{
"@context": "/terms/",
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"File",
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],
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"aliases": [
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],
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"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2641LMFU](/matrix-files/IGVFFI2641LMFU/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2641LMFU/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI2641LMFU](/matrix-files/IGVFFI2641LMFU/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI2641LMFU/"
}
]
},
"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": "2025-01-28T15:38:23.051464+00:00",
"derived_from": [
"/sequence-files/IGVFFI1373PDRD/",
"/sequence-files/IGVFFI7974OSGQ/",
"/sequence-files/IGVFFI6458EKNW/",
"/sequence-files/IGVFFI9291IGJI/",
"/sequence-files/IGVFFI5532UPHV/",
"/sequence-files/IGVFFI6544ROSI/",
"/sequence-files/IGVFFI5700XSJN/",
"/sequence-files/IGVFFI2521NNNE/"
],
"file_format": "hdf5",
"file_format_specifications": [
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],
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"accession": "IGVFDS2018URDY",
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{
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"classifications": [
"cell line",
"multiplexed sample"
],
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"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
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"status": "released",
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},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
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"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
},
{
"@id": "/multiplexed-samples/IGVFSM4547BFMA/",
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],
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{
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"modality": "interference",
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}
],
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},
{
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},
{
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},
{
"@id": "/sample-terms/NTR_0000753/",
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"term_name": "TeloHAEC"
}
],
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{
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},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
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"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
"file_size": 250701921,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI2641LMFU/@@download/IGVFFI2641LMFU.h5",
"input_file_for": [],
"integrated_in": [],
"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
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"principal_dimension": "cell",
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],
"release_timestamp": "2025-03-07T06:04:56.736345+00:00",
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"schema_version": "7",
"secondary_dimensions": [
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],
"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/igvf10/e10l1_raw_feature_bc_matrix.h5",
"summary": "cell by gene in raw feature barcode matrix",
"upload_status": "validated",
"uuid": "72d9e9b2-440f-447e-8922-c19245eebb4e",
"workflow": {
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"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}