{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5151PSMX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5151PSMX",
"aliases": [
"igvf:corces_measurementSet_X004_G4_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 [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 [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 [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/"
},
{
"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 [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 [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 [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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5151PSMX](/measurement-sets/IGVFDS5151PSMX/) has sequence file(s): [IGVFFI0130WJUI](/sequence-files/IGVFFI0130WJUI/), [IGVFFI4268HNOA](/sequence-files/IGVFFI4268HNOA/), [IGVFFI3625EMNB](/sequence-files/IGVFFI3625EMNB/), [IGVFFI5589XMMO](/sequence-files/IGVFFI5589XMMO/) 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/IGVFDS5151PSMX/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5151PSMX](/measurement-sets/IGVFDS5151PSMX/) 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/IGVFDS5151PSMX/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5151PSMX](/measurement-sets/IGVFDS5151PSMX/) 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/IGVFDS5151PSMX/"
}
]
},
"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": "2025-03-19T19:11:11.320403+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/IGVFFI0130WJUI/",
"accession": "IGVFFI0130WJUI",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G4_P003_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:06.797432+00:00",
"file_format": "fastq",
"file_size": 1531494074,
"href": "/sequence-files/IGVFFI0130WJUI/@@download/IGVFFI0130WJUI.fastq.gz",
"md5sum": "48381b86266a3be19ef6e2c1fa0c1733",
"s3_uri": "s3://igvf-files/2025/03/20/79dc510e-27bb-4abd-b5f6-dc73f87ae8b3/IGVFFI0130WJUI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_13-49_CBL_X004_S04_L004_B1_T1_P003_S18_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4268HNOA/",
"accession": "IGVFFI4268HNOA",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G4_P003_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:11.082741+00:00",
"file_format": "fastq",
"file_size": 6667082725,
"href": "/sequence-files/IGVFFI4268HNOA/@@download/IGVFFI4268HNOA.fastq.gz",
"md5sum": "4286035af4f9fc7f328b3d9d7ce5ef70",
"s3_uri": "s3://igvf-files/2025/03/20/8bd3cc20-554d-4dcf-8444-bbebe8a68efa/IGVFFI4268HNOA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_13-49_CBL_X004_S04_L004_B1_T1_P003_S18_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3625EMNB/",
"accession": "IGVFFI3625EMNB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G4_P003_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:08.094531+00:00",
"file_format": "fastq",
"file_size": 6416840853,
"href": "/sequence-files/IGVFFI3625EMNB/@@download/IGVFFI3625EMNB.fastq.gz",
"md5sum": "f4951f83373299827fc9623436f5e0b1",
"s3_uri": "s3://igvf-files/2025/03/20/0c7423ae-afbf-434b-8b61-0d1fd73879f7/IGVFFI3625EMNB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_13-49_CBL_X004_S04_L004_B1_T1_P003_S18_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5589XMMO/",
"accession": "IGVFFI5589XMMO",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X004_G4_P003_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:39:09.431227+00:00",
"file_format": "fastq",
"file_size": 3551687326,
"href": "/sequence-files/IGVFFI5589XMMO/@@download/IGVFFI5589XMMO.fastq.gz",
"md5sum": "6696ab95b940afd11a2484954048e8d1",
"s3_uri": "s3://igvf-files/2025/03/20/9a40e260-1607-4adf-a1a8-022690241aec/IGVFFI5589XMMO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_nd_13-49_CBL_X004_S04_L004_B1_T1_P003_S18_L004_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/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/IGVFDS7098UNEX/",
"accession": "IGVFDS7098UNEX",
"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": "2025-03-20T00:39:06.797432+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "5ecebebe-8a5e-4f2f-bbce-8b2e60d55ebe"
}