{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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],
"assay_titles": [
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],
"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 demultiplexed sample",
"detail": "Analysis set [IGVFDS5448FWBW](/analysis-sets/IGVFDS5448FWBW/) has `input_file_sets` with multiplexed samples: [IGVFSM2682GVVD](/multiplexed-samples/IGVFSM2682GVVD/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_analysis_set_multiplexed_samples",
"path": "/analysis-sets/IGVFDS5448FWBW/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS5448FWBW](/analysis-sets/IGVFDS5448FWBW/) 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": "/analysis-sets/IGVFDS5448FWBW/"
}
]
},
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"component": "mapping",
"contact_pi": {
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"controlled_access": false,
"creation_timestamp": "2025-01-28T05:35:01.189264+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
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"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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],
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"controlled_access": false,
"creation_timestamp": "2025-02-14T22:58:12.890513+00:00",
"derived_from": [
"/sequence-files/IGVFFI3568SBTV/",
"/sequence-files/IGVFFI1986FAVM/",
"/sequence-files/IGVFFI8652MKWJ/",
"/sequence-files/IGVFFI5795ORFY/"
],
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"href": "/tabular-files/IGVFFI9532SPYG/@@download/IGVFFI9532SPYG.tsv.gz",
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"status": "released",
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"upload_status": "validation exempted"
},
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],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-02-14T22:58:39.317295+00:00",
"derived_from": [
"/tabular-files/IGVFFI9532SPYG/"
],
"file_format": "bed",
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"md5sum": "08e56e4e9aeaf1895f7de5f509c712b4",
"s3_uri": "s3://igvf-files/2025/02/14/41079c9c-2a35-4ca4-9e45-edde57b43857/IGVFFI0480XBYK.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_peaks.bed.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI7419FNVX/",
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"aliases": [
"ansuman-satpathy:igvf0_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-02-14T23:07:50.477488+00:00",
"derived_from": [
"/tabular-files/IGVFFI9532SPYG/"
],
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"href": "/index-files/IGVFFI7419FNVX/@@download/IGVFFI7419FNVX.tbi",
"md5sum": "1a97ae3ce55552f495b0a1babf0228f3",
"s3_uri": "s3://igvf-files/2025/02/14/e41186fe-2bbc-43f2-b46e-2765086fbe86/IGVFFI7419FNVX.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI3143UHIU/",
"accession": "IGVFFI3143UHIU",
"aliases": [
"ansuman-satpathy:igvf0_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-02-14T23:18:31.500791+00:00",
"derived_from": [
"/sequence-files/IGVFFI4517STPG/",
"/sequence-files/IGVFFI8677MRVW/",
"/sequence-files/IGVFFI5758URSR/",
"/sequence-files/IGVFFI1215RCAP/"
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"file_format": "hdf5",
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"href": "/matrix-files/IGVFFI3143UHIU/@@download/IGVFFI3143UHIU.h5",
"md5sum": "1dd74e3eb4564362d01ac0df85bec162",
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"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf0/e0l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0978MWOP/",
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2025-02-19T23:37:22.781642+00:00",
"derived_from": [
"/sequence-files/IGVFFI5411OJRK/",
"/sequence-files/IGVFFI4642YKWI/",
"/sequence-files/IGVFFI5223HYRP/",
"/sequence-files/IGVFFI6088QALC/"
],
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"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e0l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS7482RDGX/",
"accession": "IGVFDS7482RDGX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf0_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6243XJYN/",
"accession": "IGVFDS6243XJYN",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf0_10x1"
],
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"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS4882ESVG/",
"accession": "IGVFDS4882ESVG",
"aliases": [
"ansuman-satpathy:multiseq_igvf0_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"protocols": [
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],
"release_timestamp": "2025-03-07T06:03:59.380337+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11)",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2682GVVD/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2682GVVD",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf0_10x1"
],
"classifications": [
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],
"disease_terms": [],
"institutional_certificates": [
{
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"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
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],
"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": "9",
"status": "released",
"submitted_by": {
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"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-02-14T22:58:12.890513+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "c78d6894-d521-4532-ba34-364310e8a357",
"workflows": [
{
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"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}