{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0287NOBE",
"aliases": [
"ansuman-satpathy:igvf6_analysis_set_10x4"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM2522EBPE](/multiplexed-samples/IGVFSM2522EBPE/) 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/IGVFSM2522EBPE/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9795MDBY](/matrix-files/IGVFFI9795MDBY/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9795MDBY/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9795MDBY](/matrix-files/IGVFFI9795MDBY/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9795MDBY/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS0287NOBE](/analysis-sets/IGVFDS0287NOBE/) has `input_file_sets` with multiplexed samples: [IGVFSM2522EBPE](/multiplexed-samples/IGVFSM2522EBPE/) 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/IGVFDS0287NOBE/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS0287NOBE](/analysis-sets/IGVFDS0287NOBE/) 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/IGVFDS0287NOBE/"
}
]
},
"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": "2025-03-21T23:04:41.278783+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO6638HIAD/",
"accession": "IGVFDO6638HIAD",
"aliases": [
"igvf:donor_of_H1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI7166LYGQ/",
"accession": "IGVFFI7166LYGQ",
"aliases": [
"ansuman-satpathy:igvf6_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:31:48.180756+00:00",
"file_format": "tsv",
"file_size": 526371,
"href": "/tabular-files/IGVFFI7166LYGQ/@@download/IGVFFI7166LYGQ.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/7cb53675-4d99-4eb1-9926-a7127f19dbbc/IGVFFI7166LYGQ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e6l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI8465FWAI/",
"accession": "IGVFFI8465FWAI",
"aliases": [
"ansuman-satpathy:igvf6_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:19.426284+00:00",
"file_format": "tbi",
"file_size": 1827846,
"href": "/index-files/IGVFFI8465FWAI/@@download/IGVFFI8465FWAI.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/e40636c1-aeed-4163-9e2f-d8fa3a2e9467/IGVFFI8465FWAI.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0224OXYI/",
"accession": "IGVFFI0224OXYI",
"aliases": [
"ansuman-satpathy:igvf6_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:00:47.191584+00:00",
"file_format": "tsv",
"file_size": 6191533900,
"href": "/tabular-files/IGVFFI0224OXYI/@@download/IGVFFI0224OXYI.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/72c0d9bb-caab-4d07-bae8-c19de6e30bde/IGVFFI0224OXYI.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI4030SCVB/",
"accession": "IGVFFI4030SCVB",
"aliases": [
"ansuman-satpathy:igvf6_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:01:21.388474+00:00",
"file_format": "bed",
"file_size": 2386432,
"href": "/tabular-files/IGVFFI4030SCVB/@@download/IGVFFI4030SCVB.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/773d9428-7af8-4854-bcd4-ee3a07aeeee2/IGVFFI4030SCVB.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l4_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI9795MDBY/",
"accession": "IGVFFI9795MDBY",
"aliases": [
"ansuman-satpathy:igvf6_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:37:27.385615+00:00",
"file_format": "hdf5",
"file_size": 148359929,
"href": "/matrix-files/IGVFFI9795MDBY/@@download/IGVFFI9795MDBY.h5",
"s3_uri": "s3://igvf-files/2025/01/28/78b84849-5f46-456f-bb8c-e1acb4a2fc0b/IGVFFI9795MDBY.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8391OPLO/",
"accession": "IGVFDS8391OPLO",
"aliases": [
"ansuman-satpathy:multiseq_igvf6_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6424PGVE/",
"accession": "IGVFDS6424PGVE",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf6_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4340TUUZ/",
"accession": "IGVFDS4340TUUZ",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf6_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": "2025-03-22T00:42:48.467534+00:00",
"sample_summary": "Homo sapiens multiplexed sample of H1-hESC",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM2522EBPE/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM2522EBPE",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf6_10x4"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e7a2058d-80fb-46ee-be82-c4d8b26d01ec/",
"certificate_identifier": "IP115-08",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H1"
],
"status": "released",
"summary": "H1-hESC",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days; Homo sapiens (male) H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 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": "2025-01-28T06:00:47.191584+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "4ebb8fbd-dcc8-4e31-b4ef-9c5bbef32484",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}