{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4026VJME",
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"ansuman-satpathy:igvf17_analysis_set_10x2"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS4026VJME](/analysis-sets/IGVFDS4026VJME/) has `input_file_sets` with multiplexed samples: [IGVFSM0198VBOA](/multiplexed-samples/IGVFSM0198VBOA/) 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/IGVFDS4026VJME/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS4026VJME](/analysis-sets/IGVFDS4026VJME/) 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/IGVFDS4026VJME/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0536JASN](/matrix-files/IGVFFI0536JASN/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0536JASN/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0536JASN](/matrix-files/IGVFFI0536JASN/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0536JASN/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM0198VBOA](/multiplexed-samples/IGVFSM0198VBOA/) 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/IGVFSM0198VBOA/"
}
]
},
"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": "2025-03-21T23:05:18.464942+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": [
{
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"accession": "IGVFFI6817WPEM",
"aliases": [
"ansuman-satpathy:igvf17_multiseq_count_matrix_10x2"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:36:21.963470+00:00",
"derived_from": [
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"/sequence-files/IGVFFI6810HQXQ/",
"/sequence-files/IGVFFI7522JWSB/"
],
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"href": "/tabular-files/IGVFFI6817WPEM/@@download/IGVFFI6817WPEM.tsv.gz",
"md5sum": "61dfcaf77a67bf584f9abbf7edee445d",
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"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e17l2_tag_mtx.tsv.gz",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI7963IGJM/",
"accession": "IGVFFI7963IGJM",
"aliases": [
"ansuman-satpathy:igvf17_fragments_10x2"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:30:55.209892+00:00",
"derived_from": [
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"/sequence-files/IGVFFI6700TSUO/",
"/sequence-files/IGVFFI8641KNFC/",
"/sequence-files/IGVFFI2126NBHO/",
"/sequence-files/IGVFFI0016IPCR/",
"/sequence-files/IGVFFI6507KNQQ/",
"/sequence-files/IGVFFI4535ILQZ/",
"/sequence-files/IGVFFI4598XWOF/",
"/sequence-files/IGVFFI9782UBAM/",
"/sequence-files/IGVFFI6520SGOM/",
"/sequence-files/IGVFFI8231HOHA/",
"/sequence-files/IGVFFI5996XIQY/",
"/sequence-files/IGVFFI1550TIXN/",
"/sequence-files/IGVFFI1071QXDC/",
"/sequence-files/IGVFFI7868TYBT/",
"/sequence-files/IGVFFI2133JUOD/"
],
"file_format": "tsv",
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"href": "/tabular-files/IGVFFI7963IGJM/@@download/IGVFFI7963IGJM.tsv.gz",
"md5sum": "d961498df113bbff7f59b0934b9d3381",
"s3_uri": "s3://igvf-files/2025/01/28/6fe14404-fc68-4a3b-bc24-613579fb3300/IGVFFI7963IGJM.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l2_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI5495WANO/",
"accession": "IGVFFI5495WANO",
"aliases": [
"ansuman-satpathy:igvf17_peaks_10x2"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:31:36.491604+00:00",
"derived_from": [
"/tabular-files/IGVFFI7963IGJM/"
],
"file_format": "bed",
"file_size": 3209643,
"href": "/tabular-files/IGVFFI5495WANO/@@download/IGVFFI5495WANO.bed.gz",
"md5sum": "85bc051604f6484a1711d0867ccec619",
"s3_uri": "s3://igvf-files/2025/01/28/d8cbf6de-43a1-4d36-ba49-dbed4a2972d9/IGVFFI5495WANO.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l2_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI2185LHSE/",
"accession": "IGVFFI2185LHSE",
"aliases": [
"ansuman-satpathy:igvf17_fragments_index_10x2"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:29:21.363431+00:00",
"derived_from": [
"/tabular-files/IGVFFI7963IGJM/"
],
"file_format": "tbi",
"file_size": 1784756,
"href": "/index-files/IGVFFI2185LHSE/@@download/IGVFFI2185LHSE.tbi",
"md5sum": "75dc9cc40d01826189220dcaf63f037f",
"s3_uri": "s3://igvf-files/2025/01/28/70655e50-e91a-4cb8-bca3-53c20e7b2dad/IGVFFI2185LHSE.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l2_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI0536JASN/",
"accession": "IGVFFI0536JASN",
"aliases": [
"ansuman-satpathy:igvf17_raw_rna_counts_10x2"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:11:21.390652+00:00",
"derived_from": [
"/sequence-files/IGVFFI5008FPTJ/",
"/sequence-files/IGVFFI5220EJPW/",
"/sequence-files/IGVFFI0089JXZC/",
"/sequence-files/IGVFFI6483HCFF/",
"/sequence-files/IGVFFI7492WFRX/",
"/sequence-files/IGVFFI9505EIAC/",
"/sequence-files/IGVFFI7663ABIS/",
"/sequence-files/IGVFFI3702EYUT/",
"/sequence-files/IGVFFI1765UYGY/",
"/sequence-files/IGVFFI7504NDRD/",
"/sequence-files/IGVFFI4050DGGL/",
"/sequence-files/IGVFFI0474PINU/",
"/sequence-files/IGVFFI1304BHQM/",
"/sequence-files/IGVFFI9687BQBU/",
"/sequence-files/IGVFFI5375GOVF/",
"/sequence-files/IGVFFI0999ZNQC/"
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"file_format": "hdf5",
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"md5sum": "a5033e1fd26776c9e5a9fd193bf867a5",
"s3_uri": "s3://igvf-files/2025/01/28/20f82419-d21d-4595-af49-f9a85240091c/IGVFFI0536JASN.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf17/e17l2_raw_feature_bc_matrix.h5",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9924UIFT/",
"accession": "IGVFDS9924UIFT",
"aliases": [
"ansuman-satpathy:multiseq_igvf17_10x2"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9737YNSX/",
"accession": "IGVFDS9737YNSX",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf17_10x2"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7207IORB/",
"accession": "IGVFDS7207IORB",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf17_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": "2025-03-22T00:44:45.454445+00:00",
"sample_summary": "Homo sapiens multiplexed sample of RUES2",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM0198VBOA/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM0198VBOA",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf17_10x2"
],
"cellular_sub_pool": "2",
"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": "2025-01-28T06:30:55.209892+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq): cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "1efab475-0583-447d-89b6-8274d340abff",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}