{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7903FOXV",
"aliases": [
"ansuman-satpathy:igvf11_analysis_set_10x3"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS7903FOXV](/analysis-sets/IGVFDS7903FOXV/) has `input_file_sets` with multiplexed samples: [IGVFSM6160ZDRZ](/multiplexed-samples/IGVFSM6160ZDRZ/) 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/IGVFDS7903FOXV/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI4495UKBO](/matrix-files/IGVFFI4495UKBO/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI4495UKBO/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI4495UKBO](/matrix-files/IGVFFI4495UKBO/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI4495UKBO/"
}
]
},
"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": "2025-03-21T23:04:48.046205+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO7411YYYE/",
"accession": "IGVFDO7411YYYE",
"aliases": [
"igvf:donor_of_h7"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/index-files/IGVFFI0347BCEG/",
"accession": "IGVFFI0347BCEG",
"aliases": [
"ansuman-satpathy:igvf11_fragments_index_10x3"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:32.735634+00:00",
"file_format": "tbi",
"file_size": 1568867,
"href": "/index-files/IGVFFI0347BCEG/@@download/IGVFFI0347BCEG.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/522cb27a-8b4d-4097-b04e-01829390e6f3/IGVFFI0347BCEG.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l3_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5952NKYY/",
"accession": "IGVFFI5952NKYY",
"aliases": [
"ansuman-satpathy:igvf11_multiseq_count_matrix_10x3"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:32:46.156090+00:00",
"file_format": "tsv",
"file_size": 245963,
"href": "/tabular-files/IGVFFI5952NKYY/@@download/IGVFFI5952NKYY.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/f298b0c6-5c1d-4851-af60-f77af5579e17/IGVFFI5952NKYY.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e11l3_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2578BIPG/",
"accession": "IGVFFI2578BIPG",
"aliases": [
"ansuman-satpathy:igvf11_fragments_10x3"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:08:20.046915+00:00",
"file_format": "tsv",
"file_size": 4483649178,
"href": "/tabular-files/IGVFFI2578BIPG/@@download/IGVFFI2578BIPG.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/0ccbb81a-9a30-464b-89b4-fc557bad8e02/IGVFFI2578BIPG.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l3_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI7472XTOL/",
"accession": "IGVFFI7472XTOL",
"aliases": [
"ansuman-satpathy:igvf11_peaks_10x3"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:08:48.541401+00:00",
"file_format": "bed",
"file_size": 1955414,
"href": "/tabular-files/IGVFFI7472XTOL/@@download/IGVFFI7472XTOL.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/eaa91d6c-4176-4fb3-aab8-2488dbb751d8/IGVFFI7472XTOL.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l3_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI4495UKBO/",
"accession": "IGVFFI4495UKBO",
"aliases": [
"ansuman-satpathy:igvf11_raw_rna_counts_10x3"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:06:35.540485+00:00",
"file_format": "hdf5",
"file_size": 147601284,
"href": "/matrix-files/IGVFFI4495UKBO/@@download/IGVFFI4495UKBO.h5",
"s3_uri": "s3://igvf-files/2025/01/28/80016d4d-66ff-4399-a63c-08b869ad3aba/IGVFFI4495UKBO.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf11/e11l3_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2891PUQE/",
"accession": "IGVFDS2891PUQE",
"aliases": [
"ansuman-satpathy:multiseq_igvf11_10x3"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4853JTJJ/",
"accession": "IGVFDS4853JTJJ",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf11_10x3"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8553CHBZ/",
"accession": "IGVFDS8553CHBZ",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf11_10x3"
],
"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": "2025-03-22T00:43:02.951664+00:00",
"sample_summary": "multiplexed sample of GM25256 (WTC-11), H7-hESC",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM6160ZDRZ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM6160ZDRZ",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf11_10x3"
],
"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"
},
{
"@id": "/institutional-certificates/f37dfa73-f4f1-4bfe-a312-9eade62d5988/",
"certificate_identifier": "IP115-15",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H7-hESC"
],
"status": "released",
"summary": "H7-hESC",
"term_name": "H7-hESC"
},
{
"@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) H7-hESC differentiated cell specimen; Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days; ... 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": "2025-01-28T06:08:20.046915+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "feb0379c-6f89-409c-8579-b32a0aa29fb3",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}