{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS8205NXKP/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8205NXKP",
"aliases": [
"ansuman-satpathy:igvf1_analysis_set",
"ansuman-satpathy:igvf1_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO9571CSNU](/human-donors/IGVFDO9571CSNU/) has in progress subobject publication [91850f8e-153a-43d6-9967-9afa98ec006a](/publications/91850f8e-153a-43d6-9967-9afa98ec006a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9571CSNU/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS8205NXKP](/analysis-sets/IGVFDS8205NXKP/) has `input_file_sets` with multiplexed samples: [IGVFSM4662QKFQ](/multiplexed-samples/IGVFSM4662QKFQ/) 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/IGVFDS8205NXKP/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS8205NXKP](/analysis-sets/IGVFDS8205NXKP/) 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/IGVFDS8205NXKP/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM4662QKFQ](/multiplexed-samples/IGVFSM4662QKFQ/) 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/IGVFSM4662QKFQ/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO2115EOOA](/human-donors/IGVFDO2115EOOA/) has in progress subobject publication [6269453b-5ac0-4651-8b89-3169466cba2b](/publications/6269453b-5ac0-4651-8b89-3169466cba2b/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO2115EOOA/"
}
]
},
"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": "2025-01-28T05:33:15.834920+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - U2OS, HAP1, HL60, K562, and HUDEP2",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2722UPGC/",
"accession": "IGVFDO2722UPGC",
"aliases": [
"igvf:donor_of_HAP-1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9571CSNU/",
"accession": "IGVFDO9571CSNU",
"aliases": [
"igvf:donor_of_U2OS"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO2115EOOA/",
"accession": "IGVFDO2115EOOA",
"aliases": [
"igvf:donor_of_HL-60"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"aliases": [
"igvf:donor_of_HUDEP-2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI4763UQQR/",
"accession": "IGVFFI4763UQQR",
"aliases": [
"ansuman-satpathy:igvf1_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:35:20.501880+00:00",
"derived_from": [
"/sequence-files/IGVFFI9476DBSV/",
"/sequence-files/IGVFFI1415ZCCR/",
"/sequence-files/IGVFFI9193AKLW/",
"/sequence-files/IGVFFI4166FQWH/",
"/sequence-files/IGVFFI6845HIAS/",
"/sequence-files/IGVFFI2636JAAE/",
"/sequence-files/IGVFFI0014KSVS/",
"/sequence-files/IGVFFI9875PICN/"
],
"file_format": "tsv",
"file_size": 3457193521,
"href": "/tabular-files/IGVFFI4763UQQR/@@download/IGVFFI4763UQQR.tsv.gz",
"md5sum": "cbe9e2a185c4cc723961e9a1fa12cb7a",
"s3_uri": "s3://igvf-files/2025/01/28/b7201f37-1bf3-4a84-97c2-22d0cdd4ca41/IGVFFI4763UQQR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf1/e1l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI0330NNDK/",
"accession": "IGVFFI0330NNDK",
"aliases": [
"ansuman-satpathy:igvf1_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:48:59.735510+00:00",
"derived_from": [
"/tabular-files/IGVFFI4763UQQR/"
],
"file_format": "bed",
"file_size": 1734011,
"href": "/tabular-files/IGVFFI0330NNDK/@@download/IGVFFI0330NNDK.bed.gz",
"md5sum": "a77e39a9c8da930515ce27c203055835",
"s3_uri": "s3://igvf-files/2025/01/28/9d179f01-61da-448c-be72-3d40aaff4c93/IGVFFI0330NNDK.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf1/e1l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI6944QFHK/",
"accession": "IGVFFI6944QFHK",
"aliases": [
"ansuman-satpathy:igvf1_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:33:29.038666+00:00",
"derived_from": [
"/sequence-files/IGVFFI2965VBOB/",
"/sequence-files/IGVFFI4293NHNU/",
"/sequence-files/IGVFFI9541RVZI/",
"/sequence-files/IGVFFI5800DGQI/",
"/sequence-files/IGVFFI6372LYLJ/",
"/sequence-files/IGVFFI5685DFEN/",
"/sequence-files/IGVFFI5543IUWE/",
"/sequence-files/IGVFFI9377FZXN/"
],
"file_format": "hdf5",
"file_size": 146675801,
"href": "/matrix-files/IGVFFI6944QFHK/@@download/IGVFFI6944QFHK.h5",
"md5sum": "49ab41a3d051e12e62e550f57484bcc8",
"s3_uri": "s3://igvf-files/2025/01/28/6fe33099-d531-4646-8e00-a1d78053e46b/IGVFFI6944QFHK.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf1/e1l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI7266GPQE/",
"accession": "IGVFFI7266GPQE",
"aliases": [
"ansuman-satpathy:igvf1_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:27:51.069405+00:00",
"derived_from": [
"/tabular-files/IGVFFI4763UQQR/"
],
"file_format": "tbi",
"file_size": 1341324,
"href": "/index-files/IGVFFI7266GPQE/@@download/IGVFFI7266GPQE.tbi",
"md5sum": "69875eac66ce244c6cce790aaf3b51b3",
"s3_uri": "s3://igvf-files/2025/01/28/529928f3-5d5a-46f8-a7b4-35bc41f3702f/IGVFFI7266GPQE.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf1/e1l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI2757DSWR/",
"accession": "IGVFFI2757DSWR",
"aliases": [
"ansuman-satpathy:igvf1_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:29:44.142596+00:00",
"derived_from": [
"/sequence-files/IGVFFI1003RFPB/",
"/sequence-files/IGVFFI2536ELTM/",
"/sequence-files/IGVFFI4549DFQQ/",
"/sequence-files/IGVFFI5932THXZ/",
"/sequence-files/IGVFFI6262QQVY/",
"/sequence-files/IGVFFI7384JIDM/",
"/sequence-files/IGVFFI0529ZSZX/",
"/sequence-files/IGVFFI9946BRRT/"
],
"file_format": "tsv",
"file_size": 474649,
"href": "/tabular-files/IGVFFI2757DSWR/@@download/IGVFFI2757DSWR.tsv.gz",
"md5sum": "d96a0a06380f932925c39a24f4ea84de",
"s3_uri": "s3://igvf-files/2025/02/19/dce6ff12-8523-479a-815e-91f194279dbb/IGVFFI2757DSWR.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e1l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3259WGKQ/",
"accession": "IGVFDS3259WGKQ",
"aliases": [
"ansuman-satpathy:multiseq_igvf1_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1555ZQOW/",
"accession": "IGVFDS1555ZQOW",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf1_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3744SQTD/",
"accession": "IGVFDS3744SQTD",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf1_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": "2025-03-07T06:04:04.309995+00:00",
"sample_summary": "Homo sapiens multiplexed sample of HAP-1, HL-60, HUDEP-2, K562, U2OS",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4662QKFQ/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM4662QKFQ",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf1_10x1"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/16883984-b168-4b68-bc2a-37ef58354571/",
"certificate_identifier": "IP115-04",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/53fbaed7-f4c0-4932-bf77-254568743089/",
"certificate_identifier": "IP115-10",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/5e0fa625-6c72-4f32-872e-bcbc6acf630b/",
"certificate_identifier": "IP115-17",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/8ef1d59e-ef62-4890-b0ea-086d37645c75/",
"certificate_identifier": "IP115-02",
"controlled_access": false,
"status": "released"
},
{
"@id": "/institutional-certificates/d997512b-2c33-48e5-ae36-a94fd2959427/",
"certificate_identifier": "IP115-19",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002793/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HL-60"
],
"status": "released",
"summary": "HL-60",
"term_name": "HL-60"
},
{
"@id": "/sample-terms/EFO_0002869/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:U2OS"
],
"status": "released",
"summary": "U2OS",
"term_name": "U2OS"
},
{
"@id": "/sample-terms/EFO_0007598/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HAP-1"
],
"status": "released",
"summary": "HAP-1",
"term_name": "HAP-1"
},
{
"@id": "/sample-terms/EFO_0022838/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HUDEP-2"
],
"status": "released",
"summary": "HUDEP-2",
"term_name": "HUDEP-2"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) HAP-1 cell line; Homo sapiens (male) HAP-1 cell line; ... and 13 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": "2025-01-28T05:35:20.501880+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "42c279f9-b8af-4b2a-9015-9c8fe1cccf45",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}