{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS4372ZZVR/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4372ZZVR",
"aliases": [
"ansuman-satpathy:igvf17_analysis_set_10x4"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI8511XOAV](/matrix-files/IGVFFI8511XOAV/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8511XOAV/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI8511XOAV](/matrix-files/IGVFFI8511XOAV/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8511XOAV/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4372ZZVR](/analysis-sets/IGVFDS4372ZZVR/) has `input_file_sets` with multiplexed samples: [IGVFSM9149ZACE](/multiplexed-samples/IGVFSM9149ZACE/) 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/IGVFDS4372ZZVR/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4372ZZVR](/analysis-sets/IGVFDS4372ZZVR/) 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/IGVFDS4372ZZVR/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM9149ZACE](/multiplexed-samples/IGVFSM9149ZACE/) 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/IGVFSM9149ZACE/"
}
]
},
"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": "2025-03-21T23:05:21.425337+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO5261UCLF/",
"accession": "IGVFDO5261UCLF",
"aliases": [
"igvf:donor_of_RUES2",
"igvf:donor_RUES2"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI1896JFVN/",
"accession": "IGVFFI1896JFVN",
"aliases": [
"ansuman-satpathy:igvf17_multiseq_count_matrix_10x4"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:36:41.266146+00:00",
"file_format": "tsv",
"file_size": 624264,
"href": "/tabular-files/IGVFFI1896JFVN/@@download/IGVFFI1896JFVN.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/6269b8d8-b4ef-49b0-9135-1c0121801c8a/IGVFFI1896JFVN.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e17l4_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4651ZHFR/",
"accession": "IGVFFI4651ZHFR",
"aliases": [
"ansuman-satpathy:igvf17_fragments_10x4"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:33:14.363368+00:00",
"file_format": "tsv",
"file_size": 5770780438,
"href": "/tabular-files/IGVFFI4651ZHFR/@@download/IGVFFI4651ZHFR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/89ada205-9472-4455-bc00-8e55e5e04d6e/IGVFFI4651ZHFR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l4_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI8511XOAV/",
"accession": "IGVFFI8511XOAV",
"aliases": [
"ansuman-satpathy:igvf17_raw_rna_counts_10x4"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:11:51.788936+00:00",
"file_format": "hdf5",
"file_size": 135556361,
"href": "/matrix-files/IGVFFI8511XOAV/@@download/IGVFFI8511XOAV.h5",
"s3_uri": "s3://igvf-files/2025/01/28/ab723d30-1789-49c8-a4af-ae0a05b06921/IGVFFI8511XOAV.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l4_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI3597DRNP/",
"accession": "IGVFFI3597DRNP",
"aliases": [
"ansuman-satpathy:igvf17_fragments_index_10x4"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:25.926492+00:00",
"file_format": "tbi",
"file_size": 1786283,
"href": "/index-files/IGVFFI3597DRNP/@@download/IGVFFI3597DRNP.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/9bdd7a66-e38c-445b-801a-4a60d209e4e2/IGVFFI3597DRNP.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l4_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI6306WEEJ/",
"accession": "IGVFFI6306WEEJ",
"aliases": [
"ansuman-satpathy:igvf17_peaks_10x4"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:33:54.535193+00:00",
"file_format": "bed",
"file_size": 3229222,
"href": "/tabular-files/IGVFFI6306WEEJ/@@download/IGVFFI6306WEEJ.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/422c317f-81f0-4645-9747-eaed044e5914/IGVFFI6306WEEJ.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l4_peaks.bed",
"upload_status": "validation exempted"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS1381KOVA/",
"accession": "IGVFDS1381KOVA",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf17_10x4"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS5763YUNI/",
"accession": "IGVFDS5763YUNI",
"aliases": [
"ansuman-satpathy:multiseq_igvf17_10x4"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9133EBOD/",
"accession": "IGVFDS9133EBOD",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf17_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": "2025-03-22T00:44:57.073160+00:00",
"sample_summary": "Homo sapiens multiplexed sample of RUES2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9149ZACE/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9149ZACE",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf17_10x4"
],
"cellular_sub_pool": "4",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/49ea766d-c6ef-4ced-be8c-4e3ba1693d31/",
"certificate_identifier": "IP115-24",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "RUES2",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 2 days; Homo sapiens (female) RUES2 differentiated cell specimen induced to gastrula for 1 day; ... 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": "2025-01-28T06:33:14.363368+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "4a338197-af00-462c-953e-bd4b3d1244be",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}