PKBDS2571DYWB
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS2571DYWB/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS2571DYWB",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS2571DYWB](/analysis-sets/PKBDS2571DYWB/) links to file set(s): [PKBDS5853LSZN](/measurement-sets/PKBDS5853LSZN/) 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/PKBDS2571DYWB/"
},
{
"category": "inconsistent parent sample",
"detail": "Primary cell [PKBSM2238OZPV](/primary-cells/PKBSM2238OZPV/) has metadata properties (`collections`, `prep_viability`, `preservation_method`, `hand_picked`, `cold_ischaemia_time`, `rrid`, `purity`, `upper_bound_age`, `isolation_center`, `islet_yield`, `age_units`, `lower_bound_age`, `sample_terms`, `islet_function_available`, `islet_histology`, `islet_morphology`, `pancreas_weight`, `organ_source`) inconsistent with its associated parent sample [PKBSM1797OQUM](/primary-islet/PKBSM1797OQUM/). Samples that are sorted from or part of a parent sample are expected to share most of the parent's metadata properties.",
"level": 60,
"level_name": "ERROR",
"name": "audit_sample_sorted_from_parent_child_check",
"path": "/primary-cells/PKBSM2238OZPV/"
},
{
"category": "audit script error",
"detail": "audit_external_reference_files: NameError(\"name 'get_audit_message' is not defined\")",
"level": 60,
"level_name": "ERROR",
"name": "audit_external_reference_files",
"path": "/reference-files/PKBFI6475GTLH/"
},
{
"category": "audit script error",
"detail": "audit_external_reference_files: NameError(\"name 'get_audit_message' is not defined\")",
"level": 60,
"level_name": "ERROR",
"name": "audit_external_reference_files",
"path": "/reference-files/PKBFI0723SUOK/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released reference file [PKBFI6475GTLH](/reference-files/PKBFI6475GTLH/) has deleted subobject award [U24DK13851](/awards/U24DK13851/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/reference-files/PKBFI6475GTLH/"
},
{
"category": "mismatched status",
"detail": "Released reference file [PKBFI0723SUOK](/reference-files/PKBFI0723SUOK/) has deleted subobject award [U24DK13851](/awards/U24DK13851/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/reference-files/PKBFI0723SUOK/"
}
],
"WARNING": [
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS2571DYWB](/analysis-sets/PKBDS2571DYWB/) links to file(s) [PKBFI6475GTLH](/reference-files/PKBFI6475GTLH/), [PKBFI0723SUOK](/reference-files/PKBFI0723SUOK/), [PKBFI0555SWYG](/alignment-files/PKBFI0555SWYG/), [PKBFI6949VUKM](/alignment-files/PKBFI6949VUKM/), [PKBFI6822EDSE](/tabular-files/PKBFI6822EDSE/) 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/PKBDS2571DYWB/"
},
{
"category": "missing age",
"detail": "Primary cell [PKBSM2238OZPV](/primary-cells/PKBSM2238OZPV/) 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/PKBSM2238OZPV/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO0568QTGJ](/human-donors/PKBDO0568QTGJ/) is missing tier 2 field `diabetes_status_hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO0568QTGJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0568QTGJ](/human-donors/PKBDO0568QTGJ/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0568QTGJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0568QTGJ](/human-donors/PKBDO0568QTGJ/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0568QTGJ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0568QTGJ](/human-donors/PKBDO0568QTGJ/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0568QTGJ/"
}
]
},
"award": {
"@id": "/awards/UC4DK112217/",
"contact_pi": {
"@id": "/users/e1c8c91f-3952-45a9-9f56-442627f60c13/",
"title": "Klaus Kaestner"
},
"title": "PENN INTEGRATED HUMAN PANCREAS PROCUREMENT AND ANALYSIS PROGRAM"
},
"collections": [
"HPAP"
],
"control_for": [],
"creation_timestamp": "2024-12-04T22:27:58.618508+00:00",
"description": "Analysis set of RNA-seq for pancreatic alpha cell of islet biosample from human donor SAMN18741978 in the HPAP database HPAP-001",
"donors": [
{
"@id": "/human-donors/PKBDO0568QTGJ/",
"accession": "PKBDO0568QTGJ",
"aliases": [
"klaus-kaestner:HPAP-001"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/reference-files/PKBFI6475GTLH/",
"accession": "PKBFI6475GTLH",
"aliases": [
"kyle-gaulton:referenceFile_GRCh38_noALT_noHLA_noDecoy"
],
"content_type": "genome reference",
"creation_timestamp": "2025-03-06T18:23:04.522268+00:00",
"file_format": "fasta",
"href": "/reference-files/PKBFI6475GTLH/@@download/PKBFI6475GTLH.fasta.gz",
"submitted_file_name": "Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta"
},
{
"@id": "/reference-files/PKBFI0723SUOK/",
"accession": "PKBFI0723SUOK",
"aliases": [
"kyle-gaulton:referenceFile_gencode_v39_GRCh38_annotation"
],
"content_type": "genes_transcripts",
"creation_timestamp": "2025-03-06T18:23:22.951195+00:00",
"file_format": "gtf",
"href": "/reference-files/PKBFI0723SUOK/@@download/PKBFI0723SUOK.gtf.gz",
"submitted_file_name": "gencode.v39.GRCh38.annotation.gtf"
},
{
"@id": "/alignment-files/PKBFI0555SWYG/",
"accession": "PKBFI0555SWYG",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_STAR-bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-03-06T18:36:12.348600+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI0555SWYG/@@download/PKBFI0555SWYG.bam"
},
{
"@id": "/alignment-files/PKBFI6949VUKM/",
"accession": "PKBFI6949VUKM",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_STAR-Transbam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2025-03-10T21:12:34.414576+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI6949VUKM/@@download/PKBFI6949VUKM.bam"
},
{
"@id": "/alignment-files/PKBFI3551GMNR/",
"accession": "PKBFI3551GMNR",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_PICARD-bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-03-10T21:13:40.375603+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI3551GMNR/@@download/PKBFI3551GMNR.bam"
},
{
"@id": "/tabular-files/PKBFI7865ARND/",
"accession": "PKBFI7865ARND",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_RSEM-gene"
],
"content_type": "element quantifications",
"creation_timestamp": "2025-03-10T21:41:53.009671+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI7865ARND/@@download/PKBFI7865ARND.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI4344UDJJ/",
"accession": "PKBFI4344UDJJ",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_RSEM-isoform"
],
"content_type": "element quantifications",
"creation_timestamp": "2025-03-10T21:42:02.059152+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI4344UDJJ/@@download/PKBFI4344UDJJ.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI6822EDSE/",
"accession": "PKBFI6822EDSE",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_STAR-log"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-03-25T22:30:16.271657+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6822EDSE/@@download/PKBFI6822EDSE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6971ASBI/",
"accession": "PKBFI6971ASBI",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_PICARD-metrics"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-03-25T22:30:29.748647+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6971ASBI/@@download/PKBFI6971ASBI.txt.gz"
},
{
"@id": "/tabular-files/PKBFI2034TPLU/",
"accession": "PKBFI2034TPLU",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-001_RNA-SeQC-metrics"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-03-25T22:30:51.545460+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI2034TPLU/@@download/PKBFI2034TPLU.tsv.gz"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS5853LSZN/",
"accession": "PKBDS5853LSZN",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_MeasurementSet_RNAseq_HPAP-001"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"publication_identifiers": [
"PMID:31127054",
"PMCID:PMC6609987",
"doi:10.2337/db19-0058",
"PMID:36206763",
"PMCID:PMC9742126",
"doi:10.1016/j.cmet.2022.09.013"
],
"release_timestamp": "2025-01-10T10:14:00.817811+00:00",
"samples": [
{
"@id": "/primary-cells/PKBSM2238OZPV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM2238OZPV",
"aliases": [
"klaus-kaestner:pancreaticAlphaCell_HPAP-001"
],
"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": "released",
"summary": "pancreatic A cell, male, Homo sapiens",
"taxa": "Homo sapiens"
}
],
"schema_version": "7",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitted_files_timestamp": "2025-03-06T18:23:04.522268+00:00",
"submitter_comment": "HPAP-001",
"summary": "intermediate analysis of RNA-seq data",
"uuid": "2ae9fd1a-7ced-4f65-9bc1-c25b6366aa1a"
}
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