{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
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],
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},
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{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7477NVAD](/measurement-sets/IGVFDS7477NVAD/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS7477NVAD/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM9059AKNM](/tissues/IGVFSM9059AKNM/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/tissues/IGVFSM9059AKNM/"
}
],
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{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7477NVAD](/measurement-sets/IGVFDS7477NVAD/) 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/IGVFDS7477NVAD/"
}
]
},
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"component": "mapping",
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"creation_timestamp": "2024-07-23T00:43:21.507281+00:00",
"donors": [
{
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"accession": "IGVFDO5114NYSN",
"aliases": [
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],
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"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI6302JZLY",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_rna_i1"
],
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"creation_timestamp": "2024-07-23T01:27:58.726782+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI6302JZLY/@@download/IGVFFI6302JZLY.fastq.gz",
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"term_name": "Illumina NovaSeq 6000"
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9653ESJV/",
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"ansuman-satpathy:igvf_mouse_bridge_102_rna_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:28:41.491127+00:00",
"file_format": "fastq",
"file_size": 4084753418,
"href": "/sequence-files/IGVFFI9653ESJV/@@download/IGVFFI9653ESJV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/c0724d10-c8fc-40f8-a332-20fe64e83412/IGVFFI9653ESJV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4454GOYF/",
"accession": "IGVFFI4454GOYF",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_rna_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:32:41.264101+00:00",
"file_format": "fastq",
"file_size": 33478585532,
"href": "/sequence-files/IGVFFI4454GOYF/@@download/IGVFFI4454GOYF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/a52ab4d8-73da-46e4-9750-55bf977aa153/IGVFFI4454GOYF.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
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"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/GEX/RNA_102_S2_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6368GQDK/",
"accession": "IGVFFI6368GQDK",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_102_rna_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:29:48.980827+00:00",
"file_format": "fastq",
"file_size": 13974248826,
"href": "/sequence-files/IGVFFI6368GQDK/@@download/IGVFFI6368GQDK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/600e7be7-642d-448d-aa84-af8937538ab0/IGVFFI6368GQDK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/GEX/RNA_102_S2_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9962SKVC/",
"accession": "IGVFFI9962SKVC",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_102_rna"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:45:35.454986+00:00",
"file_format": "yaml",
"file_size": 1400,
"href": "/configuration-files/IGVFFI9962SKVC/@@download/IGVFFI9962SKVC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/cd220d2a-9b15-43d3-a5ff-1dd1decceb23/IGVFFI9962SKVC.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_mouse_bridge_102_rna_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5230RAFR/",
"/analysis-sets/IGVFDS5717EBEY/",
"/analysis-sets/IGVFDS6347FMLT/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI8751YQRY/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-ewov1nm2kgr2/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0412WLCW/",
"accession": "IGVFDS0412WLCW",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:37.571946+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9059AKNM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9059AKNM",
"aliases": [
"ansuman-satpathy:102_CASTJ_10F_left_cortex"
],
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
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}
],
"status": "released",
"summary": "Mus musculus CAST/EiJ (female, 10 weeks) left cerebral cortex tissue",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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"title": "Christopher Mcginnis"
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"submitted_files_timestamp": "2024-07-23T01:27:58.726782+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "0d748429-2297-42d9-9468-b6b96844f85b"
}