PKBDS8010LDJC
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS8010LDJC/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS8010LDJC",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) links to file set(s): [PKBDS4480JAPN](/measurement-sets/PKBDS4480JAPN/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS8010LDJC/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary islet [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) has in progress subobject treatment [d20144fb-704c-4d62-b01a-3f2526d5f6ab](/treatments/d20144fb-704c-4d62-b01a-3f2526d5f6ab/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) has in progress subobject primary islet [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS8010LDJC/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) has in progress subobject primary islet [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS8010LDJC/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) has in progress subobject primary islet [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS8010LDJC/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) has in progress subobject primary islet [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS8010LDJC/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) has in progress subobject primary islet [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS8010LDJC/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3246QNUE](/primary-islet/PKBSM3246QNUE/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3246QNUE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM7821QYNK](/primary-islet/PKBSM7821QYNK/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM7821QYNK/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1229PGZJ](/human-donors/PKBDO1229PGZJ/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1229PGZJ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1929VVOC](/primary-islet/PKBSM1929VVOC/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1929VVOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289MFPK](/primary-islet/PKBSM6289MFPK/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289MFPK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM9387JNND](/primary-islet/PKBSM9387JNND/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM9387JNND/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS8010LDJC](/analysis-sets/PKBDS8010LDJC/) links to file(s) [PKBFI0621KDSI](/alignment-files/PKBFI0621KDSI/), [PKBFI7363FTIZ](/tabular-files/PKBFI7363FTIZ/), [PKBFI8612SXYI](/tabular-files/PKBFI8612SXYI/), [PKBFI9610AGLK](/matrix-files/PKBFI9610AGLK/), [PKBFI4051IERL](/tabular-files/PKBFI4051IERL/), [PKBFI5796FRYN](/matrix-files/PKBFI5796FRYN/), [PKBFI5758ZCTB](/matrix-files/PKBFI5758ZCTB/), [PKBFI8050DSVN](/matrix-files/PKBFI8050DSVN/), [PKBFI1271YXMB](/matrix-files/PKBFI1271YXMB/), [PKBFI6093NUSN](/matrix-files/PKBFI6093NUSN/), [PKBFI8228IPJH](/matrix-files/PKBFI8228IPJH/), [PKBFI0773XCUR](/matrix-files/PKBFI0773XCUR/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS8010LDJC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2373VJRQ](/primary-islet/PKBSM2373VJRQ/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2373VJRQ/"
}
]
},
"award": {
"@id": "/awards/U24DK138512-DK138515/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium U24DK138512-DK138515"
},
"collections": [
"IIDP"
],
"control_for": [],
"creation_timestamp": "2025-05-08T23:23:46.234432+00:00",
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{
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"accession": "PKBDO1229PGZJ",
"aliases": [
"joyce-niland:SAMN29494287"
],
"gender": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
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"accession": "PKBFI0621KDSI",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Alignment_Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T00:00:04.497452+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI0621KDSI/@@download/PKBFI0621KDSI.bam"
},
{
"@id": "/tabular-files/PKBFI7363FTIZ/",
"accession": "PKBFI7363FTIZ",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:48:16.731420+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7363FTIZ/@@download/PKBFI7363FTIZ.txt.gz"
},
{
"@id": "/tabular-files/PKBFI8612SXYI/",
"accession": "PKBFI8612SXYI",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:36:41.936157+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8612SXYI/@@download/PKBFI8612SXYI.txt.gz"
},
{
"@id": "/matrix-files/PKBFI9610AGLK/",
"accession": "PKBFI9610AGLK",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T16:48:21.199268+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI9610AGLK/@@download/PKBFI9610AGLK.mtx"
},
{
"@id": "/tabular-files/PKBFI4051IERL/",
"accession": "PKBFI4051IERL",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:42:53.828545+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI4051IERL/@@download/PKBFI4051IERL.txt.gz"
},
{
"@id": "/alignment-files/PKBFI3591THQK/",
"accession": "PKBFI3591THQK",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Alignment_before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T17:03:14.465267+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI3591THQK/@@download/PKBFI3591THQK.bam"
},
{
"@id": "/tabular-files/PKBFI4500PTOA/",
"accession": "PKBFI4500PTOA",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:25:45.936063+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI4500PTOA/@@download/PKBFI4500PTOA.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6680LMAW/",
"accession": "PKBFI6680LMAW",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_knee.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:38:02.545255+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6680LMAW/@@download/PKBFI6680LMAW.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9684LNUR/",
"accession": "PKBFI9684LNUR",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_pass.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:45:11.695159+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9684LNUR/@@download/PKBFI9684LNUR.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3964TPNA/",
"accession": "PKBFI3964TPNA",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-16T17:55:43.786502+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI3964TPNA/@@download/PKBFI3964TPNA.csv.gz"
},
{
"@id": "/matrix-files/PKBFI5796FRYN/",
"accession": "PKBFI5796FRYN",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:15:28.258495+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI5796FRYN/@@download/PKBFI5796FRYN.h5ad"
},
{
"@id": "/matrix-files/PKBFI5758ZCTB/",
"accession": "PKBFI5758ZCTB",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:23:39.491399+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI5758ZCTB/@@download/PKBFI5758ZCTB.h5ad"
},
{
"@id": "/tabular-files/PKBFI1217HNHK/",
"accession": "PKBFI1217HNHK",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T18:50:36.365051+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI1217HNHK/@@download/PKBFI1217HNHK.csv.gz"
},
{
"@id": "/tabular-files/PKBFI6387JUIM/",
"accession": "PKBFI6387JUIM",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.05_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T19:50:45.327865+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6387JUIM/@@download/PKBFI6387JUIM.txt.gz"
},
{
"@id": "/tabular-files/PKBFI7870QZOG/",
"accession": "PKBFI7870QZOG",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.15_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:31:51.100142+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7870QZOG/@@download/PKBFI7870QZOG.txt.gz"
},
{
"@id": "/matrix-files/PKBFI8050DSVN/",
"accession": "PKBFI8050DSVN",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.1.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:04:23.477380+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI8050DSVN/@@download/PKBFI8050DSVN.h5ad"
},
{
"@id": "/matrix-files/PKBFI1271YXMB/",
"accession": "PKBFI1271YXMB",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.1_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:14:19.334402+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI1271YXMB/@@download/PKBFI1271YXMB.h5ad"
},
{
"@id": "/tabular-files/PKBFI5257BLFQ/",
"accession": "PKBFI5257BLFQ",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.1_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:37:01.343888+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI5257BLFQ/@@download/PKBFI5257BLFQ.csv.gz"
},
{
"@id": "/tabular-files/PKBFI6517IYRU/",
"accession": "PKBFI6517IYRU",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.1_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:42:38.133638+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6517IYRU/@@download/PKBFI6517IYRU.txt.gz"
},
{
"@id": "/matrix-files/PKBFI6093NUSN/",
"accession": "PKBFI6093NUSN",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.15.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:05:26.773541+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI6093NUSN/@@download/PKBFI6093NUSN.h5ad"
},
{
"@id": "/matrix-files/PKBFI8228IPJH/",
"accession": "PKBFI8228IPJH",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Matrix_cellbender_FPR_0.15_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:11:07.620910+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI8228IPJH/@@download/PKBFI8228IPJH.h5ad"
},
{
"@id": "/tabular-files/PKBFI9547CNIA/",
"accession": "PKBFI9547CNIA",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_doubletfinder_assignments.txt"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:37:39.615247+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9547CNIA/@@download/PKBFI9547CNIA.txt.gz"
},
{
"@id": "/tabular-files/PKBFI7328YZPP/",
"accession": "PKBFI7328YZPP",
"aliases": [
"joyce-niland:IIDP_scRNAseq_SRR27326992_HTO_Tabular_cellbender_FPR_0.15_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:25:34.529159+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI7328YZPP/@@download/PKBFI7328YZPP.csv.gz"
},
{
"@id": "/tabular-files/PKBFI3163JFBK/",
"accession": "PKBFI3163JFBK",
"aliases": [
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],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:42:54.634812+00:00",
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"href": "/tabular-files/PKBFI3163JFBK/@@download/PKBFI3163JFBK.tsv.gz"
},
{
"@id": "/matrix-files/PKBFI0773XCUR/",
"accession": "PKBFI0773XCUR",
"aliases": [
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],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T22:30:39.706492+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI0773XCUR/@@download/PKBFI0773XCUR.mtx"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS4480JAPN/",
"accession": "PKBDS4480JAPN",
"aliases": [
"joyce-niland:IIDP_MeasurementSet_scRNAseq_SRR27326992_HTO"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/pankbase-consortium/",
"title": "Pankbase Consortium, PanKbase"
},
"notes": "GSE251912",
"release_timestamp": "2025-06-15T04:48:17.239917+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM6289MFPK/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM6289MFPK",
"aliases": [
"joyce-niland:SAMN29494287_scRNAseq_secondaryBiosample_HTO_SRR27326992_DMSO_24hr"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "in progress",
"summary": "islet of Langerhans cell, male, Homo sapiens depleted of Dimethyl sulfoxide for 24 hours",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/e37d5bf6-21d9-4a17-ad4d-86ea34dafc20/"
]
},
{
"@id": "/primary-islet/PKBSM7821QYNK/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM7821QYNK",
"aliases": [
"joyce-niland:SAMN29494287_scRNAseq_secondaryBiosample_HTO_SRR27326992_DMSO_4hr"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "in progress",
"summary": "islet of Langerhans cell, male, Homo sapiens depleted of Dimethyl sulfoxide for 4 hours",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/567e1f99-439f-4654-9889-53dbcf74141b/"
]
},
{
"@id": "/primary-islet/PKBSM3246QNUE/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM3246QNUE",
"aliases": [
"joyce-niland:SAMN29494287_scRNAseq_secondaryBiosample_HTO_SRR27326992_noTreatment"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "released",
"summary": "islet of Langerhans cell, male, Homo sapiens depleted of no treatment",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/d20144fb-704c-4d62-b01a-3f2526d5f6ab/"
]
},
{
"@id": "/primary-islet/PKBSM9387JNND/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
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"aliases": [
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],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "in progress",
"summary": "islet of Langerhans cell, male, Homo sapiens depleted of thapsigargin for 24 hours",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/fc46a9fb-fb76-4f5d-8c0e-07d7ec047442/"
]
},
{
"@id": "/primary-islet/PKBSM2373VJRQ/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
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"aliases": [
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],
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{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
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"summary": "islet of Langerhans cell, male, Homo sapiens depleted of thapsigargin for 2 hours",
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"treatments": [
"/treatments/ea8b2920-7651-4eb2-8210-cb7a2cf26711/"
]
},
{
"@id": "/primary-islet/PKBSM1929VVOC/",
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"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM1929VVOC",
"aliases": [
"joyce-niland:SAMN29494287_scRNAseq_secondaryBiosample_HTO_SRR27326992_thapsigargin_4hr"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "in progress",
"summary": "islet of Langerhans cell, male, Homo sapiens depleted of thapsigargin for 4 hours",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/aaf89ccc-2a2e-4cad-99d7-af62cf9fb5f4/"
]
}
],
"schema_version": "8",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitted_files_timestamp": "2025-05-15T23:36:41.936157+00:00",
"submitter_comment": "SRR27326992",
"summary": "intermediate analysis of scRNA-seq data",
"uuid": "a573cc34-2572-471b-b7b2-898fda05c865"
}
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
