{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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],
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"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
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{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9624INNM](/measurement-sets/IGVFDS9624INNM/) 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/IGVFDS9624INNM/"
},
{
"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 [IGVFSM2776DDRF](/tissues/IGVFSM2776DDRF/) 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/IGVFSM2776DDRF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9624INNM](/measurement-sets/IGVFDS9624INNM/) 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/IGVFDS9624INNM/"
}
]
},
"award": {
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"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": [],
"creation_timestamp": "2024-07-23T00:43:20.676576+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO2440QVYB/",
"accession": "IGVFDO2440QVYB",
"aliases": [
"ansuman-satpathy:101_CASTJ_10M"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1831EEUZ/",
"accession": "IGVFFI1831EEUZ",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_rna_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:22:22.684153+00:00",
"file_format": "fastq",
"file_size": 10824069936,
"href": "/sequence-files/IGVFFI1831EEUZ/@@download/IGVFFI1831EEUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/5615695f-be11-461b-aeda-56c3d0bf1f4d/IGVFFI1831EEUZ.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_101_S1_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7969ZWKM/",
"accession": "IGVFFI7969ZWKM",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_rna_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:24:35.847200+00:00",
"file_format": "fastq",
"file_size": 25592475844,
"href": "/sequence-files/IGVFFI7969ZWKM/@@download/IGVFFI7969ZWKM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/7b86d38a-b9f6-4c52-84fa-e51d2764cd94/IGVFFI7969ZWKM.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_101_S1_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2437QQSO/",
"accession": "IGVFFI2437QQSO",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_rna_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T00:47:48.748602+00:00",
"file_format": "fastq",
"file_size": 2913895346,
"href": "/sequence-files/IGVFFI2437QQSO/@@download/IGVFFI2437QQSO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/47096748-bcb9-44e6-a758-5100755ae450/IGVFFI2437QQSO.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_101_S1_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6962GHCW/",
"accession": "IGVFFI6962GHCW",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_101_rna_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:21:26.103336+00:00",
"file_format": "fastq",
"file_size": 3146720197,
"href": "/sequence-files/IGVFFI6962GHCW/@@download/IGVFFI6962GHCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/23/e7e4f1e9-1d07-4c5c-87b9-425e0c5f5498/IGVFFI6962GHCW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF_Bridge_McGinnis/GEX/RNA_101_S1_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7597MNBE/",
"accession": "IGVFFI7597MNBE",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_101_rna"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:45:28.482503+00:00",
"file_format": "yaml",
"file_size": 1401,
"href": "/configuration-files/IGVFFI7597MNBE/@@download/IGVFFI7597MNBE.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/37fb39de-4bd6-41bb-9d44-cae2150d7863/IGVFFI7597MNBE.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_mouse_bridge_101_rna_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5230RAFR/",
"/analysis-sets/IGVFDS5717EBEY/",
"/analysis-sets/IGVFDS7529ZWPQ/"
],
"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/IGVFDS6819TPGN/",
"accession": "IGVFDS6819TPGN",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:32.454725+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM2776DDRF/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2776DDRF",
"aliases": [
"ansuman-satpathy:101_CASTJ_10M_left_cortex"
],
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus CAST/EiJ (male, 10 weeks) left cerebral cortex tissue",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-23T00:47:48.748602+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "85970f77-048e-4409-8836-d9a453a3a32c"
}