{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0602EDSF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0602EDSF",
"aliases": [
"ansuman-satpathy:snRNA-seq_mouse_bridge_775"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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": "Measurement set [IGVFDS0602EDSF](/measurement-sets/IGVFDS0602EDSF/) 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/IGVFDS0602EDSF/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM5654SLCG](/tissues/IGVFSM5654SLCG/) 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/IGVFSM5654SLCG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0602EDSF](/measurement-sets/IGVFDS0602EDSF/) 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/IGVFDS0602EDSF/"
}
]
},
"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": [],
"creation_timestamp": "2025-01-15T23:45:04.405156+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO8962VZTT/",
"accession": "IGVFDO8962VZTT",
"aliases": [
"ali-mortazavi:775_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/IGVFFI9535QPOR/",
"accession": "IGVFFI9535QPOR",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_775_rna_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-16T00:00:07.449058+00:00",
"file_format": "fastq",
"file_size": 2714772419,
"href": "/sequence-files/IGVFFI9535QPOR/@@download/IGVFFI9535QPOR.fastq.gz",
"md5sum": "9ddf2d545405a46642f694131f1c55a8",
"s3_uri": "s3://igvf-files/2025/01/16/ce68ebca-c2c6-4f30-ad69-ead05883de14/IGVFFI9535QPOR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_RNA_775_CASTJ_10M_21_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5002QPIH/",
"accession": "IGVFFI5002QPIH",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_775_rna_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-16T00:00:26.785276+00:00",
"file_format": "fastq",
"file_size": 11058050904,
"href": "/sequence-files/IGVFFI5002QPIH/@@download/IGVFFI5002QPIH.fastq.gz",
"md5sum": "aaca730d3b2b2f24c07ee8d03164689b",
"s3_uri": "s3://igvf-files/2025/01/16/3f2349b9-cb14-4c22-afe0-42f8c710930c/IGVFFI5002QPIH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_RNA_775_CASTJ_10M_21_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1397YDQK/",
"accession": "IGVFFI1397YDQK",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_775_rna_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:59:47.880579+00:00",
"file_format": "fastq",
"file_size": 2686684284,
"href": "/sequence-files/IGVFFI1397YDQK/@@download/IGVFFI1397YDQK.fastq.gz",
"md5sum": "183c7ad7d24996d696ec734538207ad7",
"s3_uri": "s3://igvf-files/2025/01/15/2cefcebe-3c16-4ce7-b973-e9070eef47d9/IGVFFI1397YDQK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_RNA_775_CASTJ_10M_21_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1847WUHV/",
"accession": "IGVFFI1847WUHV",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_775_rna_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-16T00:01:26.986694+00:00",
"file_format": "fastq",
"file_size": 24395336166,
"href": "/sequence-files/IGVFFI1847WUHV/@@download/IGVFFI1847WUHV.fastq.gz",
"md5sum": "f864ef33c205b07123f9f2fdfcd574ff",
"s3_uri": "s3://igvf-files/2025/01/16/9c833695-c9d7-4c0c-886c-648c004786b9/IGVFFI1847WUHV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/bridge_new/IGVF_RNA_775_CASTJ_10M_21_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5546XGLH/",
"accession": "IGVFFI5546XGLH",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_775_rna"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T00:56:53.169034+00:00",
"file_format": "yaml",
"file_size": 1401,
"href": "/configuration-files/IGVFFI5546XGLH/@@download/IGVFFI5546XGLH.yaml.gz",
"md5sum": "b26cb2ff73c8c15c414a0121dc20997f",
"s3_uri": "s3://igvf-files/2025/02/26/c64847f2-641a-40ed-8dc2-b649903fc794/IGVFFI5546XGLH.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_mouse_bridge_775_rna_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8343PSUS/",
"/analysis-sets/IGVFDS8327CWJR/"
],
"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/IGVFDS2289SZHO/",
"accession": "IGVFDS2289SZHO",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:19:09.529276+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5654SLCG/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5654SLCG",
"aliases": [
"ansuman-satpathy:775_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": "2025-01-15T23:59:47.880579+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "2706c624-7ecd-4fcc-8175-8a550cd52d56"
}