{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0786WISU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0786WISU",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf18_10x3"
],
"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_0000753](/sample-terms/NTR_0000753/) 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_0000753/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2437JWUW/",
"accession": "IGVFDS2437JWUW",
"aliases": [
"ansuman-satpathy:multiseq_igvf18_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"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": "2025-01-27T22:55:49.779558+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9018OPIO/",
"accession": "IGVFDO9018OPIO",
"aliases": [
"igvf:donor_of_SKNSH"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO4200NZSV/",
"accession": "IGVFDO4200NZSV",
"aliases": [
"igvf:donor_of_IMR90"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7503RZHO/",
"accession": "IGVFDO7503RZHO",
"aliases": [
"igvf:donor_of_MCF7"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"aliases": [
"igvf:donor_of_HUDEP-2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7960QFAF/",
"accession": "IGVFFI7960QFAF",
"aliases": [
"ansuman-satpathy:igvf_exp18_rna_10x3_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:21:32.064823+00:00",
"file_format": "fastq",
"file_size": 3196835927,
"href": "/sequence-files/IGVFFI7960QFAF/@@download/IGVFFI7960QFAF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/69dc6037-bc49-4dc0-95de-997c932692fd/IGVFFI7960QFAF.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/igvf18/GEX/GEX3-CMAS23R_S27_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1858TUBD/",
"accession": "IGVFFI1858TUBD",
"aliases": [
"ansuman-satpathy:igvf_exp18_rna_10x3_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:22:02.285866+00:00",
"file_format": "fastq",
"file_size": 3196495289,
"href": "/sequence-files/IGVFFI1858TUBD/@@download/IGVFFI1858TUBD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/92a23ae2-e316-43cc-af11-b3558bc09714/IGVFFI1858TUBD.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/igvf18/GEX/GEX3-CMAS23R_S27_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9454FNFG/",
"accession": "IGVFFI9454FNFG",
"aliases": [
"ansuman-satpathy:igvf_exp18_rna_10x3_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:23:47.642500+00:00",
"file_format": "fastq",
"file_size": 43862518791,
"href": "/sequence-files/IGVFFI9454FNFG/@@download/IGVFFI9454FNFG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/53335a34-d37b-41c4-93f3-a0a2432787d9/IGVFFI9454FNFG.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/igvf18/GEX/GEX3-CMAS23R_S27_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8420OSUH/",
"accession": "IGVFFI8420OSUH",
"aliases": [
"ansuman-satpathy:igvf_exp18_rna_10x3_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-27T23:28:44.728790+00:00",
"file_format": "fastq",
"file_size": 35874258910,
"href": "/sequence-files/IGVFFI8420OSUH/@@download/IGVFFI8420OSUH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/27/c85b8d3f-055c-401a-9137-696d38678a24/IGVFFI8420OSUH.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/igvf18/GEX/GEX3-CMAS23R_S27_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9438MIAU/",
"accession": "IGVFFI9438MIAU",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp18_rna_10x3_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2025-02-26T01:45:45.101720+00:00",
"file_format": "yaml",
"file_size": 1392,
"href": "/configuration-files/IGVFFI9438MIAU/@@download/IGVFFI9438MIAU.yaml.gz",
"s3_uri": "s3://igvf-files/2025/02/26/f784e007-abc6-407e-95b4-5288efc0dce8/IGVFFI9438MIAU.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec_new/igvf_exp18_rna_10x3_NGS1_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4963SRAJ/"
],
"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 with MULTI-seq",
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS9563IPMU/",
"accession": "IGVFDS9563IPMU",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:18:22.492674+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM5815WALV/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5815WALV",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf18_10x3"
],
"cellular_sub_pool": "3",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "IMR-90",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "MCF-7",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:SK-N-SH"
],
"status": "released",
"summary": "SK-N-SH",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HUDEP-2"
],
"status": "released",
"summary": "HUDEP-2",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "25",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-27T23:21:32.064823+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "868fd9a0-ff2d-4c88-8b88-0851df06e6a4"
}