{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5771YKFQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5771YKFQ",
"aliases": [
"igvf:corces_measurementSet_X004_G2_RNA"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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 [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 [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": "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 [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": "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 [IGVFDS5771YKFQ](/measurement-sets/IGVFDS5771YKFQ/) has sequence file(s): [IGVFFI3653FAGQ](/sequence-files/IGVFFI3653FAGQ/), [IGVFFI3968SSFJ](/sequence-files/IGVFFI3968SSFJ/) 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/IGVFDS5771YKFQ/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5771YKFQ](/measurement-sets/IGVFDS5771YKFQ/) 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/IGVFDS5771YKFQ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5771YKFQ](/measurement-sets/IGVFDS5771YKFQ/) 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/IGVFDS5771YKFQ/"
}
]
},
"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": "2025-03-19T19:11:21.365141+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/IGVFFI3653FAGQ/",
"accession": "IGVFFI3653FAGQ",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G2_P004_L001_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:50.217281+00:00",
"file_format": "fastq",
"file_size": 12489860888,
"href": "/sequence-files/IGVFFI3653FAGQ/@@download/IGVFFI3653FAGQ.fastq.gz",
"md5sum": "7cd8290ee46b2ecee78bf3435a6e47cf",
"s3_uri": "s3://igvf-files/2025/03/20/288dd61f-aed0-4215-a7d0-47984517c0ee/IGVFFI3653FAGQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_20-57_CING_X004_S02_L002_B1_T1_P004_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3968SSFJ/",
"accession": "IGVFFI3968SSFJ",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G2_P004_L001_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:48.977863+00:00",
"file_format": "fastq",
"file_size": 14864268528,
"href": "/sequence-files/IGVFFI3968SSFJ/@@download/IGVFFI3968SSFJ.fastq.gz",
"md5sum": "6ed3e0e3be2b3cef7605f2427636e691",
"s3_uri": "s3://igvf-files/2025/03/20/aaf4a1c4-24ac-4867-88a4-c27d3f59722d/IGVFFI3968SSFJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_20-57_CING_X004_S02_L002_B1_T1_P004_S2_L001_R1_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/IGVFFI8751YQRY/"
],
"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/IGVFDS5462PWXH/",
"accession": "IGVFDS5462PWXH",
"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": "2025-03-20T00:40:48.977863+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "c7a779b0-b79a-4f94-85ee-1a494f95fd41"
}