{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4021UKPE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4021UKPE",
"aliases": [
"ansuman-satpathy:snATAC-seq_mouse_bridge_769"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Tissue [IGVFSM9438GDDL](/tissues/IGVFSM9438GDDL/) 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/IGVFSM9438GDDL/"
},
{
"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 [IGVFDS4021UKPE](/measurement-sets/IGVFDS4021UKPE/) 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/IGVFDS4021UKPE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4021UKPE](/measurement-sets/IGVFDS4021UKPE/) 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/IGVFDS4021UKPE/"
}
]
},
"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": "2025-01-15T23:45:03.918846+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO1345QIHE/",
"accession": "IGVFDO1345QIHE",
"aliases": [
"ali-mortazavi:769_B6J_10M"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4843GIXM/",
"accession": "IGVFFI4843GIXM",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_769_atac_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:45:21.650946+00:00",
"file_format": "fastq",
"file_size": 4085015571,
"href": "/sequence-files/IGVFFI4843GIXM/@@download/IGVFFI4843GIXM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/c1c5d573-2acb-4e82-8bc5-8d2baa045e1e/IGVFFI4843GIXM.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_ATAC_769_B6J_10M_21_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0360VNTD/",
"accession": "IGVFFI0360VNTD",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_769_atac_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:45:50.120955+00:00",
"file_format": "fastq",
"file_size": 20057558073,
"href": "/sequence-files/IGVFFI0360VNTD/@@download/IGVFFI0360VNTD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/872b9288-7bc7-4c55-a8b7-9647ebe899f4/IGVFFI0360VNTD.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_ATAC_769_B6J_10M_21_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2788FRNF/",
"accession": "IGVFFI2788FRNF",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_769_atac_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:47:27.474895+00:00",
"file_format": "fastq",
"file_size": 11008773041,
"href": "/sequence-files/IGVFFI2788FRNF/@@download/IGVFFI2788FRNF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/f4ce5ced-0978-409f-83f0-af055833d1a5/IGVFFI2788FRNF.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_ATAC_769_B6J_10M_21_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5699KRFZ/",
"accession": "IGVFFI5699KRFZ",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_769_atac_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-15T23:48:19.960932+00:00",
"file_format": "fastq",
"file_size": 19832533865,
"href": "/sequence-files/IGVFFI5699KRFZ/@@download/IGVFFI5699KRFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/15/ad243513-fd9e-4e72-842c-89bf7871d650/IGVFFI5699KRFZ.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_ATAC_769_B6J_10M_21_S2_L002_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6323NIKH/",
"accession": "IGVFFI6323NIKH",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_769_atac"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T00:56:40.295165+00:00",
"file_format": "yaml",
"file_size": 1379,
"href": "/configuration-files/IGVFFI6323NIKH/@@download/IGVFFI6323NIKH.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/2f13c6d9-037e-42d5-97fa-30ac94ea3ebe/IGVFFI6323NIKH.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_mouse_bridge_769_atac_atac_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4768JVVU/",
"/analysis-sets/IGVFDS1101THUC/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"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/IGVFDS1449TKWZ/",
"accession": "IGVFDS1449TKWZ",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:19:05.561503+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9438GDDL/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9438GDDL",
"aliases": [
"ansuman-satpathy:769_B6J_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 C57BL/6J (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": "2025-01-15T23:45:21.650946+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "b0da4af7-3e9b-4333-9f43-565aa974cf86"
}