{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS6305UWGC/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6305UWGC",
"aliases": [
"ansuman-satpathy:igvf3_analysis_set_10x2"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8818QZOF](/multiplexed-samples/IGVFSM8818QZOF/) 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/IGVFSM8818QZOF/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI6422LYRX](/matrix-files/IGVFFI6422LYRX/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI6422LYRX/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI6422LYRX](/matrix-files/IGVFFI6422LYRX/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI6422LYRX/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS6305UWGC](/analysis-sets/IGVFDS6305UWGC/) has `input_file_sets` with multiplexed samples: [IGVFSM8818QZOF](/multiplexed-samples/IGVFSM8818QZOF/) 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/IGVFDS6305UWGC/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS6305UWGC](/analysis-sets/IGVFDS6305UWGC/) 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/IGVFDS6305UWGC/"
}
]
},
"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": "2025-03-21T23:04:29.547790+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"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"
},
{
"@id": "/human-donors/IGVFDO2837BRET/",
"accession": "IGVFDO2837BRET",
"aliases": [
"igvf:donor_of_HepG2"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/index-files/IGVFFI8412SGGL/",
"accession": "IGVFFI8412SGGL",
"aliases": [
"ansuman-satpathy:igvf3_fragments_index_10x2"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:27:57.296698+00:00",
"file_format": "tbi",
"file_size": 1172525,
"href": "/index-files/IGVFFI8412SGGL/@@download/IGVFFI8412SGGL.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/50bd0a4f-1597-4d25-acac-54f52fb88d84/IGVFFI8412SGGL.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l2_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI3768EMVG/",
"accession": "IGVFFI3768EMVG",
"aliases": [
"ansuman-satpathy:igvf3_peaks_10x2"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:51:16.199776+00:00",
"file_format": "bed",
"file_size": 2017718,
"href": "/tabular-files/IGVFFI3768EMVG/@@download/IGVFFI3768EMVG.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/79add474-615e-4f67-940d-5a71b712816c/IGVFFI3768EMVG.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l2_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI6673FWIX/",
"accession": "IGVFFI6673FWIX",
"aliases": [
"ansuman-satpathy:igvf3_fragments_10x2"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:50:59.264423+00:00",
"file_format": "tsv",
"file_size": 2545543121,
"href": "/tabular-files/IGVFFI6673FWIX/@@download/IGVFFI6673FWIX.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/6b847207-11bc-4978-a16f-b6c19609bf69/IGVFFI6673FWIX.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l2_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI4101VNNU/",
"accession": "IGVFFI4101VNNU",
"aliases": [
"ansuman-satpathy:igvf3_multiseq_count_matrix_10x2"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:12.712325+00:00",
"file_format": "tsv",
"file_size": 305370,
"href": "/tabular-files/IGVFFI4101VNNU/@@download/IGVFFI4101VNNU.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/5c43f68e-9e8a-4918-a338-987abd8fcd36/IGVFFI4101VNNU.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e3l2_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI6422LYRX/",
"accession": "IGVFFI6422LYRX",
"aliases": [
"ansuman-satpathy:igvf3_raw_rna_counts_10x2"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:34:18.561991+00:00",
"file_format": "hdf5",
"file_size": 96388831,
"href": "/matrix-files/IGVFFI6422LYRX/@@download/IGVFFI6422LYRX.h5",
"s3_uri": "s3://igvf-files/2025/01/28/d7c94cc9-fed6-4edb-99bb-302f43e3fc35/IGVFFI6422LYRX.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf3/e3l2_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3579YOKV/",
"accession": "IGVFDS3579YOKV",
"aliases": [
"ansuman-satpathy:multiseq_igvf3_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2422JHIN/",
"accession": "IGVFDS2422JHIN",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf3_10x2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4602PSGH/",
"accession": "IGVFDS4602PSGH",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf3_10x2"
],
"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": "2025-03-22T00:42:18.934478+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), H9, HepG2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8818QZOF/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8818QZOF",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf3_10x2"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/90b62a08-60dc-4932-8bf1-38769f07b362/",
"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/",
"certificate_identifier": "IP115-14",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001187/",
"@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": "2025-01-28T05:50:59.264423+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "bd46d0cd-91ec-4151-902c-b261e1ac00e4",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}