{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4816GMHG",
"aliases": [
"ansuman-satpathy:igvf6_analysis_set_10x2"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2497RUGS](/matrix-files/IGVFFI2497RUGS/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2497RUGS/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2497RUGS](/matrix-files/IGVFFI2497RUGS/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2497RUGS/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8961ZZQN](/multiplexed-samples/IGVFSM8961ZZQN/) 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/IGVFSM8961ZZQN/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4816GMHG](/analysis-sets/IGVFDS4816GMHG/) has `input_file_sets` with multiplexed samples: [IGVFSM8961ZZQN](/multiplexed-samples/IGVFSM8961ZZQN/) 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/IGVFDS4816GMHG/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4816GMHG](/analysis-sets/IGVFDS4816GMHG/) 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/IGVFDS4816GMHG/"
}
]
},
"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": "2025-03-21T23:04:38.311789+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": "/matrix-files/IGVFFI2497RUGS/",
"accession": "IGVFFI2497RUGS",
"aliases": [
"ansuman-satpathy:igvf6_raw_rna_counts_10x2"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:36:58.244705+00:00",
"file_format": "hdf5",
"file_size": 142984929,
"href": "/matrix-files/IGVFFI2497RUGS/@@download/IGVFFI2497RUGS.h5",
"s3_uri": "s3://igvf-files/2025/01/28/2578bd8b-c9d6-4f99-b4cc-ebd7500fae86/IGVFFI2497RUGS.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l2_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5701AHAX/",
"accession": "IGVFFI5701AHAX",
"aliases": [
"ansuman-satpathy:igvf6_multiseq_count_matrix_10x2"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:31:32.028872+00:00",
"file_format": "tsv",
"file_size": 541798,
"href": "/tabular-files/IGVFFI5701AHAX/@@download/IGVFFI5701AHAX.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/0bfb898b-5c74-4703-8be6-1b5baa9123be/IGVFFI5701AHAX.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e6l2_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0269NGAR/",
"accession": "IGVFFI0269NGAR",
"aliases": [
"ansuman-satpathy:igvf6_peaks_10x2"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:59:24.873973+00:00",
"file_format": "bed",
"file_size": 2421958,
"href": "/tabular-files/IGVFFI0269NGAR/@@download/IGVFFI0269NGAR.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/dcf546e4-5ae8-4dbe-b2a1-070bfaed6092/IGVFFI0269NGAR.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l2_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI8020JTQX/",
"accession": "IGVFFI8020JTQX",
"aliases": [
"ansuman-satpathy:igvf6_fragments_10x2"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:58:52.601778+00:00",
"file_format": "tsv",
"file_size": 6602201771,
"href": "/tabular-files/IGVFFI8020JTQX/@@download/IGVFFI8020JTQX.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/f8a5bf39-c182-4de1-b3d0-d50b95b11d34/IGVFFI8020JTQX.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l2_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI4877UMFP/",
"accession": "IGVFFI4877UMFP",
"aliases": [
"ansuman-satpathy:igvf6_fragments_index_10x2"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:15.987299+00:00",
"file_format": "tbi",
"file_size": 1878380,
"href": "/index-files/IGVFFI4877UMFP/@@download/IGVFFI4877UMFP.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/413dd3ba-5564-4f85-88ad-73b935786f86/IGVFFI4877UMFP.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf6/e6l2_fragments.tsv.gz.tbi",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6310VXMX/",
"accession": "IGVFDS6310VXMX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf6_10x2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS7320EONJ/",
"accession": "IGVFDS7320EONJ",
"aliases": [
"ansuman-satpathy:multiseq_igvf6_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4095FWRD/",
"accession": "IGVFDS4095FWRD",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf6_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": "2025-03-22T00:42:42.864692+00:00",
"sample_summary": "Homo sapiens multiplexed sample of H1-hESC",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8961ZZQN/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8961ZZQN",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf6_10x2"
],
"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": "2025-01-28T05:58:52.601778+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "2d623a5f-ea4e-4d0c-a28c-e59ca936ac3c",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}