{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS3764KYTT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3764KYTT",
"aliases": [
"ansuman-satpathy:igvf5_analysis_set_10x4"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1885UJVU](/matrix-files/IGVFFI1885UJVU/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1885UJVU/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1885UJVU](/matrix-files/IGVFFI1885UJVU/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1885UJVU/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS3764KYTT](/analysis-sets/IGVFDS3764KYTT/) has `input_file_sets` with multiplexed samples: [IGVFSM3106AWHF](/multiplexed-samples/IGVFSM3106AWHF/) 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/IGVFDS3764KYTT/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS3764KYTT](/analysis-sets/IGVFDS3764KYTT/) 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/IGVFDS3764KYTT/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM3106AWHF](/multiplexed-samples/IGVFSM3106AWHF/) 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/IGVFSM3106AWHF/"
}
]
},
"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": "2025-03-21T23:04:36.841233+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1183RRBM/",
"accession": "IGVFDO1183RRBM",
"aliases": [
"igvf:donor_of_HEK293T"
],
"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"
},
{
"@id": "/human-donors/IGVFDO6638HIAD/",
"accession": "IGVFDO6638HIAD",
"aliases": [
"igvf:donor_of_H1"
],
"sex": "male",
"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": "/index-files/IGVFFI1356EXOT/",
"accession": "IGVFFI1356EXOT",
"aliases": [
"ansuman-satpathy:igvf5_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:11.785511+00:00",
"file_format": "tbi",
"file_size": 1818989,
"href": "/index-files/IGVFFI1356EXOT/@@download/IGVFFI1356EXOT.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/742a143d-d305-4262-8d77-951f3b304949/IGVFFI1356EXOT.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5624ZRQW/",
"accession": "IGVFFI5624ZRQW",
"aliases": [
"ansuman-satpathy:igvf5_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:31:14.074335+00:00",
"file_format": "tsv",
"file_size": 439655,
"href": "/tabular-files/IGVFFI5624ZRQW/@@download/IGVFFI5624ZRQW.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/0d8445da-8c6f-417f-8786-fc32b8eb714e/IGVFFI5624ZRQW.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e5l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI1885UJVU/",
"accession": "IGVFFI1885UJVU",
"aliases": [
"ansuman-satpathy:igvf5_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:36:24.632985+00:00",
"file_format": "hdf5",
"file_size": 162855131,
"href": "/matrix-files/IGVFFI1885UJVU/@@download/IGVFFI1885UJVU.h5",
"s3_uri": "s3://igvf-files/2025/01/28/48a9168a-86c7-409f-bf5d-41133ea2a675/IGVFFI1885UJVU.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI8232SKBR/",
"accession": "IGVFFI8232SKBR",
"aliases": [
"ansuman-satpathy:igvf5_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:56:54.134176+00:00",
"file_format": "tsv",
"file_size": 6062870119,
"href": "/tabular-files/IGVFFI8232SKBR/@@download/IGVFFI8232SKBR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/e982ff08-f1bc-44b0-b14c-aeb23799a871/IGVFFI8232SKBR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI2166HXMA/",
"accession": "IGVFFI2166HXMA",
"aliases": [
"ansuman-satpathy:igvf5_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:57:28.902220+00:00",
"file_format": "bed",
"file_size": 2390759,
"href": "/tabular-files/IGVFFI2166HXMA/@@download/IGVFFI2166HXMA.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/8de04fc5-43ac-4aff-9571-55f5798f01bd/IGVFFI2166HXMA.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l4_peaks.bed",
"upload_status": "validation exempted"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3303TULU/",
"accession": "IGVFDS3303TULU",
"aliases": [
"ansuman-satpathy:multiseq_igvf5_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1201SHMG/",
"accession": "IGVFDS1201SHMG",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf5_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3184KNYJ/",
"accession": "IGVFDS3184KNYJ",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf5_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": "2025-03-22T00:42:38.940705+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), H1-hESC, H9, HEK293T",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM3106AWHF/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM3106AWHF",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf5_10x4"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"gastruloid",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/42937768-65a6-47ee-9d4c-6d3829c7f279/",
"certificate_identifier": "IP115-03",
"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/e7a2058d-80fb-46ee-be82-c4d8b26d01ec/",
"certificate_identifier": "IP115-08",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/eaf8c672-701d-4aee-9108-8d64c472d20e/",
"certificate_identifier": "IP115-14",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001184/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HEK293T"
],
"status": "released",
"summary": "HEK293T",
"term_name": "HEK293T"
},
{
"@id": "/sample-terms/EFO_0003042/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H1"
],
"status": "released",
"summary": "H1-hESC",
"term_name": "H1-hESC"
},
{
"@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 neuron for 6 days; Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; ... and 6 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": "2025-01-28T05:56:54.134176+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "2ecb7b9f-8232-4b5a-a3c4-650e1ecfe829",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}