{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS7943IIWZ/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7943IIWZ",
"aliases": [
"jesse-engreitz:analysis_set_TeloHAEC_Perturb-seq_2kG"
],
"assay_titles": [
"Perturb-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [IGVFDS7943IIWZ](/analysis-sets/IGVFDS7943IIWZ/) links to file set(s): [IGVFDS8448SPRJ](/auxiliary-sets/IGVFDS8448SPRJ/), [IGVFDS0515YYBH](/auxiliary-sets/IGVFDS0515YYBH/), [IGVFDS7065BOZB](/auxiliary-sets/IGVFDS7065BOZB/), [IGVFDS4516AUUC](/auxiliary-sets/IGVFDS4516AUUC/), [IGVFDS2031LFEN](/auxiliary-sets/IGVFDS2031LFEN/), [IGVFDS9990NLDH](/measurement-sets/IGVFDS9990NLDH/), [IGVFDS7729SUIF](/measurement-sets/IGVFDS7729SUIF/), [IGVFDS3564YOOG](/auxiliary-sets/IGVFDS3564YOOG/), [IGVFDS9186LBQJ](/measurement-sets/IGVFDS9186LBQJ/), [IGVFDS7020OWZV](/measurement-sets/IGVFDS7020OWZV/), [IGVFDS4784DDTU](/auxiliary-sets/IGVFDS4784DDTU/), [IGVFDS4972ICEM](/auxiliary-sets/IGVFDS4972ICEM/), [IGVFDS5673IZFI](/measurement-sets/IGVFDS5673IZFI/), [IGVFDS4697CFEN](/auxiliary-sets/IGVFDS4697CFEN/), [IGVFDS8509JBZW](/auxiliary-sets/IGVFDS8509JBZW/), [IGVFDS7600PZYR](/measurement-sets/IGVFDS7600PZYR/), [IGVFDS0385ESBQ](/measurement-sets/IGVFDS0385ESBQ/), [IGVFDS8841TWDX](/measurement-sets/IGVFDS8841TWDX/), [IGVFDS0909ARVL](/measurement-sets/IGVFDS0909ARVL/), [IGVFDS9984OMGN](/auxiliary-sets/IGVFDS9984OMGN/), [IGVFDS9527RJVT](/measurement-sets/IGVFDS9527RJVT/), [IGVFDS6848XNQV](/auxiliary-sets/IGVFDS6848XNQV/), [IGVFDS4800QEKC](/auxiliary-sets/IGVFDS4800QEKC/), [IGVFDS2630GWQK](/measurement-sets/IGVFDS2630GWQK/), [IGVFDS7498VOOU](/auxiliary-sets/IGVFDS7498VOOU/), [IGVFDS1330GUQX](/measurement-sets/IGVFDS1330GUQX/), [IGVFDS7065TFMP](/measurement-sets/IGVFDS7065TFMP/), [IGVFDS4759EOBT](/measurement-sets/IGVFDS4759EOBT/), [IGVFDS7726TKVM](/measurement-sets/IGVFDS7726TKVM/), [IGVFDS7359MSBY](/auxiliary-sets/IGVFDS7359MSBY/), [IGVFDS4288VPSU](/auxiliary-sets/IGVFDS4288VPSU/), [IGVFDS7665VXNR](/measurement-sets/IGVFDS7665VXNR/), [IGVFDS5167LALN](/auxiliary-sets/IGVFDS5167LALN/), [IGVFDS4291ANNC](/measurement-sets/IGVFDS4291ANNC/), [IGVFDS0237AFZT](/measurement-sets/IGVFDS0237AFZT/), [IGVFDS0562EWQF](/measurement-sets/IGVFDS0562EWQF/), [IGVFDS6454USPN](/auxiliary-sets/IGVFDS6454USPN/), [IGVFDS2133BONK](/auxiliary-sets/IGVFDS2133BONK/), [IGVFDS0616JFOF](/auxiliary-sets/IGVFDS0616JFOF/), [IGVFDS6988JXXY](/measurement-sets/IGVFDS6988JXXY/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/IGVFDS7943IIWZ/"
}
],
"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/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Analysis set [IGVFDS7943IIWZ](/analysis-sets/IGVFDS7943IIWZ/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/analysis-sets/IGVFDS7943IIWZ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-01-18T01:49:23.106436+00:00",
"description": "TeloHAEC CAD loci Perturb-seq analysis dataset for Schnitzler et al. 2024",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "principal analysis",
"files": [],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS4291ANNC/",
"accession": "IGVFDS4291ANNC",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_5"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4784DDTU/",
"accession": "IGVFDS4784DDTU",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_1"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS8841TWDX/",
"accession": "IGVFDS8841TWDX",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_5"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7359MSBY/",
"accession": "IGVFDS7359MSBY",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_2"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0385ESBQ/",
"accession": "IGVFDS0385ESBQ",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_6"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9527RJVT/",
"accession": "IGVFDS9527RJVT",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_7"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6454USPN/",
"accession": "IGVFDS6454USPN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_2"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0237AFZT/",
"accession": "IGVFDS0237AFZT",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_5"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0562EWQF/",
"accession": "IGVFDS0562EWQF",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_4"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7600PZYR/",
"accession": "IGVFDS7600PZYR",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_1"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3564YOOG/",
"accession": "IGVFDS3564YOOG",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_5"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7498VOOU/",
"accession": "IGVFDS7498VOOU",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_5"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8509JBZW/",
"accession": "IGVFDS8509JBZW",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_7"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0515YYBH/",
"accession": "IGVFDS0515YYBH",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_4"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS1330GUQX/",
"accession": "IGVFDS1330GUQX",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_3"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6848XNQV/",
"accession": "IGVFDS6848XNQV",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_7"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4697CFEN/",
"accession": "IGVFDS4697CFEN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_6"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7729SUIF/",
"accession": "IGVFDS7729SUIF",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_4"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9186LBQJ/",
"accession": "IGVFDS9186LBQJ",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_4"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS0909ARVL/",
"accession": "IGVFDS0909ARVL",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_7"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7726TKVM/",
"accession": "IGVFDS7726TKVM",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_6"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5167LALN/",
"accession": "IGVFDS5167LALN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_1"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7065TFMP/",
"accession": "IGVFDS7065TFMP",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_3"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4800QEKC/",
"accession": "IGVFDS4800QEKC",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_4"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4516AUUC/",
"accession": "IGVFDS4516AUUC",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_1"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7020OWZV/",
"accession": "IGVFDS7020OWZV",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_2"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS5673IZFI/",
"accession": "IGVFDS5673IZFI",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_1"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8448SPRJ/",
"accession": "IGVFDS8448SPRJ",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_11AMDox_3"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS6988JXXY/",
"accession": "IGVFDS6988JXXY",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_2"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2133BONK/",
"accession": "IGVFDS2133BONK",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_2"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS9990NLDH/",
"accession": "IGVFDS9990NLDH",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_2"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS2630GWQK/",
"accession": "IGVFDS2630GWQK",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_11AMDox_6"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS4759EOBT/",
"accession": "IGVFDS4759EOBT",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_3"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9984OMGN/",
"accession": "IGVFDS9984OMGN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_6"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4972ICEM/",
"accession": "IGVFDS4972ICEM",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_3"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4288VPSU/",
"accession": "IGVFDS4288VPSU",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_3"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/measurement-sets/IGVFDS7665VXNR/",
"accession": "IGVFDS7665VXNR",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_1"
],
"file_set_type": "experimental data",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS0616JFOF/",
"accession": "IGVFDS0616JFOF",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_5"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2031LFEN/",
"accession": "IGVFDS2031LFEN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_6"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7065BOZB/",
"accession": "IGVFDS7065BOZB",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_4"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
"https://www.protocols.io/view/systematic-perturb-seq-to-discover-endothelial-cel-261ged73yv47/v1"
],
"sample_summary": "TeloHAEC cell line, modified with CRISPR modifications, transfected with a guide library",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6249JKCM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6249JKCM",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_11AMDox_3"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM0862BZMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0862BZMH",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_1"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM1061NWCP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1061NWCP",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_5"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM9689NFEU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9689NFEU",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_6"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
},
{
"@id": "/in-vitro-systems/IGVFSM3700IHHL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3700IHHL",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_4"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
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