PKBDS0269YCWP
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS0269YCWP/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS0269YCWP",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS0269YCWP](/analysis-sets/PKBDS0269YCWP/) links to file set(s): [PKBDS2009ACIW](/measurement-sets/PKBDS2009ACIW/) 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/PKBDS0269YCWP/"
}
],
"WARNING": [
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS0269YCWP](/analysis-sets/PKBDS0269YCWP/) links to file(s) [PKBFI4633SRSF](/tabular-files/PKBFI4633SRSF/), [PKBFI2383DSTA](/tabular-files/PKBFI2383DSTA/), [PKBFI9555GDAN](/tabular-files/PKBFI9555GDAN/), [PKBFI0799PYNI](/alignment-files/PKBFI0799PYNI/), [PKBFI0343WZOG](/matrix-files/PKBFI0343WZOG/), [PKBFI0199QJFP](/matrix-files/PKBFI0199QJFP/), [PKBFI2175JJXU](/matrix-files/PKBFI2175JJXU/), [PKBFI1410WEQG](/matrix-files/PKBFI1410WEQG/), [PKBFI2872IHLR](/matrix-files/PKBFI2872IHLR/), [PKBFI9314UOJR](/matrix-files/PKBFI9314UOJR/), [PKBFI4160JYBZ](/matrix-files/PKBFI4160JYBZ/), [PKBFI9974GDZJ](/matrix-files/PKBFI9974GDZJ/) 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/PKBDS0269YCWP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1147JSQB](/primary-islet/PKBSM1147JSQB/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1147JSQB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `t1d_stage`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7691YWQE](/human-donors/PKBDO7691YWQE/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7691YWQE/"
}
]
},
"award": {
"@id": "/awards/U24DK098085/",
"contact_pi": {
"@id": "/users/e385b015-66c4-48cd-b4f2-884af615dade/",
"title": "Joyce Niland"
},
"title": "Integrated Islet Distribution Program"
},
"collections": [
"Prodo"
],
"control_for": [],
"creation_timestamp": "2025-05-08T23:23:55.951020+00:00",
"description": "Analysis set of scRNA-seq for islet biosample of human donor SAMN15314807 from Prodo with infected_with_SARS-CoV-2 (SRR12831416)",
"donors": [
{
"@id": "/human-donors/PKBDO7691YWQE/",
"accession": "PKBDO7691YWQE",
"aliases": [
"joyce-niland:SAMN15314807"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/PKBFI4633SRSF/",
"accession": "PKBFI4633SRSF",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-19T18:36:13.698861+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI4633SRSF/@@download/PKBFI4633SRSF.txt.gz"
},
{
"@id": "/tabular-files/PKBFI2383DSTA/",
"accession": "PKBFI2383DSTA",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-19T18:36:19.777518+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI2383DSTA/@@download/PKBFI2383DSTA.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9555GDAN/",
"accession": "PKBFI9555GDAN",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-19T18:36:25.553586+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9555GDAN/@@download/PKBFI9555GDAN.txt.gz"
},
{
"@id": "/alignment-files/PKBFI0799PYNI/",
"accession": "PKBFI0799PYNI",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Alignment_Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-19T18:54:06.179883+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI0799PYNI/@@download/PKBFI0799PYNI.bam"
},
{
"@id": "/tabular-files/PKBFI6288KBHR/",
"accession": "PKBFI6288KBHR",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_FPR_0.15_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-20T20:31:22.979861+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI6288KBHR/@@download/PKBFI6288KBHR.csv.gz"
},
{
"@id": "/matrix-files/PKBFI0343WZOG/",
"accession": "PKBFI0343WZOG",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Matrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-19T18:46:48.332272+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI0343WZOG/@@download/PKBFI0343WZOG.mtx"
},
{
"@id": "/matrix-files/PKBFI0199QJFP/",
"accession": "PKBFI0199QJFP",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Matrix_cellbender_FPR_0.1_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-20T20:23:58.237159+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI0199QJFP/@@download/PKBFI0199QJFP.h5ad"
},
{
"@id": "/tabular-files/PKBFI6283MFMJ/",
"accession": "PKBFI6283MFMJ",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_FPR_0.1_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-20T20:31:17.034709+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6283MFMJ/@@download/PKBFI6283MFMJ.txt.gz"
},
{
"@id": "/alignment-files/PKBFI8987NWRE/",
"accession": "PKBFI8987NWRE",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Alignment_before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-19T18:54:13.586855+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI8987NWRE/@@download/PKBFI8987NWRE.bam"
},
{
"@id": "/tabular-files/PKBFI3036SQAR/",
"accession": "PKBFI3036SQAR",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-19T23:25:10.773119+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI3036SQAR/@@download/PKBFI3036SQAR.txt.gz"
},
{
"@id": "/matrix-files/PKBFI2175JJXU/",
"accession": "PKBFI2175JJXU",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-19T23:37:22.875849+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI2175JJXU/@@download/PKBFI2175JJXU.h5ad"
},
{
"@id": "/matrix-files/PKBFI1410WEQG/",
"accession": "PKBFI1410WEQG",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-19T23:37:28.540649+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI1410WEQG/@@download/PKBFI1410WEQG.h5ad"
},
{
"@id": "/tabular-files/PKBFI4671EZWK/",
"accession": "PKBFI4671EZWK",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_FPR_0.05_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-20T00:02:45.321962+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI4671EZWK/@@download/PKBFI4671EZWK.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9196SRUE/",
"accession": "PKBFI9196SRUE",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_FPR_0.15_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-20T20:31:27.942690+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9196SRUE/@@download/PKBFI9196SRUE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6538ZZZY/",
"accession": "PKBFI6538ZZZY",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-19T23:25:29.042713+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI6538ZZZY/@@download/PKBFI6538ZZZY.csv.gz"
},
{
"@id": "/tabular-files/PKBFI1338SDPB/",
"accession": "PKBFI1338SDPB",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-20T00:02:38.512266+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI1338SDPB/@@download/PKBFI1338SDPB.csv.gz"
},
{
"@id": "/matrix-files/PKBFI2872IHLR/",
"accession": "PKBFI2872IHLR",
"aliases": [
"joyce-niland:Prodo_scRNAseq_SRR12831416_infected_with_SARS-CoV-2_Matrix_cellbender_FPR_0.15_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-20T20:24:14.210233+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI2872IHLR/@@download/PKBFI2872IHLR.h5ad"
},
{
"@id": "/tabular-files/PKBFI6518FPDF/",
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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