{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3492JTPL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3492JTPL",
"aliases": [
"ansuman-satpathy:snRNA-seq_mouse_bridge_115"
],
"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": "Tissue [IGVFSM9817DJBX](/tissues/IGVFSM9817DJBX/) 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/IGVFSM9817DJBX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3492JTPL](/measurement-sets/IGVFDS3492JTPL/) 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/IGVFDS3492JTPL/"
}
]
},
"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": "2024-07-23T00:43:24.303093+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO8649RKVX/",
"accession": "IGVFDO8649RKVX",
"aliases": [
"ansuman-satpathy:115_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/IGVFFI3865CUKI/",
"accession": "IGVFFI3865CUKI",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_115_rna_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:54:34.659341+00:00",
"file_format": "fastq",
"file_size": 1457255273,
"href": "/sequence-files/IGVFFI3865CUKI/@@download/IGVFFI3865CUKI.fastq.gz",
"md5sum": "8cc865d121cfa0725de795e938c8fa4e",
"s3_uri": "s3://igvf-files/2024/07/23/1a4c81f0-2e9e-4174-aad2-e0c4746fe855/IGVFFI3865CUKI.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_115_S6_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7761PXYZ/",
"accession": "IGVFFI7761PXYZ",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_115_rna_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:55:02.711764+00:00",
"file_format": "fastq",
"file_size": 4342189500,
"href": "/sequence-files/IGVFFI7761PXYZ/@@download/IGVFFI7761PXYZ.fastq.gz",
"md5sum": "f4e89409e01370d22e2c2df7cefbca63",
"s3_uri": "s3://igvf-files/2024/07/23/b4e13462-e84d-4024-8296-a7eb3a3e03b5/IGVFFI7761PXYZ.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_115_S6_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2504VZJX/",
"accession": "IGVFFI2504VZJX",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_115_rna_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:56:04.437514+00:00",
"file_format": "fastq",
"file_size": 10362894283,
"href": "/sequence-files/IGVFFI2504VZJX/@@download/IGVFFI2504VZJX.fastq.gz",
"md5sum": "e1df6a7fe025ac6cac921aa6873707f5",
"s3_uri": "s3://igvf-files/2024/07/23/37ac273c-8a80-444f-872b-42139e79ce6c/IGVFFI2504VZJX.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_115_S6_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0849BAAC/",
"accession": "IGVFFI0849BAAC",
"aliases": [
"ansuman-satpathy:igvf_mouse_bridge_115_rna_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-23T01:54:10.261712+00:00",
"file_format": "fastq",
"file_size": 1199282573,
"href": "/sequence-files/IGVFFI0849BAAC/@@download/IGVFFI0849BAAC.fastq.gz",
"md5sum": "266e7bb6f4c4b3860af267e860546fac",
"s3_uri": "s3://igvf-files/2024/07/23/8dbbb279-0892-4c51-abfd-edd558dfb743/IGVFFI0849BAAC.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_115_S6_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6282NNDK/",
"accession": "IGVFFI6282NNDK",
"aliases": [
"ansuman-satpathy:seqspec_igvf_mouse_bridge_115_rna"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:46:04.730673+00:00",
"file_format": "yaml",
"file_size": 1394,
"href": "/configuration-files/IGVFFI6282NNDK/@@download/IGVFFI6282NNDK.yaml.gz",
"md5sum": "404352f07166225503b51b4f592dde84",
"s3_uri": "s3://igvf-files/2024/09/18/a216427d-4c06-4ec0-829e-dda82a16423c/IGVFFI6282NNDK.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_mouse_bridge_115_rna_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5230RAFR/",
"/analysis-sets/IGVFDS5717EBEY/",
"/analysis-sets/IGVFDS0608MVYZ/"
],
"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/IGVFDS1085SCZI/",
"accession": "IGVFDS1085SCZI",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:58.836337+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9817DJBX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9817DJBX",
"aliases": [
"ansuman-satpathy:115_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",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-23T01:54:10.261712+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "fc2504d7-3db4-47e9-ab8c-4ca534a260ad"
}