618', 'status': 'in progress', 'aliases': ['pankbase-consortium:treatment_knockdownRFX6'], 'purpose': 'perturbation', 'depletion': True, 'description': 'Genetic perturbation via RNAi (shRNA-mediated knockdown) resulting in RFX6 loss of function', 'submitted_by': '5e3038c4-baa5-4589-b3d8-ad2fe634e826', 'schema_version': '7', 'treatment_type': 'environmental', 'treatment_term_id': 'UniProtKB:Q8HWS3', 'creation_timestamp': '2026-01-20T19:39:54.048109+00:00', 'treatment_term_name': 'RFX6 knockdown', 'uuid': '9b713a06-8215-4af1-8426-03b72c16075b'} should not be valid under {'required': ['treatment_term_id']}.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/treatments/9b713a06-8215-4af1-8426-03b72c16075b/"
},
{
"category": "validation error: treatment_term_name",
"detail": "Treatment [9b713a06-8215-4af1-8426-03b72c16075b](/treatments/9b713a06-8215-4af1-8426-03b72c16075b/) has schema error 'RFX6 knockdown' is not one of ['stiffness'].",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/treatments/9b713a06-8215-4af1-8426-03b72c16075b/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has a sample [PKBSM2595VQBS](/primary-cells/PKBSM2595VQBS/) that lacks any `institutional_certificates` issued to the lab that submitted this file set. Measurement sets for mapping assays involving samples with a human origin are expected to link to the relevant institutional certificates issued to a matching lab and award.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/PKBDS5789FZQV/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/PKBDS5789FZQV/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS5789FZQV/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS5789FZQV](/measurement-sets/PKBDS5789FZQV/) has `assay_term` bulk RNA-seq assay, but `preferred_assay_title` RNA-seq. Measurement sets with a preferred assay title are expected to specify an appropriate assay term.",
"level": 40,
"level_name": "WARNING",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/PKBDS5789FZQV/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO3231HHPV](/human-donors/PKBDO3231HHPV/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO3231HHPV/"
},
{
"category": "missing age",
"detail": "Primary cell [PKBSM2595VQBS](/primary-cells/PKBSM2595VQBS/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/PKBSM2595VQBS/"
}
]
},
"award": {
"@id": "/awards/U24DK138512-DK138515/",
"component": "data coordination",
"name": "U24DK138512-DK138515",
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium U24DK138512-DK138515"
},
"control_for": [],
"creation_timestamp": "2026-01-28T21:01:13.454953+00:00",
"description": "Alpha cells bulk RNA-seq measurement set from human donor SAMN20478103 for GSE248853 RFX6 shRNA",
"donors": [
{
"@id": "/human-donors/PKBDO3231HHPV/",
"accession": "PKBDO3231HHPV",
"aliases": [
"joyce-niland:SAMN20478103"
],
"gender": "Male",
"status": "in progress",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS5870DVIN/"
],
"lab": {
"@id": "/labs/pankbase-consortium/"
},
"preferred_assay_title": "RNA-seq",
"publication_identifiers": [
"PMID:38064570",
"PMCID:PMC10882151",
"doi:10.2337/db23-0483"
],
"release_timestamp": "2026-02-06T23:47:42.580402+00:00",
"samples": [
{
"@id": "/primary-cells/PKBSM2595VQBS/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM2595VQBS",
"aliases": [
"pankbase-consortium:bulkRNA_GSE248853_SAMN20478103_alphaCell_RFX6shRNA_biosample"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000171/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_pancreaticAcell"
],
"status": "released",
"summary": "pancreatic A cell",
"term_name": "pancreatic A cell"
}
],
"status": "in progress",
"summary": "pancreatic A cell, Male, Homo sapiens depleted of RFX6 knockdown",
"treatments": [
{
"@id": "/treatments/9b713a06-8215-4af1-8426-03b72c16075b/",
"purpose": "perturbation",
"summary": "Depletion of RFX6 knockdown",
"treatment_type": "environmental"
}
]
}
],
"schema_version": "17",
"sequencing_library_types": [
"rRNA depleted"
],
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"uuid": "f5e65bf0-ee4e-413e-bebd-f9b7d001d9a7"
}
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
