{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS8898JDCK/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8898JDCK",
"aliases": [
"ansuman-satpathy:igvf5_analysis_set",
"ansuman-satpathy:igvf5_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM1143WWLK](/multiplexed-samples/IGVFSM1143WWLK/) 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/IGVFSM1143WWLK/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS8898JDCK](/analysis-sets/IGVFDS8898JDCK/) has `input_file_sets` with multiplexed samples: [IGVFSM1143WWLK](/multiplexed-samples/IGVFSM1143WWLK/) 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/IGVFDS8898JDCK/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS8898JDCK](/analysis-sets/IGVFDS8898JDCK/) 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/IGVFDS8898JDCK/"
}
]
},
"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": "2025-01-28T05:33:20.468903+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - H1 gastruloids, WTC11 NGN2 neurons, H9 neuron differentiation, HEK293T",
"donors": [
{
"@id": "/human-donors/IGVFDO6638HIAD/",
"accession": "IGVFDO6638HIAD",
"aliases": [
"igvf:donor_of_H1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@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/IGVFDO1183RRBM/",
"accession": "IGVFDO1183RRBM",
"aliases": [
"igvf:donor_of_HEK293T"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI0624FNHV/",
"accession": "IGVFFI0624FNHV",
"aliases": [
"ansuman-satpathy:igvf5_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:54:37.503538+00:00",
"derived_from": [
"/tabular-files/IGVFFI3412IJQJ/"
],
"file_format": "bed",
"file_size": 2346745,
"href": "/tabular-files/IGVFFI0624FNHV/@@download/IGVFFI0624FNHV.bed.gz",
"md5sum": "042e612c75cc0d8e5e2e1542a463b58b",
"s3_uri": "s3://igvf-files/2025/01/28/1c6b97a9-d2a6-4b1b-93d4-3c58fdebc1dc/IGVFFI0624FNHV.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI3412IJQJ/",
"accession": "IGVFFI3412IJQJ",
"aliases": [
"ansuman-satpathy:igvf5_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:54:07.484947+00:00",
"derived_from": [
"/sequence-files/IGVFFI4716LCQW/",
"/sequence-files/IGVFFI8766UVOC/",
"/sequence-files/IGVFFI6618LQLL/",
"/sequence-files/IGVFFI5126YZZL/",
"/sequence-files/IGVFFI3036JIDK/",
"/sequence-files/IGVFFI2993RSJW/",
"/sequence-files/IGVFFI9756XVTN/",
"/sequence-files/IGVFFI0799SCDB/",
"/sequence-files/IGVFFI6848CISU/",
"/sequence-files/IGVFFI7056KQRJ/",
"/sequence-files/IGVFFI5875NOXD/",
"/sequence-files/IGVFFI9161IXWC/",
"/sequence-files/IGVFFI1011DDAV/",
"/sequence-files/IGVFFI9071IWHT/",
"/sequence-files/IGVFFI7326FZAB/",
"/sequence-files/IGVFFI1650QNRA/"
],
"file_format": "tsv",
"file_size": 6393160644,
"href": "/tabular-files/IGVFFI3412IJQJ/@@download/IGVFFI3412IJQJ.tsv.gz",
"md5sum": "4b32cb9d82a8a9780c51005c7f9ccbdb",
"s3_uri": "s3://igvf-files/2025/01/28/f564b0cb-b085-4214-952d-ce1b6182eb1e/IGVFFI3412IJQJ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI3992LEUW/",
"accession": "IGVFFI3992LEUW",
"aliases": [
"ansuman-satpathy:igvf5_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:35:27.563926+00:00",
"derived_from": [
"/sequence-files/IGVFFI6132UEVZ/",
"/sequence-files/IGVFFI4814KAPG/",
"/sequence-files/IGVFFI5105QWTT/",
"/sequence-files/IGVFFI1341XMVN/",
"/sequence-files/IGVFFI9942CBQB/",
"/sequence-files/IGVFFI7029DELQ/",
"/sequence-files/IGVFFI2210BQAO/",
"/sequence-files/IGVFFI0560CIZS/",
"/sequence-files/IGVFFI5932BAOK/",
"/sequence-files/IGVFFI0139WHXA/",
"/sequence-files/IGVFFI3274DQST/",
"/sequence-files/IGVFFI8734QMQW/",
"/sequence-files/IGVFFI4492FTAT/",
"/sequence-files/IGVFFI0662PWBF/",
"/sequence-files/IGVFFI2520ZMKL/",
"/sequence-files/IGVFFI0180GHZK/"
],
"file_format": "hdf5",
"file_size": 200101556,
"href": "/matrix-files/IGVFFI3992LEUW/@@download/IGVFFI3992LEUW.h5",
"md5sum": "b63d2d526d0118f8784a6ab93591b3ae",
"s3_uri": "s3://igvf-files/2025/01/28/8de4bfa4-35f0-4bef-8e81-b0084f9a0735/IGVFFI3992LEUW.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI7886UBGW/",
"accession": "IGVFFI7886UBGW",
"aliases": [
"ansuman-satpathy:igvf5_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:05.120415+00:00",
"derived_from": [
"/tabular-files/IGVFFI3412IJQJ/"
],
"file_format": "tbi",
"file_size": 1849586,
"href": "/index-files/IGVFFI7886UBGW/@@download/IGVFFI7886UBGW.tbi",
"md5sum": "4244932fddb11edabc0229d19a388cf8",
"s3_uri": "s3://igvf-files/2025/01/28/b3402037-93d2-47f7-9c1e-328838f3916f/IGVFFI7886UBGW.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf5/e5l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI4899AZGW/",
"accession": "IGVFFI4899AZGW",
"aliases": [
"ansuman-satpathy:igvf5_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:45.218549+00:00",
"derived_from": [
"/sequence-files/IGVFFI8729TJQM/",
"/sequence-files/IGVFFI0085JQOD/",
"/sequence-files/IGVFFI5617ETLN/",
"/sequence-files/IGVFFI9145FMXO/",
"/sequence-files/IGVFFI5762MUQG/",
"/sequence-files/IGVFFI8874UNMK/",
"/sequence-files/IGVFFI2499PYTL/",
"/sequence-files/IGVFFI2149MFLI/",
"/sequence-files/IGVFFI5493GGSP/",
"/sequence-files/IGVFFI7607DOVX/",
"/sequence-files/IGVFFI4470PFHW/",
"/sequence-files/IGVFFI7979FJLJ/",
"/sequence-files/IGVFFI7289QBCL/",
"/sequence-files/IGVFFI6959EZEF/",
"/sequence-files/IGVFFI3941JSTF/",
"/sequence-files/IGVFFI0694HONB/"
],
"file_format": "tsv",
"file_size": 299924,
"href": "/tabular-files/IGVFFI4899AZGW/@@download/IGVFFI4899AZGW.tsv.gz",
"md5sum": "c0f76fe91a7bb0ca4f42f388daae2ce7",
"s3_uri": "s3://igvf-files/2025/02/19/d9fb092a-239b-44f3-ab8e-392346444dd1/IGVFFI4899AZGW.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e5l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5364XXRU/",
"accession": "IGVFDS5364XXRU",
"aliases": [
"ansuman-satpathy:multiseq_igvf5_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9743PIFM/",
"accession": "IGVFDS9743PIFM",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf5_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4942IIYS/",
"accession": "IGVFDS4942IIYS",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf5_10x1"
],
"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": "2025-03-07T06:04:31.325747+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), H1-hESC, H9, HEK293T",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1143WWLK/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1143WWLK",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf5_10x1"
],
"classifications": [
"cell line",
"differentiated cell specimen",
"gastruloid",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/42937768-65a6-47ee-9d4c-6d3829c7f279/",
"certificate_identifier": "IP115-03",
"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/e7a2058d-80fb-46ee-be82-c4d8b26d01ec/",
"certificate_identifier": "IP115-08",
"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_0001184/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HEK293T"
],
"status": "released",
"summary": "HEK293T",
"term_name": "HEK293T"
},
{
"@id": "/sample-terms/EFO_0003042/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H1"
],
"status": "released",
"summary": "H1-hESC",
"term_name": "H1-hESC"
},
{
"@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 neuron for 6 days; Homo sapiens (female) H9 differentiated cell specimen induced to neuron for 6 days; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T05:54:07.484947+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "26aa8a8e-d050-45da-b3d7-5d741354277f",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}