{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS1583PWNS/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1583PWNS",
"aliases": [
"ansuman-satpathy:igvf2_analysis_set"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS1583PWNS](/analysis-sets/IGVFDS1583PWNS/) has `input_file_sets` with multiplexed samples: [IGVFSM3646QLDO](/multiplexed-samples/IGVFSM3646QLDO/) 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/IGVFDS1583PWNS/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS1583PWNS](/analysis-sets/IGVFDS1583PWNS/) 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/IGVFDS1583PWNS/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2214RERT](/matrix-files/IGVFFI2214RERT/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2214RERT/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2214RERT](/matrix-files/IGVFFI2214RERT/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2214RERT/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM3646QLDO](/multiplexed-samples/IGVFSM3646QLDO/) 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/IGVFSM3646QLDO/"
}
]
},
"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": "2025-01-28T05:33:17.074784+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - teloHAEC +/- TNFa for 0hr, 4hr, or 24hr",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI6774RPHJ/",
"accession": "IGVFFI6774RPHJ",
"aliases": [
"ansuman-satpathy:igvf2_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:49:52.696812+00:00",
"file_format": "tsv",
"file_size": 6902347644,
"href": "/tabular-files/IGVFFI6774RPHJ/@@download/IGVFFI6774RPHJ.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/a7f47513-3365-43cb-9638-06af30ce84bf/IGVFFI6774RPHJ.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf2/e2l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI3993MUKU/",
"accession": "IGVFFI3993MUKU",
"aliases": [
"ansuman-satpathy:igvf2_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:50:18.400774+00:00",
"file_format": "bed",
"file_size": 1410680,
"href": "/tabular-files/IGVFFI3993MUKU/@@download/IGVFFI3993MUKU.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/aac738c9-3874-472c-ab78-deaff323c534/IGVFFI3993MUKU.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf2/e2l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/index-files/IGVFFI3495CSEB/",
"accession": "IGVFFI3495CSEB",
"aliases": [
"ansuman-satpathy:igvf2_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:27:54.544165+00:00",
"file_format": "tbi",
"file_size": 2005906,
"href": "/index-files/IGVFFI3495CSEB/@@download/IGVFFI3495CSEB.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/4f693212-65af-4357-9cd7-830748d1fb86/IGVFFI3495CSEB.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf2/e2l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/matrix-files/IGVFFI2214RERT/",
"accession": "IGVFFI2214RERT",
"aliases": [
"ansuman-satpathy:igvf2_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:33:53.808295+00:00",
"file_format": "hdf5",
"file_size": 184143171,
"href": "/matrix-files/IGVFFI2214RERT/@@download/IGVFFI2214RERT.h5",
"s3_uri": "s3://igvf-files/2025/01/28/30134fbd-ab1e-42b7-bfa1-13008d465d05/IGVFFI2214RERT.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf2/e2l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1936ETPF/",
"accession": "IGVFFI1936ETPF",
"aliases": [
"ansuman-satpathy:igvf2_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:00.636152+00:00",
"file_format": "tsv",
"file_size": 604503,
"href": "/tabular-files/IGVFFI1936ETPF/@@download/IGVFFI1936ETPF.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/b5fafcc8-e31d-471d-97cf-78c106422998/IGVFFI1936ETPF.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e2l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6369SLCB/",
"accession": "IGVFDS6369SLCB",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf2_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5111SPGA/",
"accession": "IGVFDS5111SPGA",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf2_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS9860EXKL/",
"accession": "IGVFDS9860EXKL",
"aliases": [
"ansuman-satpathy:multiseq_igvf2_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"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": "2025-03-07T06:04:09.217167+00:00",
"sample_summary": "Homo sapiens multiplexed sample of TeloHAEC, perturbed with 10 ng/mL tumor necrosis factor alpha for 1 day, 10 ng/mL tumor necrosis factor alpha for 4 hours",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM3646QLDO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM3646QLDO",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf2_10x1"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/20743336-7ae0-4e51-ab85-4ef4401b9b7d/",
"certificate_identifier": "IP115-16",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) TeloHAEC cell line treated with 10 ng/mL tumor necrosis factor alpha for 4 hours; Homo sapiens (female) TeloHAEC cell line; ... and 7 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d2d49540-dd91-49e2-b877-ce9aa0af8bb0/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 4 hours",
"treatment_type": "protein"
},
{
"@id": "/treatments/de8a9e87-d0e1-4ecb-bc9d-08e61b4ff368/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 1 day",
"treatment_type": "protein"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T05:49:52.696812+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "6582ecd1-a375-4319-b7a4-dd936b75401e",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}