{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6722QSLX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6722QSLX",
"aliases": [
"jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep2_binD_PCR2_S204"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2758XTEL](/auxiliary-sets/IGVFDS2758XTEL/) has sequence file(s): [IGVFFI9556SGOL](/sequence-files/IGVFFI9556SGOL/), [IGVFFI3516HRKT](/sequence-files/IGVFFI3516HRKT/), [IGVFFI3307JMQV](/sequence-files/IGVFFI3307JMQV/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2758XTEL/"
},
{
"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": "Measurement set [IGVFDS6722QSLX](/measurement-sets/IGVFDS6722QSLX/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS6722QSLX/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6722QSLX](/measurement-sets/IGVFDS6722QSLX/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6722QSLX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2758XTEL/",
"accession": "IGVFDS2758XTEL",
"aliases": [
"jesse-engreitz:auxiliary_NOS3_CRISPRi_FF_R1_FFrep2_binD_PCR2_S204"
],
"file_set_type": "gRNA sequencing",
"status": "released"
}
],
"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": "2024-04-16T14:54:15.096764+00:00",
"documents": [
"/documents/1d492aa4-f111-4220-aeaa-f43a3cbda78b/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2024-06-22T00:20:36.928398+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3569XFKY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3569XFKY",
"aliases": [
"jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep2_binD_PCR2_S204"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS8953DFJK/",
"accession": "IGVFDS8953DFJK",
"file_set_type": "guide library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000164867/",
"geneid": "ENSG00000164867",
"name": "nitric oxide synthase 3",
"status": "released",
"summary": "NOS3 - ENSG00000164867 (Homo sapiens)",
"symbol": "NOS3"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3"
}
],
"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": "released",
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin D for 76-100% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-04-16T21:43:51.850054+00:00",
"summary": "CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3",
"targeted_genes": [
{
"@id": "/genes/ENSG00000164867/",
"geneid": "ENSG00000164867",
"name": "nitric oxide synthase 3",
"status": "released",
"symbol": "NOS3",
"synonyms": [
"cNOS",
"constitutive NOS",
"EC-NOS",
"nitric oxide synthase, endothelial",
"eNOS",
"ECNOS",
"NOS type III",
"NOSIII",
"nitric oxide synthase 3 (endothelial cell)",
"endothelial NOS"
]
}
],
"uuid": "176d756b-1983-4f9f-8572-5bbdcd1442af"
}