{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
"assay_titles": [
"10x multiome with MULTI-seq"
],
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"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS9896QVZT](/analysis-sets/IGVFDS9896QVZT/) has `input_file_sets` with multiplexed samples: [IGVFSM8265VEJP](/multiplexed-samples/IGVFSM8265VEJP/) 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/IGVFDS9896QVZT/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7766LZDD](/matrix-files/IGVFFI7766LZDD/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7766LZDD/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI7766LZDD](/matrix-files/IGVFFI7766LZDD/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI7766LZDD/"
}
]
},
"award": {
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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": "2025-03-21T23:04:31.747106+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
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"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1756PPKO/",
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"aliases": [
"igvf:donor_of_WTC11"
],
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"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI5546FCEY/",
"accession": "IGVFFI5546FCEY",
"aliases": [
"ansuman-satpathy:igvf3_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:52:14.956915+00:00",
"file_format": "bed",
"file_size": 1895885,
"href": "/tabular-files/IGVFFI5546FCEY/@@download/IGVFFI5546FCEY.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/70bfcbcc-b74a-4cd8-9635-c771b49879c8/IGVFFI5546FCEY.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l4_peaks.bed",
"upload_status": "validation exempted"
},
{
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"accession": "IGVFFI7397VAJM",
"aliases": [
"ansuman-satpathy:igvf3_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:00.803126+00:00",
"file_format": "tbi",
"file_size": 1204390,
"href": "/index-files/IGVFFI7397VAJM/@@download/IGVFFI7397VAJM.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/b46efb79-e27e-4b77-9524-2ce98ea5cc6b/IGVFFI7397VAJM.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4451TTYR/",
"accession": "IGVFFI4451TTYR",
"aliases": [
"ansuman-satpathy:igvf3_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:51:57.297921+00:00",
"file_format": "tsv",
"file_size": 2647322613,
"href": "/tabular-files/IGVFFI4451TTYR/@@download/IGVFFI4451TTYR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/80eed827-cb9f-430d-a410-2e108c32ef8b/IGVFFI4451TTYR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI7080OLYT/",
"accession": "IGVFFI7080OLYT",
"aliases": [
"ansuman-satpathy:igvf3_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:26.855574+00:00",
"file_format": "tsv",
"file_size": 289613,
"href": "/tabular-files/IGVFFI7080OLYT/@@download/IGVFFI7080OLYT.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/5e8b902e-c63f-43ea-9575-2ec023ad3393/IGVFFI7080OLYT.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e3l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI7766LZDD/",
"accession": "IGVFFI7766LZDD",
"aliases": [
"ansuman-satpathy:igvf3_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:34:46.825936+00:00",
"file_format": "hdf5",
"file_size": 90943531,
"href": "/matrix-files/IGVFFI7766LZDD/@@download/IGVFFI7766LZDD.h5",
"s3_uri": "s3://igvf-files/2025/01/28/6aff8225-7f46-49b8-8e8d-110a3c33449a/IGVFFI7766LZDD.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0470ONXA/",
"accession": "IGVFDS0470ONXA",
"aliases": [
"ansuman-satpathy:multiseq_igvf3_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8466CGYE/",
"accession": "IGVFDS8466CGYE",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf3_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4208ZWQY/",
"accession": "IGVFDS4208ZWQY",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf3_10x4"
],
"file_set_type": "experimental data",
"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"protocols": [
"https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
],
"release_timestamp": "2025-03-22T00:42:24.923660+00:00",
"sample_summary": "multiplexed sample of GM25256 (WTC-11), H9, HepG2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8265VEJP/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8265VEJP",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf3_10x4"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
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"certificate_identifier": "IP115-06",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/eaf8c672-701d-4aee-9108-8d64c472d20e/",
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"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HepG2"
],
"status": "released",
"summary": "HepG2",
"term_name": "HepG2"
},
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
},
{
"@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 (female) H9 differentiated cell specimen induced to cardiac muscle cell for 15 days; Homo sapiens (male) HepG2 cell line grown in DMEM without serum; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/6667a92a-d202-493a-8c7d-7a56d1380356/",
"title": "Khine Lin"
},
"submitted_files_timestamp": "2025-01-28T05:51:57.297921+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "e577ad3d-dbc9-4117-93bc-f7e1d05804c3",
"workflows": [
{
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"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}