{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS4882ESVG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS4882ESVG",
"aliases": [
"ansuman-satpathy:multiseq_igvf0_10x1"
],
"audit": {
"INTERNAL_ACTION": [
{
"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": "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/"
}
]
},
"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": "2024-07-19T22:33:14.298597+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"
}
],
"file_set_type": "lipid-conjugated oligo sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI4642YKWI/",
"accession": "IGVFFI4642YKWI",
"aliases": [
"ansuman-satpathy:igvf_exp0_multi_10x1_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-19T22:42:48.735301+00:00",
"file_format": "fastq",
"file_size": 1839821154,
"href": "/sequence-files/IGVFFI4642YKWI/@@download/IGVFFI4642YKWI.fastq.gz",
"md5sum": "e0cd5d86193f65d2dc20bab60adcf9d1",
"s3_uri": "s3://igvf-files/2024/07/19/bcf8f052-eb4d-4420-ae9b-0773802602c2/IGVFFI4642YKWI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF0_McGinnis/MULTI/MULTI2_S56_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5411OJRK/",
"accession": "IGVFFI5411OJRK",
"aliases": [
"ansuman-satpathy:igvf_exp0_multi_10x1_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-19T22:42:28.125599+00:00",
"file_format": "fastq",
"file_size": 3744591369,
"href": "/sequence-files/IGVFFI5411OJRK/@@download/IGVFFI5411OJRK.fastq.gz",
"md5sum": "1e97130b5dfa0cdd859e95b39af60494",
"s3_uri": "s3://igvf-files/2024/07/19/dc9ad7b1-0997-4a7c-b5db-36a1d5a9c49c/IGVFFI5411OJRK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF0_McGinnis/MULTI/MULTI2_S56_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5223HYRP/",
"accession": "IGVFFI5223HYRP",
"aliases": [
"ansuman-satpathy:igvf_exp0_multi_10x1_NGS1_r3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-19T22:43:07.143582+00:00",
"file_format": "fastq",
"file_size": 3767864067,
"href": "/sequence-files/IGVFFI5223HYRP/@@download/IGVFFI5223HYRP.fastq.gz",
"md5sum": "9e7e768c3a69bc327cf50652ed978864",
"s3_uri": "s3://igvf-files/2024/07/19/326c7d9d-2979-4331-9046-8b6fcd7578bf/IGVFFI5223HYRP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF0_McGinnis/MULTI/MULTI2_S56_L003_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6088QALC/",
"accession": "IGVFFI6088QALC",
"aliases": [
"ansuman-satpathy:igvf_exp0_multi_10x1_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-19T22:43:26.447772+00:00",
"file_format": "fastq",
"file_size": 1090207721,
"href": "/sequence-files/IGVFFI6088QALC/@@download/IGVFFI6088QALC.fastq.gz",
"md5sum": "b9bbf6f4133d80e5062a2bed6cf37bb2",
"s3_uri": "s3://igvf-files/2024/07/19/87e87eed-06e5-4053-bbca-8461d0fcbe3b/IGVFFI6088QALC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230622_IGVF0_McGinnis/MULTI/MULTI2_S56_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6462KGWB/",
"accession": "IGVFFI6462KGWB",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp0_multi_10x1_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:20:44.092357+00:00",
"file_format": "yaml",
"file_size": 1339,
"href": "/configuration-files/IGVFFI6462KGWB/@@download/IGVFFI6462KGWB.yaml.gz",
"md5sum": "8d2655b310f2c335b8b4153966a440fd",
"s3_uri": "s3://igvf-files/2024/09/18/4dc4a2ab-fba4-4de6-a177-2c1816168dd7/IGVFFI6462KGWB.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp0_multi_10x1_NGS1_multi_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5448FWBW/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS6243XJYN/",
"accession": "IGVFDS6243XJYN",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf0_10x1"
],
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7482RDGX/",
"accession": "IGVFDS7482RDGX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf0_10x1"
],
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released"
}
],
"notes": "File_set_type enum oligo-conjugated lipids has been renamed to be lipid-conjugated oligo sequencing.",
"release_timestamp": "2025-03-07T01:10:20.645037+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": "12",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-19T22:42:28.125599+00:00",
"summary": "lipid-conjugated oligo sequencing for single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "e13689b3-4ac1-4d32-a7e4-f48d5268fb06"
}