{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1795MXXR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1795MXXR",
"aliases": [
"igvf:corces_measurementSet_X006_G3_ATAC"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7606UOXI](/human-donors/IGVFDO7606UOXI/) has in progress subobject phenotypic feature [acfae2e4-6c85-46e0-825e-6fde6ec88f0a](/phenotypic-features/acfae2e4-6c85-46e0-825e-6fde6ec88f0a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7606UOXI/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7606UOXI](/human-donors/IGVFDO7606UOXI/) has in progress subobject phenotypic feature [166bde04-bc62-42b7-9b0e-31775e50d7dd](/phenotypic-features/166bde04-bc62-42b7-9b0e-31775e50d7dd/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7606UOXI/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7606UOXI](/human-donors/IGVFDO7606UOXI/) has in progress subobject phenotypic feature [f7b2d235-fce3-4250-8abf-9a226d1f190f](/phenotypic-features/f7b2d235-fce3-4250-8abf-9a226d1f190f/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7606UOXI/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7606UOXI](/human-donors/IGVFDO7606UOXI/) has in progress subobject phenotypic feature [79174baf-cf63-4144-9cc8-050157e38fc4](/phenotypic-features/79174baf-cf63-4144-9cc8-050157e38fc4/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7606UOXI/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7606UOXI](/human-donors/IGVFDO7606UOXI/) has in progress subobject phenotypic feature [bb1e3012-380e-4519-9238-8839d272804c](/phenotypic-features/bb1e3012-380e-4519-9238-8839d272804c/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7606UOXI/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM9093ETCZ](/tissues/IGVFSM9093ETCZ/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM9093ETCZ/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM9093ETCZ](/tissues/IGVFSM9093ETCZ/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM9093ETCZ/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM9093ETCZ](/tissues/IGVFSM9093ETCZ/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM9093ETCZ/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM9093ETCZ](/tissues/IGVFSM9093ETCZ/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM9093ETCZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1795MXXR](/measurement-sets/IGVFDS1795MXXR/) has sequence file(s): [IGVFFI1410WPOR](/sequence-files/IGVFFI1410WPOR/), [IGVFFI0435GZVE](/sequence-files/IGVFFI0435GZVE/), [IGVFFI7589OCIL](/sequence-files/IGVFFI7589OCIL/), [IGVFFI4375DYIS](/sequence-files/IGVFFI4375DYIS/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS1795MXXR/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1795MXXR](/measurement-sets/IGVFDS1795MXXR/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS1795MXXR/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS1795MXXR](/measurement-sets/IGVFDS1795MXXR/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS1795MXXR/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2025-03-19T19:11:16.733935+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7606UOXI/",
"accession": "IGVFDO7606UOXI",
"aliases": [
"igvf:corces_donor_BANN1570"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1410WPOR/",
"accession": "IGVFFI1410WPOR",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X006_G3_P003_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:33.452087+00:00",
"file_format": "fastq",
"file_size": 5773653974,
"href": "/sequence-files/IGVFFI1410WPOR/@@download/IGVFFI1410WPOR.fastq.gz",
"md5sum": "453b91d560c9e9cf146644c51ab8ca78",
"s3_uri": "s3://igvf-files/2025/03/20/dfab5535-b959-414f-bf46-075f73ec3a37/IGVFFI1410WPOR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_15-70_SN_X006_S03_L003_B1_T1_P003_S29_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0435GZVE/",
"accession": "IGVFFI0435GZVE",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X006_G3_P003_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:29.177534+00:00",
"file_format": "fastq",
"file_size": 1289177366,
"href": "/sequence-files/IGVFFI0435GZVE/@@download/IGVFFI0435GZVE.fastq.gz",
"md5sum": "366c129b672476b1110b949e25b997bc",
"s3_uri": "s3://igvf-files/2025/03/20/b520e5b5-bb50-4397-b22e-a06601edd254/IGVFFI0435GZVE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_15-70_SN_X006_S03_L003_B1_T1_P003_S29_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7589OCIL/",
"accession": "IGVFFI7589OCIL",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X006_G3_P003_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:30.719495+00:00",
"file_format": "fastq",
"file_size": 5623922726,
"href": "/sequence-files/IGVFFI7589OCIL/@@download/IGVFFI7589OCIL.fastq.gz",
"md5sum": "0f21c9b9b844796a6e2b0f2537991c7a",
"s3_uri": "s3://igvf-files/2025/03/20/7e7ce401-4758-4fd7-9188-2579d08b6226/IGVFFI7589OCIL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_15-70_SN_X006_S03_L003_B1_T1_P003_S29_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4375DYIS/",
"accession": "IGVFFI4375DYIS",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X006_G3_P003_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:32.161139+00:00",
"file_format": "fastq",
"file_size": 3084094450,
"href": "/sequence-files/IGVFFI4375DYIS/@@download/IGVFFI4375DYIS.fastq.gz",
"md5sum": "fe221d577044f0334671911c54a01f55",
"s3_uri": "s3://igvf-files/2025/03/20/44277c47-084c-4711-96a0-a0b69aefd0a2/IGVFFI4375DYIS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_15-70_SN_X006_S03_L003_B1_T1_P003_S29_L004_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS4064ZVTG/",
"accession": "IGVFDS4064ZVTG",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM9093ETCZ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9093ETCZ",
"aliases": [
"igvf:corces_tissue_BANN1570_SN_B1-singleplex"
],
"classifications": [
"tissue"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_14330/",
"status": "in progress",
"term_name": "Parkinson's disease"
},
{
"@id": "/phenotype-terms/DOID_9246/",
"status": "in progress",
"term_name": "cerebral amyloid angiopathy"
},
{
"@id": "/phenotype-terms/DOID_0080832/",
"status": "in progress",
"term_name": "mild cognitive impairment"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
"certificate_identifier": "IP115-05",
"controlled_access": false,
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "substantia nigra",
"term_name": "substantia nigra"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 73 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-20T00:39:29.177534+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "a9f895e7-b01b-49c1-80bd-874f836e5b08"
}