{
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{
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{
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{
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{
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{
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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9087SPJI](/measurement-sets/IGVFDS9087SPJI/) has sequence file(s): [IGVFFI6781YNAW](/sequence-files/IGVFFI6781YNAW/), [IGVFFI9204TUQB](/sequence-files/IGVFFI9204TUQB/), [IGVFFI9008GTBA](/sequence-files/IGVFFI9008GTBA/), [IGVFFI8950TRFA](/sequence-files/IGVFFI8950TRFA/), [IGVFFI6712HKBG](/sequence-files/IGVFFI6712HKBG/), [IGVFFI1665TVSZ](/sequence-files/IGVFFI1665TVSZ/), [IGVFFI1877VTEQ](/sequence-files/IGVFFI1877VTEQ/), [IGVFFI4546VFVF](/sequence-files/IGVFFI4546VFVF/) 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.",
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},
{
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{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS9087SPJI](/measurement-sets/IGVFDS9087SPJI/) 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/IGVFDS9087SPJI/"
}
]
},
"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": "2025-03-19T19:57:32.559025+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
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"accession": "IGVFDO4015EJFT",
"aliases": [
"igvf:corces_donor_BANN0526"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0180JQCL/",
"accession": "IGVFDO0180JQCL",
"aliases": [
"igvf:corces_donor_BANN1344"
],
"sex": "female",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7109IWDJ/",
"accession": "IGVFDO7109IWDJ",
"aliases": [
"igvf:corces_donor_BANN2005"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9028PIDF/",
"accession": "IGVFDO9028PIDF",
"aliases": [
"igvf:corces_donor_BANN1637"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1464XWYC/",
"accession": "IGVFDO1464XWYC",
"aliases": [
"igvf:corces_donor_BANN1809"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0112XZXT/",
"accession": "IGVFDO0112XZXT",
"aliases": [
"igvf:corces_donor_BANN0218"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO5410JIJT/",
"accession": "IGVFDO5410JIJT",
"aliases": [
"igvf:corces_donor_BANN0919"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7678VYKP/",
"accession": "IGVFDO7678VYKP",
"aliases": [
"igvf:corces_donor_BANN1235"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI6781YNAW",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L005_I1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:51.775137+00:00",
"file_format": "fastq",
"file_size": 1415017627,
"href": "/sequence-files/IGVFFI6781YNAW/@@download/IGVFFI6781YNAW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/51104f74-75be-4f32-8da3-b281e99896e6/IGVFFI6781YNAW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9204TUQB/",
"accession": "IGVFFI9204TUQB",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L005_R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:55.806971+00:00",
"file_format": "fastq",
"file_size": 13263798907,
"href": "/sequence-files/IGVFFI9204TUQB/@@download/IGVFFI9204TUQB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/94945ab8-2bef-4d13-ba9c-827d347be0d5/IGVFFI9204TUQB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9008GTBA/",
"accession": "IGVFFI9008GTBA",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L005_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:59.404842+00:00",
"file_format": "fastq",
"file_size": 3167803227,
"href": "/sequence-files/IGVFFI9008GTBA/@@download/IGVFFI9008GTBA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/65011c16-6646-4981-af24-215e67380ac7/IGVFFI9008GTBA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8950TRFA/",
"accession": "IGVFFI8950TRFA",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L004_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:44.032127+00:00",
"file_format": "fastq",
"file_size": 3165035221,
"href": "/sequence-files/IGVFFI8950TRFA/@@download/IGVFFI8950TRFA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/9f4dfc74-9367-4530-9457-87ddb8bd93ef/IGVFFI8950TRFA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6712HKBG/",
"accession": "IGVFFI6712HKBG",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L004_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:47.883567+00:00",
"file_format": "fastq",
"file_size": 12625561527,
"href": "/sequence-files/IGVFFI6712HKBG/@@download/IGVFFI6712HKBG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/bfa4dbd7-1394-4dcd-b8da-b79da4034965/IGVFFI6712HKBG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L004_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1665TVSZ/",
"accession": "IGVFFI1665TVSZ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L004_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:38.037866+00:00",
"file_format": "fastq",
"file_size": 1423223643,
"href": "/sequence-files/IGVFFI1665TVSZ/@@download/IGVFFI1665TVSZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/7ee77d12-b7c9-4beb-a8fd-d911b2eff4b0/IGVFFI1665TVSZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1877VTEQ/",
"accession": "IGVFFI1877VTEQ",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L004_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:04:40.472213+00:00",
"file_format": "fastq",
"file_size": 13205517614,
"href": "/sequence-files/IGVFFI1877VTEQ/@@download/IGVFFI1877VTEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/aa7f6d84-fe38-41f9-8798-198779eb6857/IGVFFI1877VTEQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4546VFVF/",
"accession": "IGVFFI4546VFVF",
"aliases": [
"igvf:corces_sequenceFile_ATAC_RP027_G6_P075_L005_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-21T01:05:03.448023+00:00",
"file_format": "fastq",
"file_size": 12714363830,
"href": "/sequence-files/IGVFFI4546VFVF/@@download/IGVFFI4546VFVF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/21/da4c3682-892c-4dc2-a2fe-b2962f0a7d53/IGVFFI4546VFVF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_RP027_G6_L006_P075_S30_L005_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/IGVFDS9238GAGW/",
"accession": "IGVFDS9238GAGW",
"status": "preview"
}
],
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7247VDCH/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7247VDCH",
"aliases": [
"igvf:corces_multiplexedSample_RP027_G6"
],
"classifications": [
"tissue",
"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_0080832/",
"status": "in progress",
"term_name": "mild cognitive impairment"
},
{
"@id": "/phenotype-terms/DOID_14330/",
"status": "in progress",
"term_name": "Parkinson's disease"
},
{
"@id": "/phenotype-terms/DOID_9246/",
"status": "in progress",
"term_name": "cerebral amyloid angiopathy"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
"certificate_identifier": "IP115-05",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001874/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "putamen",
"term_name": "putamen"
},
{
"@id": "/sample-terms/UBERON_0002038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "substantia nigra",
"term_name": "substantia nigra"
},
{
"@id": "/sample-terms/UBERON_0002740/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "posterior cingulate gyrus",
"term_name": "posterior cingulate gyrus"
},
{
"@id": "/sample-terms/UBERON_0002771/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "middle temporal gyrus",
"term_name": "middle temporal gyrus"
}
],
"status": "preview",
"summary": "multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment; Homo sapiens (male, 85 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-21T01:04:38.037866+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "63bea93d-2c4e-4b2f-8f14-20d1b398b76c"
}