{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5462PWXH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5462PWXH",
"aliases": [
"igvf:corces_measurementSet_X004_G2_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 [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [bd6f3062-edeb-4a6b-8894-efd13d5f6d1a](/phenotypic-features/bd6f3062-edeb-4a6b-8894-efd13d5f6d1a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [c474daa4-7513-404e-94d5-875f37a7c343](/phenotypic-features/c474daa4-7513-404e-94d5-875f37a7c343/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [c2483f59-ee42-47e9-855b-4121902f7e6e](/phenotypic-features/c2483f59-ee42-47e9-855b-4121902f7e6e/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [088a9bc3-3c47-43fb-a433-e98b083f05b0](/phenotypic-features/088a9bc3-3c47-43fb-a433-e98b083f05b0/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [688afed8-9edc-4232-aad4-2342093c1c09](/phenotypic-features/688afed8-9edc-4232-aad4-2342093c1c09/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4825ZGIS](/human-donors/IGVFDO4825ZGIS/) has in progress subobject phenotypic feature [a0d65347-a21f-439b-bd5d-7232f0b1ee5e](/phenotypic-features/a0d65347-a21f-439b-bd5d-7232f0b1ee5e/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4825ZGIS/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM6036OELU](/tissues/IGVFSM6036OELU/) 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/IGVFSM6036OELU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5462PWXH](/measurement-sets/IGVFDS5462PWXH/) has sequence file(s): [IGVFFI5463IJII](/sequence-files/IGVFFI5463IJII/), [IGVFFI2211YBKB](/sequence-files/IGVFFI2211YBKB/), [IGVFFI9588QOWM](/sequence-files/IGVFFI9588QOWM/), [IGVFFI5511LYXX](/sequence-files/IGVFFI5511LYXX/) 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/IGVFDS5462PWXH/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5462PWXH](/measurement-sets/IGVFDS5462PWXH/) 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/IGVFDS5462PWXH/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5462PWXH](/measurement-sets/IGVFDS5462PWXH/) 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/IGVFDS5462PWXH/"
}
]
},
"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": "2025-03-19T19:11:08.785965+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4825ZGIS/",
"accession": "IGVFDO4825ZGIS",
"aliases": [
"igvf:corces_donor_BANN2057"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5463IJII/",
"accession": "IGVFFI5463IJII",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G2_P003_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:12.399628+00:00",
"file_format": "fastq",
"file_size": 1572667362,
"href": "/sequence-files/IGVFFI5463IJII/@@download/IGVFFI5463IJII.fastq.gz",
"md5sum": "c617091f1e4e5605feb9097a3a7a7223",
"s3_uri": "s3://igvf-files/2025/03/20/e375f11f-ac15-41c6-a641-ab3ae5406fa2/IGVFFI5463IJII.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_20-57_CING_X004_S02_L002_B1_T1_P003_S16_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2211YBKB/",
"accession": "IGVFFI2211YBKB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G2_P003_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:15.623108+00:00",
"file_format": "fastq",
"file_size": 3714556144,
"href": "/sequence-files/IGVFFI2211YBKB/@@download/IGVFFI2211YBKB.fastq.gz",
"md5sum": "68e5f6bb0a2ea5da4dc996e4827344db",
"s3_uri": "s3://igvf-files/2025/03/20/eaccc4ca-6cc0-4b85-888c-30f7cfa01aec/IGVFFI2211YBKB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_20-57_CING_X004_S02_L002_B1_T1_P003_S16_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9588QOWM/",
"accession": "IGVFFI9588QOWM",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G2_P003_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:14.136361+00:00",
"file_format": "fastq",
"file_size": 6741038818,
"href": "/sequence-files/IGVFFI9588QOWM/@@download/IGVFFI9588QOWM.fastq.gz",
"md5sum": "66c9931d913e1d67d1650b451c2af174",
"s3_uri": "s3://igvf-files/2025/03/20/2264e647-154d-4044-83a3-7ad6cfe9f552/IGVFFI9588QOWM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_20-57_CING_X004_S02_L002_B1_T1_P003_S16_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5511LYXX/",
"accession": "IGVFFI5511LYXX",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G2_P003_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:17.284899+00:00",
"file_format": "fastq",
"file_size": 6976530869,
"href": "/sequence-files/IGVFFI5511LYXX/@@download/IGVFFI5511LYXX.fastq.gz",
"md5sum": "c3bf5b0d28dc9cb4c846c84d68057f54",
"s3_uri": "s3://igvf-files/2025/03/20/25db1119-54e3-488a-8e3d-c066ac2634d1/IGVFFI5511LYXX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_20-57_CING_X004_S02_L002_B1_T1_P003_S16_L004_R3_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/IGVFDS5771YKFQ/",
"accession": "IGVFDS5771YKFQ",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM6036OELU/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6036OELU",
"aliases": [
"igvf:corces_tissue_BANN2057_CING_B1-singleplex"
],
"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_0002740/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "posterior cingulate gyrus",
"term_name": "posterior cingulate gyrus"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 81 years) posterior cingulate gyrus tissue",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-20T00:39:12.399628+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "dc8a15f9-32ee-4b10-a3da-b8a741fd0ea2"
}