{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI5252BPFG/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI5252BPFG",
"aliases": [
"ansuman-satpathy:igvf18_raw_rna_counts_10x2"
],
"analysis_step_version": "/analysis-step-versions/072beaf9-db5c-4bb3-9d63-e5cf7ee29dd6/",
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI5252BPFG](/matrix-files/IGVFFI5252BPFG/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5252BPFG/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI5252BPFG](/matrix-files/IGVFFI5252BPFG/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI5252BPFG/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"checkfiles_version": "v14",
"content_summary": "cell by gene in raw feature barcode matrix",
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:12:28.832229+00:00",
"derived_from": [
"/sequence-files/IGVFFI1269DVSB/",
"/sequence-files/IGVFFI5402LZTX/",
"/sequence-files/IGVFFI3746JMAE/",
"/sequence-files/IGVFFI1287UCCZ/"
],
"file_format": "hdf5",
"file_format_specifications": [
"/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS4963SRAJ/",
"accession": "IGVFDS4963SRAJ",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM3125MLLP/",
"accession": "IGVFSM3125MLLP",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"status": "released",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"status": "released",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"status": "released",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_term_name": "Yoda1"
}
]
},
{
"@id": "/multiplexed-samples/IGVFSM4392KEFB/",
"accession": "IGVFSM4392KEFB",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"status": "released",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"status": "released",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"status": "released",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_term_name": "Yoda1"
}
]
},
{
"@id": "/multiplexed-samples/IGVFSM9642EHZY/",
"accession": "IGVFSM9642EHZY",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"status": "released",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"status": "released",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"status": "released",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_term_name": "Yoda1"
}
]
},
{
"@id": "/multiplexed-samples/IGVFSM5815WALV/",
"accession": "IGVFSM5815WALV",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001196/",
"status": "released",
"term_name": "IMR-90"
},
{
"@id": "/sample-terms/EFO_0001203/",
"status": "released",
"term_name": "MCF-7"
},
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
},
{
"@id": "/sample-terms/EFO_0003072/",
"status": "released",
"term_name": "SK-N-SH"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: IMR-90 cell line, female, Homo sapiens; MCF-7 cell line, female, Homo sapiens; ... and 17 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
"purpose": "perturbation",
"status": "in progress",
"summary": "Treatment of 3 μM Yoda1 for 4 hours",
"treatment_term_name": "Yoda1"
}
]
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
"file_size": 170860184,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI5252BPFG/@@download/IGVFFI5252BPFG.h5",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "cda80554a82a9bc2364f5871e24bfbec",
"principal_dimension": "cell",
"quality_metrics": [],
"reference_files": [
"/reference-files/IGVFFI8311QXYM/",
"/reference-files/IGVFFI3944QOJF/"
],
"release_timestamp": "2025-03-07T06:05:36.485184+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/ef601288-105b-44e6-a61b-bbe7b2cf2fff/IGVFFI5252BPFG.h5",
"schema_version": "7",
"secondary_dimensions": [
"gene"
],
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l2_raw_feature_bc_matrix.h5",
"summary": "cell by gene in raw feature barcode matrix",
"upload_status": "validated",
"uuid": "ef601288-105b-44e6-a61b-bbe7b2cf2fff",
"workflow": {
"@id": "/workflows/IGVFWF1453HVEC/",
"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}