{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5735HWHA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5735HWHA",
"aliases": [
"igvf:corces_measurementSet_X004_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": "missing CCF ID",
"detail": "Tissue [IGVFSM9133DPZS](/tissues/IGVFSM9133DPZS/) 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/IGVFSM9133DPZS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [3722891d-0d84-4ede-8520-3db83e7a6b16](/phenotypic-features/3722891d-0d84-4ede-8520-3db83e7a6b16/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [c0ce9b04-e7ed-4b93-a2eb-beb1600b8a07](/phenotypic-features/c0ce9b04-e7ed-4b93-a2eb-beb1600b8a07/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [45dc979b-555f-4b01-8d0f-a743d2314876](/phenotypic-features/45dc979b-555f-4b01-8d0f-a743d2314876/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [973e8365-f16f-4cd4-b8d8-3810cfb6de08](/phenotypic-features/973e8365-f16f-4cd4-b8d8-3810cfb6de08/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [633b00ad-b194-4a5e-996f-0e6e7d188a4b](/phenotypic-features/633b00ad-b194-4a5e-996f-0e6e7d188a4b/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5735HWHA](/measurement-sets/IGVFDS5735HWHA/) has sequence file(s): [IGVFFI3053KWAU](/sequence-files/IGVFFI3053KWAU/), [IGVFFI0299YQWT](/sequence-files/IGVFFI0299YQWT/), [IGVFFI2223FWVN](/sequence-files/IGVFFI2223FWVN/), [IGVFFI4341IBJU](/sequence-files/IGVFFI4341IBJU/) 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/IGVFDS5735HWHA/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5735HWHA](/measurement-sets/IGVFDS5735HWHA/) 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/IGVFDS5735HWHA/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5735HWHA](/measurement-sets/IGVFDS5735HWHA/) 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/IGVFDS5735HWHA/"
}
]
},
"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": "2025-03-19T19:11:09.966087+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9236YUAT/",
"accession": "IGVFDO9236YUAT",
"aliases": [
"igvf:corces_donor_BANN0227"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3053KWAU/",
"accession": "IGVFFI3053KWAU",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G3_P003_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:05.644962+00:00",
"file_format": "fastq",
"file_size": 6204238185,
"href": "/sequence-files/IGVFFI3053KWAU/@@download/IGVFFI3053KWAU.fastq.gz",
"md5sum": "455a0eb682c726e98eee9db5a59d27cc",
"s3_uri": "s3://igvf-files/2025/03/20/bf8186eb-92c3-4a4d-8d86-e8ac9c7c2c2f/IGVFFI3053KWAU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_02-27_CBL_X004_S03_L003_B1_T1_P003_S17_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0299YQWT/",
"accession": "IGVFFI0299YQWT",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G3_P003_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:04.211757+00:00",
"file_format": "fastq",
"file_size": 3145274248,
"href": "/sequence-files/IGVFFI0299YQWT/@@download/IGVFFI0299YQWT.fastq.gz",
"md5sum": "a97a5e019286d47d758422ee68ab6c2e",
"s3_uri": "s3://igvf-files/2025/03/20/baf4c504-180d-4da5-b86d-d42a6c3fb177/IGVFFI0299YQWT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_02-27_CBL_X004_S03_L003_B1_T1_P003_S17_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2223FWVN/",
"accession": "IGVFFI2223FWVN",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G3_P003_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:02.785396+00:00",
"file_format": "fastq",
"file_size": 5987513802,
"href": "/sequence-files/IGVFFI2223FWVN/@@download/IGVFFI2223FWVN.fastq.gz",
"md5sum": "7bf41d5cd0d0a65dedcdd6f5742b31a7",
"s3_uri": "s3://igvf-files/2025/03/20/c0e11e07-7586-4779-9f75-5c404b15ea42/IGVFFI2223FWVN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_02-27_CBL_X004_S03_L003_B1_T1_P003_S17_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4341IBJU/",
"accession": "IGVFFI4341IBJU",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G3_P003_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:00.964787+00:00",
"file_format": "fastq",
"file_size": 1322289808,
"href": "/sequence-files/IGVFFI4341IBJU/@@download/IGVFFI4341IBJU.fastq.gz",
"md5sum": "f733b36c9e479e04cfb8da58e57ae17f",
"s3_uri": "s3://igvf-files/2025/03/20/6be74cce-0931-4ce5-8ac2-9bf5b68db1a5/IGVFFI4341IBJU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_02-27_CBL_X004_S03_L003_B1_T1_P003_S17_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/IGVFDS5528ZTLH/",
"accession": "IGVFDS5528ZTLH",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM9133DPZS/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9133DPZS",
"aliases": [
"igvf:corces_tissue_BANN0227_CBL_B1"
],
"classifications": [
"tissue"
],
"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_0002129/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "cerebellar cortex",
"term_name": "cerebellar cortex"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 86 years) cerebellar cortex tissue",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-20T00:39:00.964787+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "3f4e7b90-0dab-4431-818a-ced533377375"
}