{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9661AXWU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9661AXWU",
"aliases": [
"igvf:corces_measurementSet_X004_G1_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 [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [9987347f-6f4d-4d82-88c9-0c4c4317a278](/phenotypic-features/9987347f-6f4d-4d82-88c9-0c4c4317a278/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [67b114cf-7764-4391-8fd6-ac46ac9bc7a4](/phenotypic-features/67b114cf-7764-4391-8fd6-ac46ac9bc7a4/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [0fd0acf9-94ba-4952-9984-7d1e562d121a](/phenotypic-features/0fd0acf9-94ba-4952-9984-7d1e562d121a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [2215de1b-9e0d-47cd-a69d-7f4faf6b0976](/phenotypic-features/2215de1b-9e0d-47cd-a69d-7f4faf6b0976/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [be5d84fc-8dc2-496a-8ecf-440a2092a07c](/phenotypic-features/be5d84fc-8dc2-496a-8ecf-440a2092a07c/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7227BIXW](/human-donors/IGVFDO7227BIXW/) has in progress subobject phenotypic feature [fb128197-8fc4-4ae2-90ee-244353c5c115](/phenotypic-features/fb128197-8fc4-4ae2-90ee-244353c5c115/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7227BIXW/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM7491SDBL](/tissues/IGVFSM7491SDBL/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM7491SDBL/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM7491SDBL](/tissues/IGVFSM7491SDBL/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM7491SDBL/"
},
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM7491SDBL](/tissues/IGVFSM7491SDBL/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM7491SDBL/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM7491SDBL](/tissues/IGVFSM7491SDBL/) 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/IGVFSM7491SDBL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9661AXWU](/measurement-sets/IGVFDS9661AXWU/) has sequence file(s): [IGVFFI3967QNUQ](/sequence-files/IGVFFI3967QNUQ/), [IGVFFI9676XGIW](/sequence-files/IGVFFI9676XGIW/), [IGVFFI4331NBIB](/sequence-files/IGVFFI4331NBIB/), [IGVFFI8031MMGX](/sequence-files/IGVFFI8031MMGX/) 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/IGVFDS9661AXWU/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9661AXWU](/measurement-sets/IGVFDS9661AXWU/) 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/IGVFDS9661AXWU/"
}
]
},
"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": "2025-03-19T19:11:07.329648+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7227BIXW/",
"accession": "IGVFDO7227BIXW",
"aliases": [
"igvf:corces_donor_BANN1614"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI3967QNUQ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G1_P003_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:37.297121+00:00",
"file_format": "fastq",
"file_size": 3429776134,
"href": "/sequence-files/IGVFFI3967QNUQ/@@download/IGVFFI3967QNUQ.fastq.gz",
"md5sum": "d9651143945fc3d85fbcd9aa1633e420",
"s3_uri": "s3://igvf-files/2025/03/20/21f6d042-0580-4262-810c-a25827e29ed2/IGVFFI3967QNUQ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_16-14_CING_X004_S01_L001_B1_T1_P003_S15_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9676XGIW/",
"accession": "IGVFFI9676XGIW",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G1_P003_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:36.130176+00:00",
"file_format": "fastq",
"file_size": 6205105522,
"href": "/sequence-files/IGVFFI9676XGIW/@@download/IGVFFI9676XGIW.fastq.gz",
"md5sum": "81d749ace65c7d466a6fd3b18c7fc6f5",
"s3_uri": "s3://igvf-files/2025/03/20/e8fe6dd0-b738-4af9-a91c-99e0afc88b75/IGVFFI9676XGIW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_16-14_CING_X004_S01_L001_B1_T1_P003_S15_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4331NBIB/",
"accession": "IGVFFI4331NBIB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G1_P003_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:38.573313+00:00",
"file_format": "fastq",
"file_size": 6424197129,
"href": "/sequence-files/IGVFFI4331NBIB/@@download/IGVFFI4331NBIB.fastq.gz",
"md5sum": "fb891be038951e12b422198017c1fe7d",
"s3_uri": "s3://igvf-files/2025/03/20/2f255097-84d0-4db9-a524-e7c530dc2912/IGVFFI4331NBIB.fastq.gz",
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"status": "released",
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},
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"submitted_file_name": "Multiome_ATAC_PD_16-14_CING_X004_S01_L001_B1_T1_P003_S15_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8031MMGX/",
"accession": "IGVFFI8031MMGX",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G1_P003_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:34.894559+00:00",
"file_format": "fastq",
"file_size": 1435750711,
"href": "/sequence-files/IGVFFI8031MMGX/@@download/IGVFFI8031MMGX.fastq.gz",
"md5sum": "feffbc010d07b7841224dcb7f5671eff",
"s3_uri": "s3://igvf-files/2025/03/20/ae3a09b9-c713-432c-a18d-8911a82a3709/IGVFFI8031MMGX.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_16-14_CING_X004_S01_L001_B1_T1_P003_S15_L004_I1_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/IGVFDS8311GMRY/",
"accession": "IGVFDS8311GMRY",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM7491SDBL/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7491SDBL",
"aliases": [
"igvf:corces_tissue_BANN1614_CING_B1"
],
"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_0002740/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "posterior cingulate gyrus",
"term_name": "posterior cingulate gyrus"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 80 years) posterior cingulate gyrus 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": "2025-03-20T00:39:34.894559+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "8ed9e87e-748f-4189-a070-ec34bb8ef9eb"
}