PKBDS1784ZYFY
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS1784ZYFY/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS1784ZYFY",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS1784ZYFY](/analysis-sets/PKBDS1784ZYFY/) links to file set(s): [PKBDS0529GPTE](/measurement-sets/PKBDS0529GPTE/) 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/PKBDS1784ZYFY/"
}
],
"WARNING": [
{
"category": "incorrect classifications format",
"detail": "Human beta cell line [PKBSM6207TNSY](/human-beta-cell-line/PKBSM6207TNSY/) has `classifications` ['human beta cell line'] but should be [\"cell line\"]. Human beta cell lines are expected to have classifications as an array.",
"level": 40,
"level_name": "WARNING",
"name": "audit_classifications_format_check",
"path": "/human-beta-cell-line/PKBSM6207TNSY/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `bmi`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `diabetes_status_description`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `cause_of_death`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `genetic_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `collections`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `pancreas_tissue_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `url`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `derived_diabetes_status`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS1784ZYFY](/analysis-sets/PKBDS1784ZYFY/) links to file(s) [PKBFI7941WLPY](/alignment-files/PKBFI7941WLPY/), [PKBFI7194OSYA](/alignment-files/PKBFI7194OSYA/), [PKBFI9029IAJT](/tabular-files/PKBFI9029IAJT/) 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/PKBDS1784ZYFY/"
}
]
},
"award": {
"@id": "/awards/U24DK138512-DK138515/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium U24DK138512-DK138515"
},
"control_for": [],
"creation_timestamp": "2025-10-30T18:44:41.043267+00:00",
"description": "Analysis set of EndoC-bh1 cells treated with T-antigen (460) siRNA and stable expression of SIX2 from GSE79469",
"donors": [
{
"@id": "/human-donors/PKBDO8293TLPA/",
"accession": "PKBDO8293TLPA",
"aliases": [
"pankbase-consortium:EndoC_donor"
],
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/PKBFI6169NSMB/",
"accession": "PKBFI6169NSMB",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.rsem.genes.results"
],
"content_type": "element quantifications",
"creation_timestamp": "2026-01-07T18:11:41.620832+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI6169NSMB/@@download/PKBFI6169NSMB.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI3471DUNP/",
"accession": "PKBFI3471DUNP",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.rsem.isoforms.results"
],
"content_type": "element quantifications",
"creation_timestamp": "2026-01-07T18:11:42.524780+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3471DUNP/@@download/PKBFI3471DUNP.tsv.gz"
},
{
"@id": "/alignment-files/PKBFI7941WLPY/",
"accession": "PKBFI7941WLPY",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-01-07T18:06:27.911271+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI7941WLPY/@@download/PKBFI7941WLPY.bam"
},
{
"@id": "/alignment-files/PKBFI7194OSYA/",
"accession": "PKBFI7194OSYA",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.Aligned.toTranscriptome.out.bam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2026-01-07T18:06:30.093140+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI7194OSYA/@@download/PKBFI7194OSYA.bam"
},
{
"@id": "/alignment-files/PKBFI7478CAFK/",
"accession": "PKBFI7478CAFK",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.Aligned.sortedByCoord.out.md.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-01-07T18:06:33.172288+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI7478CAFK/@@download/PKBFI7478CAFK.bam"
},
{
"@id": "/tabular-files/PKBFI7266CIOD/",
"accession": "PKBFI7266CIOD",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.metrics.tsv"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-07T18:11:39.180670+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI7266CIOD/@@download/PKBFI7266CIOD.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI1534VUIM/",
"accession": "PKBFI1534VUIM",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.Aligned.sortedByCoord.out.md.marked_dup_metrics.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-07T18:11:37.682672+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI1534VUIM/@@download/PKBFI1534VUIM.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9029IAJT/",
"accession": "PKBFI9029IAJT",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_AnalysisSet.SRR3546387.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-07T18:11:36.097452+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9029IAJT/@@download/PKBFI9029IAJT.txt.gz"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS0529GPTE/",
"accession": "PKBDS0529GPTE",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469_MeasurementSet"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/pankbase-consortium/"
},
"publication_identifiers": [
"PMID:27133132",
"PMCID:PMC4864151",
"doi:10.1016/j.cmet.2016.04.002"
],
"release_timestamp": "2025-11-15T06:59:52.130559+00:00",
"samples": [
{
"@id": "/human-beta-cell-line/PKBSM6207TNSY/",
"@type": [
"HumanBetaCellLines",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM6207TNSY",
"aliases": [
"pankbase-consortium:EndoC-bh1_treated_T-antigen460SIX2_GSE79469"
],
"sample_terms": [
{
"@id": "/sample-terms/CVCL_909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_EndoC-betaH1"
],
"status": "released",
"summary": "EndoC-βH1",
"term_name": "EndoC-βH1"
}
],
"status": "released",
"summary": "EndoC-βH1 cell line, depleted of SIX2",
"treatments": [
"/treatments/b0c9b32d-e8e8-4469-86a0-1661b0878545/"
]
}
],
"schema_version": "8",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitted_files_timestamp": "2026-01-07T18:06:27.911271+00:00",
"uuid": "f1323c7d-65ba-4456-98b6-5004c6d5c84f"
}
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
