{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6243XJYN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6243XJYN",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf0_10x1"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS4882ESVG](/auxiliary-sets/IGVFDS4882ESVG/) 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": "/auxiliary-sets/IGVFDS4882ESVG/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2682GVVD](/multiplexed-samples/IGVFSM2682GVVD/) 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": "/multiplexed-samples/IGVFSM2682GVVD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6243XJYN](/measurement-sets/IGVFDS6243XJYN/) 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/IGVFDS6243XJYN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4882ESVG/",
"accession": "IGVFDS4882ESVG",
"aliases": [
"ansuman-satpathy:multiseq_igvf0_10x1"
],
"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": [],
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:13:41.571099+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1215RCAP/",
"accession": "IGVFFI1215RCAP",
"aliases": [
"ansuman-satpathy:igvf_exp0_rna_10x1_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:34:28.461196+00:00",
"file_format": "fastq",
"file_size": 29775558820,
"href": "/sequence-files/IGVFFI1215RCAP/@@download/IGVFFI1215RCAP.fastq.gz",
"md5sum": "f604d5334ebe9b3e177fc2eca39f73a1",
"s3_uri": "s3://igvf-files/2024/07/21/dd1e5648-3c47-420a-b5ec-3f4a03e9e507/IGVFFI1215RCAP.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_IGVF0_McGinnis/GEX/GEX2_S2_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5758URSR/",
"accession": "IGVFFI5758URSR",
"aliases": [
"ansuman-satpathy:igvf_exp0_rna_10x1_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:32:39.547777+00:00",
"file_format": "fastq",
"file_size": 12566704925,
"href": "/sequence-files/IGVFFI5758URSR/@@download/IGVFFI5758URSR.fastq.gz",
"md5sum": "561d02b7194cbe502f6c59f83f870fa4",
"s3_uri": "s3://igvf-files/2024/07/21/178a7c19-aac4-443e-97d1-4f728a38269b/IGVFFI5758URSR.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_IGVF0_McGinnis/GEX/GEX2_S2_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4517STPG/",
"accession": "IGVFFI4517STPG",
"aliases": [
"ansuman-satpathy:igvf_exp0_rna_10x1_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:31:35.106083+00:00",
"file_format": "fastq",
"file_size": 3685770313,
"href": "/sequence-files/IGVFFI4517STPG/@@download/IGVFFI4517STPG.fastq.gz",
"md5sum": "941ffd66e760083aac296930588dde7a",
"s3_uri": "s3://igvf-files/2024/07/21/a2147c44-4fe5-4518-a8f1-a27523171c09/IGVFFI4517STPG.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_IGVF0_McGinnis/GEX/GEX2_S2_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8677MRVW/",
"accession": "IGVFFI8677MRVW",
"aliases": [
"ansuman-satpathy:igvf_exp0_rna_10x1_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:31:58.245359+00:00",
"file_format": "fastq",
"file_size": 4123653973,
"href": "/sequence-files/IGVFFI8677MRVW/@@download/IGVFFI8677MRVW.fastq.gz",
"md5sum": "29533c378fb087699837e0e799c18e20",
"s3_uri": "s3://igvf-files/2024/07/21/378e4584-2523-4ce0-8274-24458bb0f337/IGVFFI8677MRVW.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_IGVF0_McGinnis/GEX/GEX2_S2_L003_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5164YYMG/",
"accession": "IGVFFI5164YYMG",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp0_rna_10x1_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:20:48.381528+00:00",
"file_format": "yaml",
"file_size": 1397,
"href": "/configuration-files/IGVFFI5164YYMG/@@download/IGVFFI5164YYMG.yaml.gz",
"md5sum": "c63e138fc5dfea7ca2ffeadc64a2aabb",
"s3_uri": "s3://igvf-files/2024/09/18/7768b6f4-306c-48d3-83d0-b3d6b55c3dc4/IGVFFI5164YYMG.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp0_rna_10x1_NGS1_rna_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5448FWBW/"
],
"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/IGVFDS7482RDGX/",
"accession": "IGVFDS7482RDGX",
"status": "released"
}
],
"release_timestamp": "2025-03-07T01:10:24.009037+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2682GVVD/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2682GVVD",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf0_10x1"
],
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to endothelial cell for 3 days; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to endothelial cell for 4 days; ... and 21 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"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": "2024-07-19T22:42:28.125599+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "1e8e2e64-8106-4875-886b-e8cded32dbd9"
}