{
"@context": "/terms/",
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2649QXJV",
"aliases": [
"ansuman-satpathy:igvf4_analysis_set",
"ansuman-satpathy:igvf4_analysis_set_10x1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM8594ZCZM](/multiplexed-samples/IGVFSM8594ZCZM/) 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/IGVFSM8594ZCZM/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9060FTBW](/matrix-files/IGVFFI9060FTBW/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9060FTBW/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI9060FTBW](/matrix-files/IGVFFI9060FTBW/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI9060FTBW/"
},
{
"category": "missing demultiplexed sample",
"detail": "Analysis set [IGVFDS2649QXJV](/analysis-sets/IGVFDS2649QXJV/) has `input_file_sets` with multiplexed samples: [IGVFSM8594ZCZM](/multiplexed-samples/IGVFSM8594ZCZM/) 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/IGVFDS2649QXJV/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS2649QXJV](/analysis-sets/IGVFDS2649QXJV/) 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/IGVFDS2649QXJV/"
}
]
},
"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": "2025-01-28T05:33:19.324153+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"description": "Quality-control workflow performed by Satpathy Lab - WTC11 macrophage perturbation (M0, M1, M2, preMac, cholesterol)",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI8225EESE/",
"accession": "IGVFFI8225EESE",
"aliases": [
"ansuman-satpathy:igvf4_fragments_10x1"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:52:31.562657+00:00",
"file_format": "tsv",
"file_size": 5867111794,
"href": "/tabular-files/IGVFFI8225EESE/@@download/IGVFFI8225EESE.tsv.gz",
"s3_uri": "s3://igvf-files/2025/01/28/ff0b1bc1-c199-412a-ad28-41bda9de710d/IGVFFI8225EESE.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf4/e4l1_fragments.tsv.gz",
"upload_status": "validation exempted"
},
{
"@id": "/tabular-files/IGVFFI7585TQDT/",
"accession": "IGVFFI7585TQDT",
"aliases": [
"ansuman-satpathy:igvf4_peaks_10x1"
],
"assembly": "GRCh38",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:53:00.545056+00:00",
"file_format": "bed",
"file_size": 1962296,
"href": "/tabular-files/IGVFFI7585TQDT/@@download/IGVFFI7585TQDT.bed.gz",
"s3_uri": "s3://igvf-files/2025/01/28/3ec1f728-c8dd-4558-92dd-923e8962f30e/IGVFFI7585TQDT.bed.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf4/e4l1_peaks.bed",
"upload_status": "validation exempted"
},
{
"@id": "/matrix-files/IGVFFI9060FTBW/",
"accession": "IGVFFI9060FTBW",
"aliases": [
"ansuman-satpathy:igvf4_raw_rna_counts_10x1"
],
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T15:35:01.316491+00:00",
"file_format": "hdf5",
"file_size": 225464492,
"href": "/matrix-files/IGVFFI9060FTBW/@@download/IGVFFI9060FTBW.h5",
"s3_uri": "s3://igvf-files/2025/01/28/6629ec1b-9b24-454f-81e7-599deace700f/IGVFFI9060FTBW.h5",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf4/e4l1_raw_feature_bc_matrix.h5",
"upload_status": "validated"
},
{
"@id": "/index-files/IGVFFI8513NQCU/",
"accession": "IGVFFI8513NQCU",
"aliases": [
"ansuman-satpathy:igvf4_fragments_index_10x1"
],
"content_type": "index",
"controlled_access": false,
"creation_timestamp": "2025-01-28T15:28:02.573098+00:00",
"file_format": "tbi",
"file_size": 1737102,
"href": "/index-files/IGVFFI8513NQCU/@@download/IGVFFI8513NQCU.tbi",
"s3_uri": "s3://igvf-files/2025/01/28/1787b75f-5710-4237-bbbb-263ac2eccedf/IGVFFI8513NQCU.tbi",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf4/e4l1_fragments.tsv.gz.tbi",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI0407NUDH/",
"accession": "IGVFFI0407NUDH",
"aliases": [
"ansuman-satpathy:igvf4_multiseq_count_matrix_10x1"
],
"content_type": "cell hashing barcodes",
"controlled_access": false,
"creation_timestamp": "2025-02-19T23:30:33.648258+00:00",
"file_format": "tsv",
"file_size": 1150129,
"href": "/tabular-files/IGVFFI0407NUDH/@@download/IGVFFI0407NUDH.tsv.gz",
"s3_uri": "s3://igvf-files/2025/02/19/5e76e99c-e847-40df-b017-19a61f28984f/IGVFFI0407NUDH.tsv.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e4l1_tag_mtx.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8226YTNI/",
"accession": "IGVFDS8226YTNI",
"aliases": [
"ansuman-satpathy:multiseq_igvf4_10x1"
],
"file_set_type": "lipid-conjugated oligo sequencing",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9581AWPV/",
"accession": "IGVFDS9581AWPV",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf4_10x1"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2045SDGW/",
"accession": "IGVFDS2045SDGW",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf4_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": "2025-03-07T06:04:22.220405+00:00",
"sample_summary": "Homo sapiens multiplexed sample of GM25256 (WTC-11), differentiated with 0.025 ng/mL acetylated low density lipoprotein for 1 day, 100 ng/mL macrophage colony-stimulating factor 1 for 7 days, 20 ng/mL interferon gamma for 1 day, 50 ng/mL interleukin 4 for 1 day",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM8594ZCZM/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM8594ZCZM",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf4_10x1"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
"@id": "/institutional-certificates/e5598331-9e7c-4bd5-8e7b-64d5a4529006/",
"certificate_identifier": "IP115-21",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
"@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 (male) GM25256 (WTC-11) cell line treated with 50 ng/mL interleukin 4 for 1 day; Homo sapiens (male) GM25256 (WTC-11) cell line treated with 100 ng/mL macrophage colony-stimulating factor 1 for 7 days; ... and 13 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/2987f643-86dc-4113-af7e-d4b5d162b5c8/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 0.025 ng/mL acetylated low density lipoprotein for 1 day",
"treatment_type": "chemical"
},
{
"@id": "/treatments/729630f8-aa05-47f5-9cba-ee7a264da593/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 50 ng/mL interleukin 4 for 1 day",
"treatment_type": "protein"
},
{
"@id": "/treatments/ae8065d2-85f3-498e-b4f2-01a38756d48e/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 20 ng/mL interferon gamma for 1 day",
"treatment_type": "protein"
},
{
"@id": "/treatments/bec71d5e-97ef-489a-acb7-5336691b6c39/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 100 ng/mL macrophage colony-stimulating factor 1 for 7 days",
"treatment_type": "protein"
}
]
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2025-01-28T05:52:31.562657+00:00",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
"uuid": "46812185-4fc0-4a78-8deb-8f6afa73f402",
"workflows": [
{
"@id": "/workflows/IGVFWF1453HVEC/",
"accession": "IGVFWF1453HVEC",
"name": "Satpathy Cell Ranger",
"status": "released",
"uniform_pipeline": false
}
]
}