{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7098UNEX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7098UNEX",
"aliases": [
"igvf:corces_measurementSet_X004_G4_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": "missing CCF ID",
"detail": "Tissue [IGVFSM8408MAMT](/tissues/IGVFSM8408MAMT/) 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/IGVFSM8408MAMT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [95491ef2-b590-4c18-b81d-6c903ed626a4](/phenotypic-features/95491ef2-b590-4c18-b81d-6c903ed626a4/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [29048a47-9d7d-4ad1-bc30-b97bd2c5e4d7](/phenotypic-features/29048a47-9d7d-4ad1-bc30-b97bd2c5e4d7/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [c9ecdf8e-7c0f-473e-a8be-77797167794c](/phenotypic-features/c9ecdf8e-7c0f-473e-a8be-77797167794c/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [721cdbe5-854d-428a-85b6-a444e6fe94c3](/phenotypic-features/721cdbe5-854d-428a-85b6-a444e6fe94c3/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [6a8d3945-6600-4f71-bc2d-3aa7cd079713](/phenotypic-features/6a8d3945-6600-4f71-bc2d-3aa7cd079713/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [793031fc-a40d-4951-9abf-09dcf84149cb](/phenotypic-features/793031fc-a40d-4951-9abf-09dcf84149cb/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO7387JZDV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7098UNEX](/measurement-sets/IGVFDS7098UNEX/) has sequence file(s): [IGVFFI4715UXES](/sequence-files/IGVFFI4715UXES/), [IGVFFI9759EMHS](/sequence-files/IGVFFI9759EMHS/) 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/IGVFDS7098UNEX/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7098UNEX](/measurement-sets/IGVFDS7098UNEX/) 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/IGVFDS7098UNEX/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS7098UNEX](/measurement-sets/IGVFDS7098UNEX/) 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/IGVFDS7098UNEX/"
}
]
},
"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": "2025-03-19T19:11:24.085940+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7387JZDV/",
"accession": "IGVFDO7387JZDV",
"aliases": [
"igvf:corces_donor_BANN1349"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4715UXES/",
"accession": "IGVFFI4715UXES",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G4_P004_L001_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:46.804273+00:00",
"file_format": "fastq",
"file_size": 11722738271,
"href": "/sequence-files/IGVFFI4715UXES/@@download/IGVFFI4715UXES.fastq.gz",
"md5sum": "791be623a87dbe80bb02e946a0756d13",
"s3_uri": "s3://igvf-files/2025/03/20/4f53b179-e1dd-4da5-8493-a2cd627086d8/IGVFFI4715UXES.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_13-49_CBL_X004_S04_L004_B1_T1_P004_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9759EMHS/",
"accession": "IGVFFI9759EMHS",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G4_P004_L001_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:47.853766+00:00",
"file_format": "fastq",
"file_size": 9697227141,
"href": "/sequence-files/IGVFFI9759EMHS/@@download/IGVFFI9759EMHS.fastq.gz",
"md5sum": "7047b01bfdebfd335d2c56f5353e30d1",
"s3_uri": "s3://igvf-files/2025/03/20/4a8733a0-75bf-49dc-b4f0-a3b7bf53baad/IGVFFI9759EMHS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_13-49_CBL_X004_S04_L004_B1_T1_P004_S4_L001_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/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/IGVFDS5151PSMX/",
"accession": "IGVFDS5151PSMX",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM8408MAMT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8408MAMT",
"aliases": [
"igvf:corces_tissue_BANN1349_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 (female, 75 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": "2025-03-20T00:40:46.804273+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "a7554911-c7a9-4612-8180-5b71750e7514"
}